Fermentation doi: 10.3390/fermentation12110518

Authors: Yongsheng Yang Haoqian Cheng Xiaoxiao Zhang Qian Lin Yukun Zhang

Bamboo is an abundant plant resource with potential for use as an unconventional feed ingredient; however, its application in animal production remains relatively limited. This study aimed to evaluate the effects of partially replacing the basal diet with fermented bamboo powder (FBP) on the growth performance, slaughter traits, meat quality, serum biochemical parameters, antioxidant status, immune-related parameters, and intestinal digestive enzyme activities of yellow-feathered broilers. Two-year-old bamboo was used as the raw material and subjected to microbial fermentation for 14 d, followed by drying and sieving to obtain FBP. A total of 480 one-day-old yellow-feathered broilers were randomly assigned to four dietary treatment groups, with six replicate cages per treatment and 20 birds per cage. The control group received a basal diet, whereas the experimental groups received diets in which 0.5%, 1.0%, or 1.5% of the basal diet was replaced with FBP. The feeding trial lasted 56 d. During the starter phase, dietary FBP replacement significantly increased final body weight and average daily gain (ADG). During the grower phase, final body weight and ADG increased with increasing FBP inclusion levels. Over the entire experimental period, the overall treatment effect on ADG was not statistically significant, whereas dietary replacement with 1.0% and 1.5% FBP significantly reduced the feed-to-gain ratio (F/G) (p < 0.05). FBP replacement also significantly reduced abdominal fat percentage and increased breast muscle redness (a*) at 24 h postmortem (p < 0.05). Serum triglyceride (TG) and total cholesterol (TC) concentrations decreased, whereas high-density lipoprotein cholesterol (HDL-C) concentrations increased in FBP-fed broilers (p < 0.05). Regarding antioxidant and immune-related parameters, FBP significantly affected catalase (CAT) activity, total superoxide dismutase (T-SOD) activity, and total antioxidant capacity (T-AOC) (p < 0.05). CAT activity was highest in the 1.0% FBP group, whereas serum immunoglobulin A (IgA) concentrations were significantly higher in the 1.0% and 1.5% FBP groups than in the control group (p < 0.05); the 0.5% group did not differ significantly from the control. No significant effects were observed on organ indices or intestinal digestive enzyme activities (p > 0.05). In conclusion, partial replacement of the basal diet with FBP improved feed conversion efficiency and was associated with reduced abdominal fat deposition and favorable changes in selected serum lipid, antioxidant, and immune-related parameters. Although phase-specific improvements in growth performance were observed, overall ADG did not differ significantly among dietary treatments. These findings suggest that FBP has potential as a partial substitute for conventional feed ingredients in yellow-feathered broiler diets. Further studies are needed to confirm these effects and establish the optimal inclusion level under different production conditions.

Fermentation doi: 10.3390/fermentation12110517

Authors: Nova Henna Jemimah Kaila Jahnavi Pasaluri Narayan Vasudev Megha Reddy Chintapalli Narayanaswamy Naveen Kumar Chetana Ramakrishna Punil Kumar Hulikerekoppal Ningegowda Manohar Sita Rama Manohar Siva Naga Suresh Purama Prakash Motiram Halami Muthukumar Serva Peddha

Pearl millet (Pennisetum glaucum) was fermented with Lactiplantibacillus plantarum DHCU 70 to develop a cereal-based matrix for microbial encapsulation. A re-parameterized modified logistic model was fitted to viable cell growth data to identify a fermentation harvest interval associated with high cell density and fermentation-metabolite accumulation. Based on the composite desirability analysis, desirability was maximal at 17.5 h and remained on a plateau (D ≥ 0.97) from 17 to 22 h; a harvest interval of 18.0 to 20.5 h within its plateau was selected, during which viable counts reached 9.15 to 9.25 log CFU mL−1 and total measured organic acids were 27.9 to 28.7 g L−1 (maximum 29.9 g L−1 at 17.5 h). The selected fermented matrix, containing viable cells, residual soluble carbohydrate fractions and constituents derived from fermentation was incorporated into calcium-alginate–gelatin microbeads with 0.8 to 1.2 mm diameters. The bead formulation showed high retention of viable cells and measured fermentation-derived constituents during encapsulation. Under sequential simulated oral, gastric and intestinal conditions, the Ca-alginate–millet–gelatin formulation retained 6.45 log CFU mL−1, compared with 3.45 log CFU mL−1 for free cells, corresponding to a lower viability loss for encapsulated cells. FTIR analysis showed retention of characteristic hydroxyl, carboxylate and spectral bands associated with carbohydrates following encapsulation. Relative to the non-encapsulated fermented matrix, microbeads showed reduced amylolysis during the applied in vitro assays. Lyophilised microbeads exhibited a water activity of 0.40 ± 0.02, hygroscopicity of 56 ± 2.26% and 71.66 ± 26.30% rehydration after 10 min. The selection of the harvest time for encapsulation was guided by fermentation kinetics and metabolite profiles of the fermented matrix. The resulting alginate–gelatin microbeads improved the survival of Lpb. plantarum DHCU 70 relative to free cells under simulated gastrointestinal conditions tested. The formulation provides a cereal-based platform for further development of fermented functional food delivery systems.

Fermentation doi: 10.3390/fermentation12110516

Authors: Rommel Angel Mayorga Vargas Yoisdel Castillo Alvarez Reinier Jiménez Borges

Regional assessments of livestock manure often treat excreted organic matter as available feedstock and methane volume as an unequivocal climate benefit. This study builds a four-level resource cascade (theoretical, collectable, recoverable, and deployment-constrained methane) for 20 Latin American countries from 2024 FAOSTAT inventories of cattle, pigs, and poultry with IPCC-consistent parameters, and evaluates each level across energy, exergy, nitrogen, and climate. The theoretical envelope of 73.88 × 109 m3 CH4 a−1 contracts by 82.1% to 13.22 recoverable and to a deployment corridor of 6.74 (95% interval 5.05–9.27); cattle fall from 85.4% of the theoretical to 32.5% of the recoverable resource, whereas poultry rises to 40.4%, a share conditional on controlling ammonia inhibition. Energy and climate hierarchies diverge: pigs hold 27.1% of recoverable methane yet deliver all positive manure-management mitigation (+29.14 Mt CO2eq a−1 at 5% leakage), and the central net balance including grid displacement is +43.96 Mt CO2eq a−1, with a production-based break-even leakage of 15.00%. On an exergy-equivalent basis (81.52 TWhx a−1), recovered nitrogen (25.26 TWhx; 3.77 Mt N a−1) exceeds useful heat (10.24 TWhx). Monte Carlo propagation (20,000 iterations) identifies cattle collectability as the dominant resource uncertainty (Spearman ρs=0.774) and digester leakage as the dominant climate uncertainty (ρs=−0.613; 99.4% probability of positive management mitigation). Intensification scenarios raise recoverable methane to 16.97–20.73 × 109 m3 a−1 by 2035, and published techno-economic evidence shows that profitability depends on scale, incentives, and coproducts. Abundance, recoverability, climate effectiveness, and economic viability are four distinct quantities that must be evaluated jointly.

Fermentation doi: 10.3390/fermentation12110515

Authors: Yu-Na Oh Hack-Youn Kim

Mushroom mycelium is gaining attention as a sustainable protein source because it can be produced reliably through submerged fermentation and has a low environmental impact. In this study, we investigated the physicochemical and sensory characteristics of plant-based (PB) patties formulated with Lentinula edodes mycelium (LM) and pork backfat at respective levels of 15/0, 10/5, 5/10, and 0/15% (w/w, wet basis), based on the total formulation weight, and compared them with pork patties. Proximate composition analysis showed that the PB patty treatments had lower fat content (0–10.68%) than the control (p < 0.05). The water-holding capacity of the treatment groups was approximately 1.8 times that of the control (p < 0.05). The treatment groups exhibited generally lower texture profile values compared to the control. Electronic nose analysis showed that higher LM inclusion was generally associated with greater peak intensities for tentatively assigned volatile compounds, including ethanol, dimethyl sulfide, ethyl acetate, 3-methylbutanal, and hexanal. Electronic tongue analysis results showed that sourness and umami increased as the LM content increased. Sensory evaluation revealed no significant differences in overall acceptability among the treatments (p > 0.05). These results suggest the feasibility of developing low-fat plant-based patty formulations using LM.

Fermentation doi: 10.3390/fermentation12110514

Authors: Kingsley O. Omeje Benjamin O. Ezema Sabinus Oscar O. Eze Nonso E. Nnolim

The search for novel proteases with robust bioprocessing tendencies will benefit industrial production. Consequently, Aspergillus flavus KIGC protease was immobilised on iron oxide magnetic nanoparticles (IOMNPs) for the potential digestion of soybean protein. The protease was produced, partially purified, and used to functionalize the IOMNPs. Free and immobilized proteases were characterised and used to hydrolyze soybean protein. The results showed maximum protease production on day 7, with orange peel being the best carbon source. Characterization showed light scattering measurements of 72 and 81 nm for the IOMNPs and protease–IOMNP complex, respectively. The differential scanning calorimetry thermogram showed endothermic peaks at 193.97 °C and 150.93 °C for the IOMNPs and protease–IOMNP complex, respectively. The X-ray diffraction intensities differed between angles. Free and immobilized proteases showed optimal temperatures of 50 °C and 55 °C and pH values of 5.0 and 7.5, respectively. Km and Vmax were 0.002 mg/mL and 2 mg/min/mL for free protease and 0.0019 mg/mL and 3.85 mg/min/mL for immobilized protease, respectively. The immobilized protease showed 86.15% hydrolysis at 1.5 mg/mL of soybean protein after 18 h. The significant digestion of soybean protein by the IOMNP–protease compared to free protease points to the conjugate’s possible future applications pending further detailed study.

Fermentation doi: 10.3390/fermentation12110513

Authors: Raúl Ricardo Gamba Ana Florencia Moretti Néstor Gabriel Iglesias Marina Alejandra Golowczyc

Lactiplantibacillus species are widely recognized for their probiotic potential, yet the genetic determinants underlying strain-specific functional traits remain incompletely characterized. This study aimed to obtain the draft genome sequence of Lactiplantibacillus plantarum CIDCA 83114, a kefir-derived strain with previously demonstrated probiotic and antimicrobial properties, and to identify genetic features potentially associated with these traits and with strain safety. Whole-genome sequencing was performed on an Illumina MiSeq platform, genome assembly was generated using SPAdes, and functional annotation was conducted using Prokka and KEGG-based tools. The genome comprises a 3.27 Mb chromosome and five putative plasmid sequences. KEGG analysis identified 36 complete metabolic pathways, including biosynthetic routes for amino acid and vitamin biosynthesis. A plantaricin gene cluster was identified, consistent with the genetic potential for bacteriocin production. Core-genome phylogenetic analysis positioned Lpb. plantarum CIDCA 83114 among dairy-associated Lpb. plantarum isolates. Importantly, genomic screening revealed no acquired antibiotic-resistance or virulence-associated genes. The few resistance-related loci detected were annotated as resistance-associated but could not be confirmed as acquired resistance determinants; they were chromosomally located and showed no association with the plasmid sequences or prophage-associated regions identified in this assembly. Overall, the genomic features identified in Lpb. plantarum CIDCA 83114 provide a molecular basis consistent with its previously characterized metabolic, probiotic, and antimicrobial properties, while supporting its genomic safety profile.

Fermentation doi: 10.3390/fermentation12110512

Authors: Zhehuan Pu Huixin Su Shihong Yang Dong Chen Yin Ma Guohong Yuan Guishan Xu Halidai Rehemujiang

Machine-harvested cotton residue is a major byproduct of cotton processing whose utilization is limited by a lignocellulosic matrix and antinutritional factors. This study combined an L49(76) orthogonal design with entropy-weighted TOPSIS for multi-indicator selection and then used Plackett–Burman screening and Box–Behnken response surface methodology (RSM) to optimize NDF degradability as a response-specific objective. Range analysis showed that fermentation time was the dominant factor for several fiber-related indices. TOPSIS selected A4B3C6D2E6F1 as the preferred multi-indicator treatment, corresponding to 15% glucose, 10% urea, 65% moisture, 14 days, a bacterial ratio of Enterococcus faecium: Bacillus licheniformis: Bacillus amyloliquefaciens = 15:10:5, and an enzyme ratio of cellulase: laccase: lignin peroxidase = 5:10:15. Relative to the raw residue, NDF, cellulose, hemicellulose, and ADL contents decreased by 25.83%, 43.54%, 74.40%, and 45.65%, respectively. In the subsequent NDF-oriented RSM stage, PBD identified fermentation time, urea, and glucose as the three quantitative factors taken forward to BBD. The model predicted an NDF degradability of 39.054% at 20.449 days, 9.865% urea, and 9.901% glucose; a rounded operating point of 20 days, 10% urea, and 10% glucose yielded a mean of 37.03% in three replicate runs. Thus, TOPSIS and RSM provided complementary results for different optimization objectives rather than a single global optimum.

Fermentation doi: 10.3390/fermentation12110511

Authors: Gundega Gulbe Signe Vessere Viktorija Dika Agnese Brūvere Vineta Aniņa Anda Valdovska

Biofilms in dairy production lines, including milking equipment, can contribute to persistent microbial contamination. This exploratory study screened 32 formulations derived from Lactobacillus acidophilus, Lactobacillus helveticus, Lacticaseibacillus rhamnosus, and Saccharomyces cerevisiae to identify candidates for further biofilm-control studies. Nine bacterial targets, including isolates from milking equipment and reference strains, were tested individually. The attached biomass was measured using crystal-violet staining, with De Man–Rogosa–Sharpe (MRS) controls adjusted to pH 3.8 and 6.8. Planktonic growth was assessed after exposure to native-pH cell-free supernatants (CFSs). The screening comprised one independent experiment with three technical replicates per formulation target combination. All four native-pH CFSs inhibited attached-biomass formation by the six strong biofilm-forming targets, with displayed inhibition values of 71–100% and no or low formulation-only staining. The three lactobacillus-derived CFSs also generally reduced planktonic turbidity to near-background levels, whereas the effect of S. cerevisiae CFS on planktonic growth varied among targets. L. acidophilus pH-adjusted CFS and S. cerevisiae heat-inactivated whole-culture preparation also retained broad antibiofilm activity. Meanwhile, several other cell-containing or pH-adjusted formulations showed target-dependent effects or produced substantial surface-associated material. Native-pH CFSs were the most consistent candidates for independent confirmation and further testing on equipment-relevant surfaces.

Fermentation doi: 10.3390/fermentation12110510

Authors: Lilyana Nacheva Lyudmila Kabaivanova Boryana Yakimova Ivanka Boyadzhieva Kaloyan Berberov Dessislava Todorova Ralitza Alexova Vanyo Mitev Ivanka Stoineva

Surfactants are widely used in industrial applications, creating a growing demand for sustainable and cost-effective production processes. Biosurfactants, on the other hand, are environmentally friendly alternatives to synthetic surfactants because of their biodegradability, low toxicity, and diverse functional properties. Among biosurfactant-producing microorganisms, filamentous fungi remain comparatively underexplored despite their considerable biotechnological potential. This study evaluated the biosurfactant-producing ability of filamentous fungi isolated from petrochemical waste-contaminated soil collected near a fuel station in Sofia, Bulgaria. Three isolates grown on n-hexadecane and olive oil were selected as promising fungi for biosurfactant production, following surface tension reduction and enhancement of emulsification. Based on ITS region sequencing, the isolates were identified as Penicillium cavernicola LL-1 (LC899784.1), Trichoderma longibrachiatum LL-2 (LC899785.1), and Aspergillus niger LL-3 (LC899786.1). Culture conditions were optimized, and the use of mineral–organic media supplemented with 2% sunflower seed oil at pH 7 was found most appropriate. The optimal cultivation temperature was 28 °C for P. cavernicola LL-1 and 35 °C for both T. longibrachiatum LL-2 and A. niger LL-3. Maximum biosurfactant activity occurred during the stationary growth phase. Among the isolates, T. longibrachiatum LL-2 reduced the surface tension to 31.8 mN/m and achieved an emulsification index (E24) of 58% with motor oil, whereas P. cavernicola LL-1 reduced the surface tension to 34.8 mN/m and E24 = 56% for gasoline, and A. niger LL-3 reduced the surface tension to 37.4 mN/m and E24 was 57% for triolein. E24 assay was performed with the same hydrophobic substrates (gasoline, diesel fuel, motor oil, olive oil or trioleins) for all of the studied strains. Based on the primary screening experiments (E24 assay and surface tension measurement), T. longibrachiatum LL-2 was chosen as the most promising biosurfactant producer. For this reason, subsequent experiments were conducted with this strain for a deeper investigation, as it is the least researched. The combined chromatographic, spectroscopic, and mass-spectrometric analyses suggest that the bioproduct obtained from T. longibrachiatum LL-2 exhibits features consistent with a glycolipid compound and certain characteristics reported for sophorolipid-like compounds. However, these preliminary findings do not allow the carbohydrate moiety to be identified conclusively. This novel bioproduct exhibited pronounced surface-active properties, indicating its potential as a fungal-derived biosurfactant for sustainable biotechnological applications.

Fermentation doi: 10.3390/fermentation12110509

Authors: Grace Enzien Anika G. Klein Anja Urbanz Jee-Hwan Oh Timothy J. Donohue Daniel R. Noguera

The dairy industry produces large quantities of lactose-rich residues which could be fermented into a suite of valuable products. In this study, we sought to ferment concentrated cheese whey (CCW), with an initial lactose concentration of about 150 g/L, into D-lactic acid (D-LA) using an engineered strain of Lactiplantibacillus plantarum ATCC BAA-793 that lacks the L-lactate dehydrogenase gene (ldhL1), referred to as LdhL1. In experiments using lactose-supplemented laboratory MRS media, greater than 99% of the lactic acid generated by LdhL1 was the D-stereoisomer, compared to equimolar production of D- and L-lactic acid (L-LA) with the wild-type (WT) strain. When CCW was used as the major source of lactose and essential nutrients, most lactose was fermented in 7 days. However, in mixtures of CCW and MRS, fermentations with high-density LdhL1 cultures took less than 1 day, yielding D-LA titers of ~75 g D-LA/L, with 94% of the LA being the D-LA isomer, and with a production rate of ~3.7 g D-LA/(L h). This fermentation process achieves some of the highest titers and rates of D-LA production from dairy residues, an important step toward valorizing lactose-rich dairy residues.

Fermentation doi: 10.3390/fermentation12110508

Authors: Zhixin Wan Yuyang Li Ni Wang Peng Wu Xiao Dong Chen

Current in vitro colon models predominantly employ planktonic fecal bacterial fermentation. We designed a colonic microbial culture model consisting of bionic mucus, mucosa and muscularis. The bionic mucus contained bacterial quorum sensing molecule, autoinducer-2 (AI-2), for stimulating biofilm formation. The bionic mucosa was a UV-curable 15% GelMA/1% HAMA/0.5% PVAMA composite hydrogel, serving as a biocompatible biofilm attachment interface. The bionic muscularis made of silicone was designed as a physical barrier isolating the anaerobic microbial ecosystem and external environment. The experiment of culturing infant feces showed that this culture model can construct a microbial microecosystem that enables microorganisms to attach. Confocal laser scanning microscopy and scanning electron microscopy demonstrated bacterial colonization attached within the hydrogel pores. Quantitative PCR revealed that biofilm-associated bacterial abundance could reach 7.56 × 108 gene copies/g, which was approximately two orders of magnitude higher than that in the mucus. AI-2 further modulated microbial community assembly by promoting the enrichment of Bifidobacterium, increasing its abundance from 9.20 × 107 to 1.77 × 108 gene copies/g, while suppressing Escherichia-Shigella from 2.98 × 108 to 2.00 × 108 gene copies/g after 24 h cultivation. This study aimed to construct a bionic colon model that supports the colonization of fecal microbiota for survival, growth, attachment and community succession. Serving as a microbial culture bioreactor, this model provided a physiologically relevant in vitro platform to investigate the characteristics of colonic biofilm-associated microbial ecology and corresponding microbiota intervention strategies.

Fermentation doi: 10.3390/fermentation12110507

Authors: René Alejandro Flores-Estrella Rubén Fernando Gutiérrez-Hernández Hugo Alejandro Nájera-Aguilar José Luis Cabellos Jesús Mauricio Ernesto Hernández-Méndez Abumalé Cruz-Salomón Victor Alcaraz-Gonzalez

Background: The anaerobic digestion (AD) of the organic fraction of municipal solid waste (OFMSW) is a widely used waste-to-energy technology. However, inhibition effects can drive the process toward acidification or washout, with a consequent loss of treatment efficiency. Feedback control can prevent these undesirable conditions, but the biomass concentration is not measurable online. Methods: This work proposes an observer-based control scheme for the AD of the soluble fraction of OFMSW near an inhibited nominal operating condition. An extended Kalman filter (EKF) estimates the acidogenic biomass from the online measurement of the soluble organic substrate. A proportional–integral (PI) controller regulates the estimated biomass by manipulating the dilution rate. Three tuning methods are compared: approximate M-constrained integral gain optimization (AMIGO), Skogestad internal model control (SIMC), and frequency-domain auto-tuning. The convergence of the scheme is analyzed through Lyapunov and input-to-state stability arguments. The evaluation is simulation-based. Results: In an open loop, the observer converged under initial offsets of up to 35%, with steady-state error norms below 0.31 mg/L. The convergence time ranged from 45.3 to 81.3 d, depending on the initial estimation error. In a closed loop, nine controller designs tracked the reference and rejected feed perturbations over a 1000 d horizon. Under a stoichiometric mismatch of ±5%, the true-state tracking error of design S2 increased from 459.5 to 1783.5 mg d/L. The estimated-state error remained at 558.4 mg d/L. Estimated-state tracking can therefore conceal substantial true-state errors. The fastest design achieved the lowest estimated-state IAE, 501.1 mg d/L, but exhibited the lowest gain margin, 5.8 dB. The lowest true-state IAE, 450.2 mg d/L, corresponded to a design with a phase margin of 60∘. Conversely, the most conservative designs paired the largest IAE values with the largest gain margins, up to 15.2 dB. Conclusions: The proposed scheme maintains the anaerobic process around its inhibited nominal operating condition under the tested feed disturbances. The scheme uses a standard analytical measurement. The results support its feasibility as a soft sensor-based control strategy for anaerobic reactors near this operating condition. The prevention of acidification or washout under increased inhibition disturbances is beyond the tested scope.

Fermentation doi: 10.3390/fermentation12110506

Authors: Marta A. Piva Ismael Mayo Jamal A. Chambers Allison S. Olivier Jon Ignacio Moreno

We compared the initial ethanol production capacity of Saccharomyces cerevisiae ρ0 mutants with that of isogenic wild types to prevent alcohol toxicity from affecting the fermentation results. This study used meiotic segregants from a cross between the BY 4741 strain and the Δccm1 mutant to account for biological variability. We measured the dextrose fermentation rate using a CO2 sensor during the first 10 min and biomass spectrophotometrically at 600 nm. Colorimetric assays determined alcohol concentration and the NAD+/NADH ratio. RNA sequencing assessed expression of genes involved in glycolysis, fermentation, NAD+-dependent regulation, and generation of the electrogenic mitochondrial membrane potential. Reverse transcription quantitative PCR measured cytoplasmic ribosomal RNA levels. The ρ0 mutants produced 63% more CO2 per biomass unit than their wild-type counterparts, as confirmed by ethanol production. However, their doubling time was significantly longer, as is characteristic of ρ0 mutants. They also had a lower NAD+/NADH ratio, higher cytoplasmic ribosomal RNA, and upregulation of several glycolytic and alcoholic fermentation genes, including TDH3, which increased more than 4-fold, all of which favor a better ethanol yield per unit of biomass. These findings highlight the genetic and biochemical factors that influence alcohol production under conditions not affected by alcohol toxicity.

Fermentation doi: 10.3390/fermentation12110505

Authors: Virginia Prieto-Santiago Sarah H. E. Verkempinck Tara Grauwet Ingrid Aguiló-Aguayo Maribel Abadias

This study characterized a protein-fortified peach-and-grape beverage, focusing on the effects of fermentation and protein particle size on protein digestibility and the bioaccessibility of minerals and antioxidants. Beverages were formulated with 3.5% pea protein isolate (PPI), added directly to peach-and-grape juice (PGJ) or subjected to high-pressure homogenization (HPH) before incorporation. The resulting beverages (PGJ + PPI and PGJ + PPIHPH) were evaluated before and after lactic fermentation for 48 h. HPH significantly reduced PPI particle size while increasing polyphenol content (11.27%) and antioxidant activity (ABTS: 11.09%; FRAP: 12.83%). Fermentation resulted in the detection of glutamine (1.32 ± 0.23 mg/g d.w.) and increased lactic acid content (61.44 ± 0.83 mg/g d.w.) and the levels of the essential amino acids phenylalanine and valine. Both fermentation and HPH increased the readily bioaccessible hydrolyzed protein fraction (13.27% and 11.94%, respectively), although neither significantly affected mineral or antioxidant bioaccessibility. Probiotic viability during fermentation and simulated gastrointestinal digestion was assessed using viable counts, with the quantitative results needed to establish the extent of viability retention. However, fermented beverages showed lower consumer acceptability. Overall, protein fortification and fermentation improved selected nutritional and in vitro digestive properties, although fermentation adversely affected sensory acceptance. These findings highlight the need to balance nutritional and functional improvements with consumer acceptability in the development of fermented, protein-fortified plant-based beverages.

Fermentation doi: 10.3390/fermentation12110504

Authors: Aida Esther Peñuela-Martínez Aristófeles Ortiz Camila Buitrago-Zuluaga Arley David Zapata-Zapata María Manuela Hincapié-Gomez Magally Romero-Tabarez

Starter cultures enhance coffee sensory quality by producing yeast-derived volatile organic compounds (VOCs). This study evaluated five native yeast strains—Hanseniaspora guilliermondii, Pichia membranifaciens, Schizosaccharomyces pombe, Torulaspora globosa, and Rhodotorula aurantiaca—for their VOC contributions in mucilage, green beans, and roasted coffee. A 2×2+1 factorial randomized complete block design assessed two consortia (c1, c2), two inoculation growth phases (lag, t1; exponential, t2), and a spontaneous fermentation control. VOCs were analyzed via HS-SPME-GC-MS, and sensory quality was evaluated per SCA protocols. Multivariate and univariate statistical analyses were conducted across matrices, demonstrating a shift from fermentation-derived alcohols and esters in mucilage and green beans to thermally generated pyrazines, furans, and aldehydes in roasted coffee. Treatment c2t2 exhibited higher metabolic activity in mucilage, with increased peak areas for acids, alcohols, and aldehydes, while c1t1 showed a greater chromatographic response for acids and ketones in green coffee. In roasted coffee, peak areas of compounds associated with enhanced aroma and body, such as 1-(2-furanyl)ethanone, 1-(2-furanyl)-1-propanone, and pyrazines, were significantly higher for c2, whereas 1-hydroxy-2-propanone, 1-hydroxy-2-butanone, and 1-acetyloxy-2-propanone were higher for t1. Although non-parametric sensory tests did not reveal statistically significant differences among treatments, c1t1 achieved the highest numerical overall cupping score (82.63 SCA points) due to improved flavor, acidity, and balance. Yeast inoculation obtained SCA total scores 2.6 to 3.5 points higher than that of spontaneous fermentation (79.13 points) without developing defective off-flavors. The evaluated yeasts show potential in modulating specific volatile profiles and sensory attributes in coffee effectively.

Fermentation doi: 10.3390/fermentation12110503

Authors: Weiqin Zhang Cuijiao Feng Tao Zhang Lai-Yu Kwok Qiuwen He

Inflammatory bowel disease (IBD) is a chronic non-specific gut inflammatory disease. Conventional treatments are insufficient to support long-term disease remission, so there is an urgent need to search for new IBD treatment options. This study evaluated the alleviation effect of Lactobacillus (L.) helveticus H9 on dextran sodium sulfate (DSS)-induced colitis rats. We found that administering L. helveticus H9 significantly reduced DAI (disease activity index) scores (p ≤ 0.05), spleen weights (p ≤ 0.05), and colonic tissue damage in the colitis rats, while increasing the body weight gain rate. Compared with the DSS group, L. helveticus H9-receiving rats had less serum tumor necrosis factor-α (p ≤ 0.05) and interleukin-1β (p < 0.01), a higher gut microbiota diversity, and significantly more Alistipes senegalensis (p ≤ 0.05) and Parabacteroides distasonis (p < 0.01). On the metabolomics level, 65 significantly differential metabolites (VIP > 1, p < 0.05, fold change > 2 or <0.5) were identified between the probiotic and DSS groups. Some significantly enriched pathways were identified in the fecal metabolome of the probiotic group, including Sphingolipid metabolism, Linoleic acid metabolism, alpha-Linolenic acid metabolism, Arachidonic acid metabolism, Glycerophospholipid metabolism, Pyrimidine metabolism, Tryptophan metabolism, Fatty acid biosynthesis and Steroid hormone biosynthesis metabolic pathways, and lecithin is an important differential metabolite interconnecting several of the enriched pathways. In summary, administering L. helveticus H9 modulated the gut microbiota, metabolome, and host immune response, which could relate to symptom alleviation in the colitis rats. Our study provides interesting data regarding the use of probiotics in managing chronic colitis.

Fermentation doi: 10.3390/fermentation12110502

Authors: Pável Padilla-Tamayo Armando Quintero-Ramos Miguel Ángel Sánchez-Madrigal José Carlos Espinoza-Hicks Ever Hernández-Olivas Iván Salmerón José Rafael Linares-Morales María del Cielo Valdez-Cárdenas Martha Graciela Ruiz-Gutiérrez

Water kefir is a fermented beverage produced by a consortium of diverse microorganisms that can adapt to different substrate sources, modifying the beverage’s physicochemical and functional properties. Apple pomace is an agro-industrial by-product with nutrients and compounds that can enhance microbial activity and influence metabolite production, leading to subsequent physicochemical and phytochemical changes. In this study, apple pomace extract served as the substrate for water kefir fermentation at 30 °C for 120 h. Changes in total sugar content, pH, total polyphenols, antioxidant activity, microbial growth, organic acids, and volatile compounds were evaluated. The results showed a significant difference between substrates during fermentation. The process with apple pomace extract decreased total sugars, pH, and total polyphenols and increased antioxidant activity and microbial growth. Using apple pomace extract, acids such as acetic, lactic, malic, and citric, along with volatile compounds such as ethanol, isobutanol, isoamyl alcohol, and ethyl acetate, were detected, highlighting the water kefir consortium’s metabolic activity during fermentation. Apple pomace proved to be a suitable substrate for water kefir fermentation, as it promoted microbial growth and metabolite production; thus, it could serve as an alternative for developing fermented beverages with potential functional properties.

Fermentation doi: 10.3390/fermentation12110501

Authors: Jázmin Molnár László Varga Ronald H. J. Scholten Károly Tempfli Eszter Zsédely Bernadett Bana Loretta Sárvári Georgina Takács Balázs Ásványi Erika Lakatos Viktória Kapcsándi Tamás Tóth

Evidence on liquid-fermented pea–wheat supplementation in broilers remains limited. This 42-day exploratory trial evaluated growth and biological responses using basal diets formulated for semi-intensive production. Eight hundred one-day-old male Ross 308 broilers were randomly assigned to two treatments (eight pens per treatment; 50 birds per pen): a freshly hydrated, unfermented mixture (CONTROL) or a mixture fermented for 24 h at 37 °C (FERMENT). Both mixtures supplied 3% (w/w) ground substrate relative to basal feed. During fermentation, pH decreased from 6.11 to 3.78. Compared with CONTROL, FERMENT birds had higher final body weight (1725 vs. 1649 g; p = 0.006) and feed intake, with no significant difference in feed conversion ratio. Tissue-specific cytokine-gene expression differences and lower litter Escherichia coli and coliform counts on days 28 and 42 were observed. Relative wing yield, breast drip loss and thigh thawing loss were significantly higher in FERMENT, whereas raw-carcass microbial counts and sensory attributes did not differ significantly. Because fermentation status was confounded with storage duration, treatment responses cannot be attributed exclusively to fermentation. The findings indicate greater growth accompanied by increased feed consumption, without demonstrated improvements in feed efficiency or general health.

Fermentation doi: 10.3390/fermentation12110500

Authors: Vanesa Postigo Margarita García Julia Crespo Alice Agarbati Francesca Comitini Laura Canonico

The global beverage market is experiencing a growing demand for low- and reduced-alcohol wines and beers, driven by shifting consumer preferences toward healthier lifestyles and stricter regulations. While conventional physical dealcoholization methods often compromise the sensory profile and texture of the final product, biological approaches using non-Saccharomyces yeasts have emerged as a sustainable and innovative alternative. This review provides a comprehensive overview of the metabolic diversity of the main non-Saccharomyces genera, assessing their potential for ethanol reduction in both grape juice and wort. We compare the different carbon transport and diversion strategies employed by these yeasts across distinct matrices, from the redirection of hexoses toward glycerol or lactic acid pathways in winemaking to the utilization of maltose-negative phenotypes that naturally limit attenuation in brewing. Furthermore, this review addresses the crucial role of non-Saccharomyces metabolism in sensory compensation, detailing how specific enzymatic activities and the production of volatile compounds (esters, higher alcohols) counteract the loss of mouthfeel and aroma volatility typically associated with ethanol reduction. Finally, critical technological bottlenecks, such as controlled aeration strategies, the nutritional impact of micro-oxygenation and subsequent nutrient competition (primarily nitrogen) between non-Saccharomyces and Saccharomyces yeasts in co-inoculations, and microbiological stability under low-alcohol conditions, are discussed. By providing a direct comparative analysis between wine and beer applications, this review highlights how exploiting biodiversity can reshape the technological landscape of low-alcohol beverage production.

Fermentation doi: 10.3390/fermentation12110499

Authors: Luis Guillermo González-Olivares Ana Fátima Chávez-Olvera Carlos Farfán-Flores María Fernanda Escamilla-Rosales Elizabeth Contreras-López Emmanuel Pérez-Escalante Laura Berenice Olvera-Rosales

Bioactive peptides derived from food proteins have gained attention as potential functional food components. This study evaluated proteolytic and functional changes during whey fermentation with Lactococcus lactis NCFB 724, with emphasis on the in vitro inhibition of angiotensin-converting enzyme (ACE) and dipeptidyl peptidase IV (DPP-IV). Whey was fermented for 48 h, monitoring microbial growth, pH, titratable acidity, free amino group concentration, electrophoretic profile, and ACE- and DPP-IV-inhibitory activities. Pearson correlation analysis and principal component analysis (PCA) were additionally performed as exploratory approaches. During fermentation, pH decreased from 6.07 to 4.00, while cell viability increased from 5.9 to 8.8 log CFU/mL and free amino group concentration increased from 407.02 to 539.20 µg/mL. Electrophoretic analysis revealed changes in signal distribution in the low-molecular-weight region (<10 kDa). DPP-IV-inhibitory activity showed no significant differences among fermentation times, with values of 35.49% at 0 h and 37.80% at 48 h, whereas ACE inhibition showed a time-dependent response, reaching its highest value (57.14%) at 24 h. The first two principal components explained 82.69% of the total variance, providing an exploratory visualization of the temporal patterns among the evaluated variables. Overall, greater proteolysis did not correspond to greater enzyme-inhibitory activity. These findings identify 24 h as a fermentation stage of interest for further characteriza tion.

Fermentation doi: 10.3390/fermentation12110498

Authors: Guiqin Zhao Xingdi Liang Jingchao Liu Hao Wang Wei Gao

Lycopene is a carotenoid with potent antioxidant activity. Microbial fermentation has emerged as a promising production platform owing to its natural origin, safety, and independence from seasonal constraints. However, most high-yield studies rely on extensive metabolic engineering and are conducted at the 3–7 L laboratory scale, with limited research on pilot-scale process development. In this study, a recombinant Komagataella phaffii (formerly Pichia pastoris) strain Pp-F2-G1-035 producing lycopene was used to systematically investigate shake-flask medium optimization, high-density fermentation, and 50 L pilot-scale process development, using a pre-engineered strain, with no further metabolic engineering performed in this study. The optimal shake-flask medium was identified as 0.8× BSM basal salts medium supplemented with 5 g/L peptone, achieving a lycopene titer of 261.4 mg/L—approximately 172% higher than with standard BSM. After iterative optimization in 5 L and 10 L bioreactors, the 50 L pilot trial employed a three-stage high-density seed train. A representative batch reached 3.37 g/L after 139 h of fermentation, while an extended fermentation batch (198 h) yielded 3.70 g/L. The specific lycopene yield per unit biomass in the 50 L bioreactor was comparable to that in the 10 L system, providing a preliminary 50 L-scale demonstration. Notably, a basal level of lycopene accumulation (0.045–0.19 g/L) was detected during the glycerol feeding phase prior to methanol induction, suggestive of possible partial derepression of P_AOX1. The production strain exhibited stable lycopene production across 9 serial passages (mean 228.3 mg/L, CV 9.7%), indicating good phenotypic production stability across passages. This work provides a preliminary 50 L-scale process demonstration, establishing a technical basis for further scale-up evaluation of lycopene production by K. phaffii.

Fermentation doi: 10.3390/fermentation12110497

Authors: José M. Benito-Ventoso Ángela Peirotén José Abellán José Antonio Curiel Iván Palomino Pilar Sabuquillo Susana Langa José María Landete

The fermentation of cow’s milk and soy beverages, a plant-based alternative, by lactic acid bacteria (LAB) and bifidobacteria strains shares the goal of creating functional products, but differs significantly in the substrates and final properties. The aim of this study was to compare the functional properties offered by 21 selected strains of LAB and bifidobacteria in the fermentation of soy beverages and cow’s milk. LAB and bifidobacteria strains showed a greater pH decrease in soy beverages, particularly in Lactiplantibacillus plantarum and Bifidobacterium pseudocatenulatum strains, which were only able to grow and ferment in soy beverages. Lacticaseibacillus rhamnosus and Lacticaseibacillus paracasei strains showed high proteolytic activity in both milk and soy beverages, while Streptococcus thermophilus and Lactococcus lactis strains showed greater proteolytic activity in cow’s milk, and most bifidobacteria strains did not show proteolytic activity. Fermentation mostly resulted in an increase in antioxidant activity in soy beverages, as measured by DPPH, and in cow’s milk by FRAP. Finally, all L. paracasei, L. rhamnosus, and bifidobacteria strains showed efficient production of daidzein and genistein in soy beverages. In conclusion, soy beverages are a better substrate for L. plantarum and bifidobacteria strains, and the production of bioactive isoflavones by many selected strains increases the functional potential of soy beverages.

Fermentation doi: 10.3390/fermentation12110496

Authors: Mingyu Shi Ting Guo Qinlu Lin Feng Lin

Mi Zhen, a nutrient-dense by-product generated via AI-guided targeted rice milling, is rich in lipids, proteins, dietary fibers, and bioactive compounds, holding significant potential for high-value applications. However, processing readily activates endogenous lipases, triggering lipid hydrolysis and oxidative deterioration that compromise quality and shelf life, thereby severely constraining its commercial utilization. This review comprehensively summarizes and critically discusses the compositional profile and instability mechanisms of Mi Zhen, critically evaluating the efficacy and limitations of mainstream stabilization strategies, including physical, chemical, and biological approaches. While conventional thermal and chemical treatments are industrially established, they are constrained by suboptimal nutrient retention, high energy demands, and limited flavor control. In contrast, microbial fermentation emerges as a sustainable bioprocessing alternative that synergistically suppresses lipid rancidity, degrades anti-nutritional factors, and enhances both nutritional value and functional bioactivity. To address the inherent bottlenecks of traditional fermentation-namely, empirical process control, unresolved mechanistic pathways, and poor standardization-this work highlights how integrated multi-omics technologies bridge the microbial–molecular–quality continuum. By providing a systems-level analytical framework, multi-omics serves as a pivotal engine for transitioning Mi Zhen fermentation from experience-dependent practices toward data-driven optimization, mechanistic transparency, and precision engineering. Ultimately, this review establishes a theoretical foundation and technical roadmap for advancing stabilization protocols, rational bioprocess design, and the sustainable, high-value valorization of rice milling by-products.

Fermentation doi: 10.3390/fermentation12110495

Authors: Yuan Fang Wenting Song Xuefeng Guo

Bamboo residues are a potential sugar source for polyhydroxyalkanoate (PHA) production, yet their suitability depends on the coupling of saccharification, microbial conversion and polymer recovery. This critical narrative review examined bamboo composition and pretreatment, direct PHA experiments and comparative evidence from other lignocellulosic feeds. It focused on enzymatic sugar hydrolysates, with lignin-rich pretreatment liquor considered separately. Bamboo studies demonstrated substantial tissue-dependent variation and production of concentrated glucose–xylose streams. Four related Halomonas studies established PHA production from selected bamboo-derived feeds, mainly in liquor-based, mixed-carbon or split-vessel configurations. Their results supported further sugar-hydrolysate development but did not validate a recovery-inclusive process across heterogeneous residues. Comparative experiments identified strain-specific pentose uptake, matrix tolerance and nutrient-dependent polymer accumulation as major selection criteria. Carbohydrate retention, conditioning losses and feeding strategy were more informative than maximum residual-solid digestibility alone. Recovery methods and selective cultivation introduced additional resource and product-quality trade-offs, while agricultural valorization of the separated liquor remained conditional. The central development need is to connect representative residue batches to sugar consumption, sustained PHA production and recovered material of specified quality. Economic and environmental assessments should use these linked measurements rather than isolated conversion maxima.

Fermentation doi: 10.3390/fermentation12110494

Authors: Xuyang Guan Jiachen Li Yiwen Shao Sen Bian Xiujin Li Hairong Yuan Xiaoyu Zuo

This study evaluated an ethylene glycol–sodium hydroxide (EG–NaOH, 8:1 molar ratio) mixture pretreatment for enhancing dark fermentative biohydrogen production from corn stover. Two separate single-factor screening series examined pretreatment temperature (30–110 °C at 3 h) and process time (1–9 h at 70 °C). In the temperature series, pretreatment at 70 °C for 3 h produced a reducing sugar concentration of 29.58 g L−1 after enzymatic hydrolysis and gave the highest reported measured hydrogen yield of 109.82 mL g−1 VS (549.09 mL), approximately 9.12 times that of the untreated control. In the independent pretreatment-time series, hydrogen yields ranged from 75.46 to 84.95 mL g−1 VS across 1–9 h. The 1 h treatment is therefore considered a candidate that prioritizes shorter process time rather than a validated optimum. For the 70 °C treatment in the temperature series, the modified Gompertz fit gave a fitted Pmax of 110.16 mL g−1 VS, a fitted Rmax of 3.30 mL g−1 VS h−1, and a fitted lag parameter λ of 4.63 h; these parameters are interpreted descriptively. Metabolite and oxidation–reduction potential (ORP) profiles changed during fermentation; however, the observed hydrogen production did not support a universal ORP threshold as a necessary or sufficient condition for hydrogen formation. Endpoint 16S rRNA gene sequencing showed a greater relative representation of several Clostridium groups in the treated profile, while PICRUSt2 predicted a higher relative representation of the hydrogenase-related COG4624 category (0.170% versus 0.0482% in the untreated profile). These results are descriptive and do not establish direct ecological filtering, differential hydrogenase expression, or increased enzyme activity. Overall, the EG–NaOH mixture pretreatment increased reducing sugar release and hydrogen production from corn stover, while process optimization, energy performance, and the proposed causal mechanisms require further validation.

Fermentation doi: 10.3390/fermentation12110493

Authors: Jin Sun Jiancheng Luo Zhiqiang Qi Run Yang Wenli Zhang

Solid-state fermentation (SSF) with multi-strain inoculants is widely used to upgrade complete feed, yet how it reallocates nutrients in starch–protein diets has rarely been quantified on a dry-matter basis. Complete feeds for growing-finishing pigs and laying hens were inoculated with a six-strain composite inoculant (two Bacillus strains, two lactic acid bacteria and two yeasts) and fermented anaerobically for 5 d (n = 3; uninoculated feed as received served as the control, n = 1). Both feeds acidified to pH ≈ 4.5. The soluble-protein-to-crude-protein ratio rose by 36.7% and 36.8%, and acid-detergent insoluble protein fell by 21.4% and 23.1%. Soluble carbon was consumed: starch decreased by 17.4% and 3.9%, and linolenic acid by 70.5% and 24.2%, with the magnitude of starch loss tracking the fermentable-carbon supply of each feed. Dry-matter loss concentrated crude protein, ash and fiber fractions, while total digestible nutrients changed by only −2.1% and −1.4%. None of the six strains showed hemolysis (γ-hemolysis) on sheep-blood agar. Fermentation therefore raised protein availability rather than protein quantity, consumed starch and essential fatty acids, and left energy essentially unchanged; the inoculant may be better suited to ruminant roughage than to complete feed.

Fermentation doi: 10.3390/fermentation12110492

Authors: Ana Catarina Pereira Cordeiro António M. Peres Lígia R. Rodrigues Cláudia Amorim

Olive industry by-products, particularly olive pomace (OLP), extracted olive pomace (EOLP), and olive stones (OLS), are promising alternative substrates for oligosaccharide (OS) production, as their polysaccharides can be converted into OS by physicochemical treatment, enzymatic hydrolysis, or direct fermentation. However, OS mixtures and one-step strategies integrating enzyme production and substrate conversion remain underexplored. This review evaluates OLP, EOLP, and OLS as raw materials for producing XOS-rich and POS-related oligosaccharides, as well as OS mixtures with prebiotic and technological potential, emphasising direct fermentation. A structured literature mapping was used to compare substrate types, product classes, and production strategies. Conventional physicochemical and enzymatic strategies are compared with the emerging direct fermentation strategy in terms of substrate accessibility, OS yield, degree of polymerisation, product composition, downstream requirements. Physicochemical processes enable rapid solubilisation but require careful control to limit over-depolymerisation, whereas enzymatic hydrolysis provides greater selectivity but depends on substrate accessibility and enzyme inputs. Direct fermentation integrates enzyme production and substrate conversion, although product control and recovery remain challenging. Human evidence is strongest for XOS, while POS and OS mixtures require direct validation. Further progress requires linking substrate composition and process selection to product standardisation, biological validation, and application-oriented testing.

Fermentation doi: 10.3390/fermentation12110491

Authors: Maite Villalobos Carmine Mattia Verosimile Belén Sepúlveda Claudio D’Onofrio Marcelo Lanino Ingrid Poblete Alexis Velásquez

Viticulture in hyper-arid environments represents an emerging frontier in non-traditional winegrowing regions, where extreme climatic conditions may be associated with distinctive grape and wine chemical composition. In this study, four wines produced from Vitis vinifera cv. Tamarugal cultivated in the Atacama Desert (Chile) were characterized based on their volatile organic compound composition, with particular emphasis on free and glycosylated aroma-related volatile fractions. Wines from four production years (2019–2022), obtained under different vinification approaches, were analyzed using solid-phase extraction followed by GC–MS. The free volatile fraction was dominated by lipid-derived compounds, including fatty acid-derived alcohols, acids, and esters, whereas the glycosylated fraction was enriched in C13-norisoprenoids and benzenoid/phenylpropanoid-derived precursors, highlighting a substantial pool of bound volatile compounds. Multivariate analyses, including principal component analysis (PCA) and supervised partial least squares–discriminant analysis (PLS-DA), were applied to explore patterns in volatile composition and support visualization of variables associated with sample differentiation. The observed compositional differences were associated with the combined influence of vintage and vinification conditions, which could not be experimentally disentangled in the present study. This study provides the first characterization of free and glycosylated volatile profiles in wines produced in the Atacama Desert and contributes to the understanding of wines from non-traditional hyper-arid viticultural conditions.

Fermentation doi: 10.3390/fermentation12100490

Authors: Qiyuan Deng Li Gao Shan Zhang Ruirui Tian Fan Yang Zhijun Zhang

The use of cottonseed hulls as a feed resource is constrained by their high fiber content and residual free gossypol. This study evaluated the effects of steam explosion combined with fermentation using a microbial–enzyme preparation on the nutrient composition, fermentation quality, bacterial communities, and in vitro digestion and fermentation characteristics of cottonseed hulls. Four treatments were evaluated using physicochemical analyses, 16S rRNA gene sequencing, and in vitro incubation: an untreated control (CK), steam explosion (BP), fermentation with a microbial–enzyme preparation (FJ), and steam explosion followed by fermentation with the same preparation (BF). All processing treatments significantly reduced free gossypol content (p < 0.05), with BF showing the lowest concentration (70.42 mg/kg), representing a 77.89% reduction relative to CK. The neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents of BF were 573.38 and 446.23 g/kg dry matter (DM), respectively, both significantly lower than those of CK (p < 0.05) but not significantly different from those of BP. Crude protein content did not differ significantly among treatments. BF had the highest lactic acid content (27.94 g/kg DM) and the lowest endpoint pH (4.12). Bacterial community analysis showed that Firmicutes was the dominant phylum in all three fermented groups. At the end of fermentation, Lentilactobacillus was the dominant genus in the BF group, with a relative abundance of 97.55%. No associations between bacterial taxa and fermentation parameters remained significant after correction for multiple testing. KEGG functional prediction indicated differences in potential functional composition among treatments. In vitro DM digestibility in BF reached 43.99% at 48 h; however, NDF digestibility did not differ significantly among treatments at any incubation time. Cumulative gas production and total volatile fatty acid concentration in BF at 48 h were 154.28 mL/g DM and 64.58 mmol/L, respectively, neither of which differed significantly from FJ. In conclusion, steam explosion combined with microbial–enzyme fermentation reduced free gossypol content, promoted lactic acid accumulation, and altered bacterial community composition, providing experimental evidence to support further development of cottonseed hulls as a feed resource.

Fermentation doi: 10.3390/fermentation12100489

Authors: Amairany Carrasco-López Arizbeth G. Villanueva-Flores Natividad Castro-Alarcón Nelda X. Martínez-Galero Arturo Ramírez-Peralta Roxana Reyes-Ríos Octavio T. Barrera-Perales Elisa López-Loeza Freddy M. Torres-Antonio Agustín Reyes-Pérez César Sotelo-Leyva Alberto Patricio-Hernández Jeiry Toribio-Jiménez

Spontaneous fermentations contribute to the identity of ancestral mezcal, although duration and yield may vary. This study selected an indigenous yeast and evaluated it as a starter candidate. Four native isolates (Torulaspora delbrueckii A1GM and A6GM, Kluyveromyces marxianus A2GM, and Saccharomyces cerevisiae A5GM) and a spontaneous control were compared in Agave cupreata microfermentations. Selection considered distillate alcohol content and preliminary ethanol-tolerance assays. A5GM was subsequently evaluated in three production batches containing A. angustifolia + A. karwinskii, A. angustifolia, or A. cupreata + A. angustifolia, with three independent vats per treatment. Fermentation profiles, distillate composition, yield, and sensory acceptance were assessed. A5GM produced the highest microfermentation distillate alcohol content (43.91 ± 0.89% Alc. Vol.) and grew at 16% ethanol (v/v). In the first two production batches, inoculated vats showed higher volumes standardized to 45% Alc. Vol. and lower calculated agave requirements than the controls; these were batch-specific observations under the operating conditions studied. Sensory evaluation used pooled vat-derived distillate composites, and the A5GM composites received the highest mean hedonic scores. Because strain-level establishment and persistence of A5GM were not confirmed, the observed outcomes cannot be attributed exclusively to this strain. Sensory interpretation is limited by fixed presentation order. Further independent batches, standardized management, and strain-level monitoring are needed to assess reproducibility.

Fermentation doi: 10.3390/fermentation12100487

Authors: Ying Wang Wei Guo Ding Dong Kai Ji Shuang Li Weiyi Tao

Rhamnolipids are promising biosurfactants with diverse applications, but their efficient production from glucose remains challenging. In this study, a glucose-based fermentation process was developed using Pseudomonas aeruginosa YM4 through sequential evaluation of nitrogen source, pH, C/N ratio, glucose concentration, and Fe2+ supplementation in a 5 L bioreactor. A mixed NH4+/NO3− nitrogen source resulted in higher rhamnolipid production than either NH4+ or NO3− alone. Maintaining the culture pH at 7.2 prevented excessive acidification and promoted glucose consumption and rhamnolipid production. The highest rhamnolipid titer (29.7 g/L) was achieved using 100 g/L glucose, a C/N ratio of 35, and 10.8 μM Fe2+. Fermentation kinetics indicated that biomass accumulated rapidly during the early fermentation stage, whereas rhamnolipid production continued after cell growth had slowed. Under the selected conditions, YM4 produced a rhamnolipid mixture containing 73.8% di-rhamnolipids and showed substantially higher rhamnolipid production than three additional P. aeruginosa strains cultivated under identical conditions. This study developed a glucose-based fermentation process for producing di-rhamnolipid-rich products and demonstrated the efficient rhamnolipid-producing capability of P. aeruginosa YM4 under the evaluated conditions.

Fermentation doi: 10.3390/fermentation12100488

Authors: José A. D. López-Coronado Zelin Li Joe L. Jacobs Edward Nagul Sharon R. Aarons

Increasing the solids concentration in farm dairy effluent is necessary to operate a biogas plant at optimal parameters; however, conventional chemicals reduce CH4 production. This study evaluated the effects of the tannin-based coagulant–flocculant Tanfloc SG® on anaerobic digester performance using biomethane potential (BMP) tests with centrifuged solids produced at 50–300 mg Tanfloc g TS−1, and semi-continuous fermentation tests with settled solids at 150 mg g TS−1 (Tanfloc150). In the fermentation tests, the control and Tanfloc-treated solids were fed into two reactors, operating at 37 °C, at 2.1 kg VS m−3 d−1 with a 12- to 15-day hydraulic retention time. In the BMP tests, the Tanfloc-treated solids showed delayed degradation and produced 168.2–303.1 L CH4 kg VS−1, values not significantly different from the untreated solids (250.0 L CH4 kg VS−1). However, semi-continuous feeding reduced the volatile solids degradation, biogas, and specific CH4 yield by 23.3%, 17.9%, and 24.1%, while the pH, volatile fatty acids, and ammonia-N remained stable. However, Tanfloc150 reduced the biogas H2S and NH3 concentrations and increased the digestate N and S. The lower performance was associated with lower substrate biodegradability, which was consistent with the delayed degradation observed in the BMP tests. These findings highlight the importance of assessing coagulated solids under conditions representative of long-term performance.

Fermentation doi: 10.3390/fermentation12100486

Authors: Xiudi Zhang Fuqiang Xu Xia Liu Xiaohua Du Yanbin Zhu Yuan Gao Changhui Xu Miaoyin Dong Fengyu Mao Yaxiong Ren Dawa Jiangcuo

Lactic acid bacteria combining probiotic properties with acidification capacity and stress tolerance are valuable for food fermentation but remain insufficiently characterized. In this study, a strain of Pediococcus acidilactici, designated PA-X1, was isolated from pastoral fermented yak yogurt collected from the Qinghai–Tibet Plateau. Its in vitro probiotic-related properties, acidification performance, genomic characteristics, and expression patterns of key genes associated with acidification-related metabolism were investigated. After 24 h of fermentation, the broth pH decreased to 3.75 ± 0.02 and the L-lactic acid concentration reached 8.53 ± 0.23 g/L. The glucose concentration decreased from the measured initial value of 20.0 g/L at 0 h to 6.00 g/L at 24 h, corresponding to 70.0% glucose consumption. PA-X1 showed a survival rate of 94.64 ± 0.10% at pH 3.0, and its culture supernatant inhibited all three tested indicator bacteria, namely Escherichia coli, Salmonella enterica, and Staphylococcus aureus, in vitro. Genomic analysis identified multiple genes associated with acidification-related metabolism, including those involved in the phosphotransferase system (PTS), the Embden–Meyerhof–Parnas pathway, pyruvate metabolism and lactate synthesis. Additionally, the PTS-related genes ptsI, ptsH, and crr were significantly upregulated under high-glucose conditions (40 g/L), whereas low-pH conditions induced varying degrees of upregulation of glycolysis- and pyruvate-metabolism-related genes, including pgk, eno, tpiA, ldhA, ldhL, and ackA. Together, these phenotypic, genomic, and gene-expression results suggest that the acidification phenotype of PA-X1 may be associated with carbohydrate uptake, glycolysis, pyruvate metabolism, and organic acid formation. Overall, the combined probiotic-related, acidification, and antibacterial properties of PA-X1 support its potential as a functional starter culture for developing probiotic fermented foods with improved microbial safety and functional value.

Fermentation doi: 10.3390/fermentation12100485

Authors: Xiaoyan Wang Xianlin He Guo Tang Ting Yuan Siqi Li Chunyan Wu Jiyingcong Shen Yunjiang Liu

The global restriction or elimination of antibiotic growth promoters (AGPs) has intensified the search for effective and sustainable alternatives in livestock production. Among the proposed strategies, probiotic supplementation has received increasing attention due to its potential to enhance animal health and productivity while reducing reliance on antibiotics. Lactobacillus acidophilus (L. acidophilus), a well-characterized lactic acid bacterium commonly found in the gastrointestinal tract of animals, has been widely investigated as a probiotic candidate in livestock systems. This review summarizes current knowledge regarding the biological characteristics and mechanisms of action of L. acidophilus, including pathogen inhibition, modulation of intestinal barrier function, and regulation of host immune responses. Practical considerations, including the effects of feed processing on bacterial viability, strain stabilization technologies, and dose–response relationships, are also discussed. Reported supplementation doses in livestock trials typically range from 106 to 109 CFU/kg feed or per animal per day, although dose–response relationships remain poorly defined. Furthermore, recent advances in the application of L. acidophilus in major livestock species—including swine, poultry, and ruminants—are critically evaluated, with emphasis on growth performance, gut microbiota modulation, and disease resistance. Emerging approaches such as postbiotic utilization and probiotic-based vaccine adjuvants are also discussed. In addition, the potential contribution of L. acidophilus to environmental sustainability and mitigation of antimicrobial resistance dissemination in livestock systems is examined. Overall, L. acidophilus represents a promising component of integrated strategies aimed at improving animal health and promoting sustainable livestock production, although further research is required to clarify strain-specific effects and optimize practical applications.

Fermentation doi: 10.3390/fermentation12100484

Authors: Zeynep Gürbüz-Kaçan Hacer Meral-Aktaş Tuba Erkaya-Kotan Bülent Çetin

This study investigated the effects of quince seed mucilage powder (QSMP; 0.05, 0.10, 0.15, and 0.20%) on the microbiological, physicochemical, rheological, and microstructural properties of probiotic ayran fermented with a commercial starter culture and Lactiplantibacillus plantarum ACC66 during 14 days of refrigerated storage. QSMP completely prevented serum separation at all concentrations, whereas the control exhibited progressive whey separation throughout storage. This improvement was associated with the formation of a denser and more continuous protein network, as confirmed by scanning electron microscopy, rather than with increased apparent viscosity. QSMP also reduced post-acidification, moderated lactic acid accumulation, and enhanced the survival of L. plantarum ACC66, with the 0.15% treatment showing the highest viable counts. All samples complied with the microbiological criteria specified by the Turkish Food Codex throughout storage. Multivariate analyses further confirmed QSMP concentration as the primary factor influencing the physicochemical and microbiological characteristics of ayran. Overall, the results demonstrate that QSMP is an effective natural stabilizer for improving the physical stability of probiotic ayran while maintaining its microbiological quality, suggesting its potential application as a functional ingredient in industrial ayran production.

Fermentation doi: 10.3390/fermentation12100483

Authors: Xiuwen Wang Xinai Liu Wu Yang Youpeng Fan Yuanda Song

Nitrogen metabolite repression (NMR) represents a conserved regulatory system governing nitrogen utilization in filamentous fungi. The GATA-type transcription factor AreA serves as an activator under nitrogen-limited conditions, while AreB functions as a negative antagonist that competes with AreA for GATA cis-elements within target promoters. Previous studies in Mucor circinelloides have demonstrated that AreA can regulate key nitrogen metabolic genes and orchestrates carbon–nitrogen balance to promote lipid accumulation. Nevertheless, the function of AreB remains uncharacterized in this oleaginous fungus. In this study, the areB homologous gene was identified from the genome of M. circinelloides through bioinformatic prediction. Subsequently, we constructed the areB-knockout and areB-overexpression strains to elucidate the regulatory role of AreB in cell growth, carbon and nitrogen utilization, and lipid accumulation. Fermentation phenotypic assays showed that deletion of areB significantly improved cell growth, yielding a 15.81% increase in biomass compared with the wild-type, while the lipid content showed a moderate increase of 9.7%. In contrast, overexpression of areB exerted negligible effects on biomass (17.84 g/L versus 17.08 g/L in the control) and slightly reduced the lipid content (from 25.85% to 25.17%). When cultivated under diverse nitrogen sources, the ΔareB strain displayed markedly enhanced lipid content with glutamate as the sole nitrogen source. Subsequent transcriptomic analysis revealed that deletion of areB redirects carbon flux towards fatty acid biosynthesis. This work extends the nitrogen regulatory network in M. circinelloides and provides potential targets for metabolic engineering aimed at improving lipid production.

Fermentation doi: 10.3390/fermentation12100482

Authors: Wanting Xia Li Fang Fangmin Chen Xinqi Ji Simiao Li Xinyao Yang

Insect guts harbor microorganisms with carbohydrate-active enzymes, yet their potential as enzyme-production strains and the benefits of co-cultivation remain insufficiently characterized. In this study, 180 bacterial isolates from nine insect species were screened for carboxymethyl cellulose (CMC)-hydrolyzing activity. Two non-hemolytic isolates, H11 and Q5-3, were assigned to the genus Bacillus based on morphological characteristics and 16S rRNA gene analysis. Their initial extracellular endoglucanase activities were 156.67 ± 4.17 and 190.36 ± 4.29 U/mL, respectively, and increased to 228.01 ± 2.73 and 283.28 ± 2.06 U/mL after orthogonal array optimization. Central composite design predicted a maximum volumetric activity of 340.81 U/mL at approximately 16% (v/v) total inoculum and a Q5-3/H11 inoculum ratio of 2.08; independent validation yielded 339.17 ± 3.97 U/mL. Additional H11 and Q5-3 monoculture controls evaluated at the same total inoculum proportion showed lower mean volumetric activities than the validated co-culture. PCR screening produced expected-size amplicons for five putative endoglucanase-related targets in both isolates. These results indicate that H11 and Q5-3 are promising insect-gut-derived candidates for extracellular endoglucanase production and that co-cultivation can enhance volumetric enzyme activity on CMC without genetic modification. This study establishes candidate strains and a validated co-cultivation process in a controlled soluble-CMC model system, providing a process-development basis for subsequent evaluation of strain interactions and performance on insoluble cellulose and representative lignocellulosic substrates.

Fermentation doi: 10.3390/fermentation12100481

Authors: Emanuel Vamanu Laura-Dorina Dinu Alina Orțan

Vineyard management and winemaking leave behind large residue streams that are still rarely used as fermentation feedstocks. This review considers how pomace, skins, seeds, stems, canes, pruning wood, leaves and wine lees can be directed toward microbial bioconversion, fermentation-assisted recovery of bioactive compounds, and circular biorefinery schemes. Their composition (phenolics, stilbenes, dietary fiber, lignocellulose, sugars, minerals and yeast-derived material) makes them workable in either solid-state or submerged fermentation. We describe the routes that lead to enzymes, organic acids, ethanol, microbial biomass, biosurfactants, pigments and functional ingredients, together with the mechanisms by which bound phenolics are released and transformed. Green extraction, downstream purification, analytical standardization and process intensification are treated next, since market-ready consistency depends on them. The remaining obstacles are then set out: feedstock variability, phenolic inhibition, strain safety, scale-up, product stability, regulatory demands and economics. The data show grapevine waste as a versatile and valuable fermentation substrate and identify the reasons why laboratory results have not yet reached industrial scale.

Fermentation doi: 10.3390/fermentation12100480

Authors: Limei Chen Liucheng Long Xizhen Liu Wenqin Bai Yixin Cao Bingxuan Liu Guanyi Chen Beibei Yan Demao Li

To obtain thermotolerant Cyberlindnera jadinii strains with high-efficiency utilization of ethanol–acetate carbon sources, serial-batch-transfer adaptive laboratory evolution (ALE) under 37 °C was performed on the wild-type strain C. jadinii TU389, and a thermotolerant evolved strain C. jadinii X131 was acquired. Results demonstrated that C. jadinii X131 exhibited superior biomass accumulation compared to the wild-type strain at both the optimal temperature of 31 °C and 37 °C. Specifically, the X131 strain showed 43.4% higher biomass and 45.1% higher protein yield than wild-type strain at 37 °C in 5 L fermenters, with complete amino acid composition, high amino acid score and relative coefficient. Transcriptomic analysis indicated that temperature ALE reprogrammed ethanol oxidation from the cytoplasm to mitochondria to realize in situ detoxification of acetaldehyde, comprehensively activated DNA replication, chromosome segregation, and chromatin remodeling pathways to sustain cell cycle progression under high temperature, and simultaneously reduced peroxisomal metabolic load and redundant transport pathways. C. jadinii X131 can efficiently utilize ethanol–acetate carbon sources without adaptive trade-offs, which reduces cooling energy consumption in industrial fermentation.

Fermentation doi: 10.3390/fermentation12100479

Authors: Darío Cruz Valeria Hidalgo José Miguel Fernández Débora Masache Paola Duque-Sarango David Apolo Andrea Jaramillo-Riofrío Ángel Benítez

The organoleptic profile of coffee is modulated by microbially mediated fermentation processes; thus, characterizing the coffee microbiome is essential for the specialty coffee industry. This research investigated three coffee farms in Loja, Ecuador, to determine the cultivable bacterial diversity in coffee cherries (Coffea arabica var. Geisha) subjected to different post-harvest processing methods. Bacteria were isolated on Trypticase Soy Agar (TSA), Blood Agar Base, and MacConkey Agar after a broth enrichment step. Isolates were initially grouped into 14 morphotypes (MT) based on colony morphology and Gram staining. Molecular identification was performed by 16S rRNA gene sequencing, followed by phylogenetic analysis and Operational Taxonomic Unit (OTU) delimitation at a 99% identity threshold. Although 45 purified strains (19 Gram-positive and 26 Gram-negative) were initially clustered, morphological characterization showed significant taxonomic limitations compared with molecular tools. Molecular analysis identified nine genera and 19 bacterial genotypes, with Lactococcus lactis and Enterobacter spp. being the most frequently recovered and resilient taxa across all treatments. Statistical analyses (PERMANOVA and PCA) revealed no significant differences in bacterial community composition among post-harvest processes (Natural or Carbonic Maceration) or among farms, indicating that the predominant cultivable isolates remained consistent under the conditions evaluated, as presented here. According to the literature, several of the recovered species have functional roles in coffee fermentation, providing a baseline for the future development of starter cultures to optimize and standardize coffee sensory quality in southern Ecuador.

Fermentation doi: 10.3390/fermentation12100478

Authors: Qiulin Wei Yongdi Wen Jialu Liu Fuqiang Yu Zhenqiang Wu Xiaofei Tian

Hypocrellin A (HA) is a perylenequinone photosensitizer produced by Shiraia bambusicola during submerged fermentation, but its accumulation during submerged fermentation remains limited by low biosynthetic efficiency. Building on our previous finding that 32 °C increased HA accumulation and induced broad transcriptional changes, we reanalyzed that transcriptome to guide amino acid (AA) supplementation. Five AAs (Ala, Lys, Gly, Val, and Ile) were selected from eight residues showing nominal enrichment in proteins encoded by 32 °C upregulated genes because their catabolic routes are among those connected to central carbon metabolism and the generation of acetyl-CoA, the immediate precursor of the HA polyketide backbone. Single AAs and binary combinations were screened for their effects on intracellular HA content in S. bambusicola GDMCC 60438. At 32 °C, single supplementation with Ala (50 mg/L), Lys (200 mg/L), or Gly (100 mg/L) increased intracellular HA content by 71%, 74%, and 36%, respectively. Three binary combinations, Ala + Lys, Ile + Gly, and Val + Gly, further enhanced intracellular HA content by 71%, 75%, and 80%, respectively, with Val + Gly producing the largest increase in intracellular HA content despite Val alone being inactive. The AA response was markedly weaker at 28 °C, with larger response magnitudes observed at 32 °C in separate experiments. Transcriptomic re-analysis of previously published data revealed upregulation of AA transporter genes, including amino acid permeases (AAPs) and major facilitator superfamily (MFS) transporters, at 32 °C. Proteins encoded by highly expressed genes at 32 °C showed enrichment in eight AAs at an unadjusted p < 0.05, seven of which remained significant after Benjamini–Hochberg correction (q < 0.05). Intracellular acetyl-CoA was elevated in AA-supplemented cultures during the early fermentation phase (0–12 h). These findings support a working model in which elevated temperature is associated with a metabolically permissive state under which targeted AA supplementation may enhance HA biosynthesis in independent experiments.

Fermentation doi: 10.3390/fermentation12100477

Authors: Nasib Qureshi Thaddeus C. Ezeji Haibo Huang Ronald E. Hector

Sustainable production of biofuels and chemicals by green fermentation routes is becoming attractive. In this paper, the production of butyric acid by fermentation of wheat straw is studied. This conversion process requires biomass milling, pretreatment, hydrolysis, fermentation, and recovery. Of these five processing steps, pretreatment, hydrolysis, fermentation, and recovery are particularly cost-intensive. In the current study we combined simultaneous saccharification and fermentation in one unit operation for the substrate of wheat straw. In the integrated process, 90 g L−1 of wheat straw was simultaneously saccharified and fermented to 20.8 g L−1 of total acetic and butyric acids, of which butyric acid is the main product. As a result of the integration of saccharification with fermentation into a single streamlined workflow, the economics of the process significantly improved. In the fermentation process in which water was recycled, 39.9 g L−1 total acid (acetic acid + butyric acids) was produced. This is comparable to 40.8 g L−1 total acid produced in the glucose-fed control fermentation. Using cell-recycling technology, acid productivity was increased by 8–10 fold (800–1000%) from wheat straw hydrolysate as a feed. In this article, product yield, productivity, and selectivity were deemed to have high potential.

Fermentation doi: 10.3390/fermentation12100476

Authors: HyunHo Yun Hwee Won Ji Yeonju Lim Ju-Sik Min Sang Hyun Kim Geon-Hee Lee Seonggon Kim Sung-Oh Sohn

Gastric mucosal injury is associated with acute epithelial damage, inflammatory cytokine release, and disruption of the protective mucus barrier. NPKE6-FM is a fermented metabolite preparation produced from puffed soybean and rice inoculated with Bacillus amyloliquefaciens NPKE6, a strain isolated from Korean water kimchi. Although NPKE6-FM has shown antioxidant and anti-inflammatory potential in previous in vitro and in vivo studies, its gastroprotective efficacy against acute gastric injury has not been fully evaluated. This study investigated the protective effects of NPKE6-FM in an HCl/ethanol-induced acute gastritis model in ICR mice. Male ICR mice were randomly assigned to six groups after weight measurement (n = 5 per group): normal control (distilled water only), model group (HCl/ethanol plus distilled water), positive control (HCl/ethanol plus rebamipide, 50 mg/kg), and NPKE6-FM treatment groups receiving 10, 50, or 100 mg/kg. Test substances or vehicle were orally administered for 14 consecutive days. Following an approximately 18 h fast on Day 15, acute gastric mucosal injury was induced by oral administration of 200 mM HCl in 80% ethanol. Gastric tissues were collected approximately 1 h after injury induction for macroscopic lesion assessment, histopathological examination, cytokine analysis, and quantitative real-time PCR analysis of inflammation- and mucin-related genes. HCl/ethanol administration induced marked hemorrhagic and erosive gastric lesions, histopathological mucosal damage, and increased levels of TNF-α and IL-6. NPKE6-FM treatment reduced gross gastric lesion scores in a dose-dependent manner, with the 100 mg/kg group showing the greatest protective effect. Histological evaluation further indicated improved preservation of gastric mucosal architecture in NPKE6-FM-treated mice. In addition, NPKE6-FM significantly suppressed TNF-α and IL-6 levels and downregulated the mRNA expression of inflammatory mediators, including COX-2, iNOS, TNF-α, and IL-6. Conversely, the HCl/ethanol-induced reduction in Muc5ac expression was substantially restored by NPKE6-FM treatment. These findings demonstrate that NPKE6-FM protects against HCl/ethanol-induced acute gastric mucosal injury through anti-inflammatory activity and reinforcement of the gastric mucus barrier. NPKE6-FM may therefore represent a promising functional food ingredient or nutraceutical candidate for the prevention or attenuation of gastric mucosal injury.

Fermentation doi: 10.3390/fermentation12100475

Authors: Gilson C. A. Chagas-Junior César R. Balcázar-Zumaeta Nelson Rosa Ferreira Roberto Mori Efrain M. Castro-Alayo Guilherme Chagas Neto Emanuela da Conceição Cardoso Alessandra Santos Lopes Gustavo Araujo Pereira Rosinelson da Silva Pena

Defined starter cultures may improve the control and consistency of traditional fermentations. Therefore, this study evaluated the effects of Pediococcus acidilactici inoculation (Pa) on the physicochemical and chemical characteristics of traditional Amazonian cassava flour fermentation compared with spontaneous fermentation (CT). Changes in pH, total titratable acidity (TTA), sugars, and hydrogen cyanide (HCN) were monitored throughout 120 h of fermentation, and the resulting flour was characterized by physicochemical properties, color, HCN, and biogenic amines. Pa promoted pronounced acidification during the final fermentation stages, reaching pH 4.77 and TTA 6.49 mEq NaOH/100 g at 120 h, and produced distinct temporal profiles of sugars and cyanogenic compounds. However, enhanced acidification did not correspond to greater cyanide removal during fermentation. Subsequent flour processing markedly reduced residual total HCN to 0.44 and 0.42 mg/kg in CT and Pa, respectively, while free HCN responses were below the calibration range in both flour samples. Among the ten biogenic amines investigated, four were quantitatively determined. Compared with CT, Pa showed significantly higher concentrations of putrescine and spermidine and a significantly lower concentration of cadaverine, whereas phenylethylamine did not differ significantly between treatments. Overall, P. acidilactici modulated fermentation and final-product characteristics, supporting further investigation of its technological potential as a starter culture for traditional fermented cassava flour production.

Fermentation doi: 10.3390/fermentation12100474

Authors: İnci Cerit Ayşe Avcı Recep Gunes Elif Sezer Eliza Altynova Omca Demirkol

This study evaluated sunflower meal, a protein- and carbohydrate-rich by-product of sunflower oil processing, as a sustainable feedstock for the supplement-free cultivation of Saccharomyces cerevisiae var. boulardii. Sequential acid and enzymatic hydrolysis were applied to release fermentable sugars. During this process, the formation of fermentation inhibitors, such as hydroxymethyl furfural (HMF) and furfural, was also monitored. Hydrolysates were analyzed by high-performance liquid chromatography over 72 h to determine sugar profiles and inhibitor concentrations. The selected hydrolysis conditions yielded up to 25.76 g/L glucose, whereas HMF and furfural concentrations remained relatively low, ranging from 0.09 to 0.52 g/L and 0.02 to 0.11 g/L, respectively. The resulting hydrolysate was evaluated as a cultivation medium for S. cerevisiae var. boulardii under submerged fermentation conditions (30 °C, 120 rpm) without additional nutrient supplementation. Viable cell counts reached 8.3–8.4 log CFU/mL, comparable to those obtained in a yeast extract-peptone-malt extract (YPM) control medium. The sunflower meal hydrolysate exhibited substantially higher antioxidant activity than YPM throughout the cultivation period, with high initial values indicating a major contribution from sunflower-derived compounds. These findings demonstrate that sunflower meal can be converted into a hydrolysate with relatively low HMF and furfural concentrations that supports substantial S. cerevisiae var. boulardii growth. The resulting fermentation broth also exhibited high antioxidant activity, highlighting the potential of sunflower meal hydrolysate as a sustainable alternative medium for probiotic yeast production.

Fermentation doi: 10.3390/fermentation12100473

Authors: Ji-Eung Kim Sung-Chul Jung Mi-Hwa Lee Su-Kyoung Lee

Nuruk, a traditional Korean fermentation starter, largely determines the quality of makgeolli; however, data on nuruk produced from novel wheat cultivars remain limited. In this descriptive case study, nuruk made from the novel wheat cultivar ‘Wooju’ (A) was characterized alongside commercial Jinju-gokja (B) and a Korea Food Research Institute reference nuruk (C), with three independently manufactured batches per type. Physicochemical, enzymatic, antioxidant, and microbiological properties were analyzed, together with qualitative Q-ToF LC-MS/MS metabolite profiles. Nuruk A showed the highest total acidity (1.19%), total polyphenol (1090 ± 15 µg GAE/g) and flavonoid (1927 ± 10 µg QE/g) contents, total fungal count, and levels of phenylalanine, tryptophan, and GABA, but the lowest α-amylase and protease activities. Of the 22 compounds detected (20 tentatively identified), six differed in detection: two lysophospholipids and a nucleotide sugar were detected only in C, two oxylipins only in A and B, and LPI(18:2) was not detected in A. Wooju-based nuruk may be suited to antioxidant-oriented applications, although its lower saccharification and proteolytic activities may require process optimization. Because the samples differed simultaneously in cultivar, starter type, and manufacturing conditions, these differences should be regarded as preliminary and cannot be attributed to the Wooju cultivar alone.

Fermentation doi: 10.3390/fermentation12100472

Authors: Tomás García-Cayuela

Food systems are currently under increasing pressure to reduce waste and by-product generation, improve resource-use efficiency, and transition towards more sustainable production models [...]

Fermentation doi: 10.3390/fermentation12100471

Authors: Ángel González-Amador Luis-Fernando Patlan-Velázquez Gabriela Rodríguez-Serrano Lorena Gómez-Ruiz Francisco Guzmán-Rodríguez Sergio Alatorre-Santamaría Aurora Pintor-Jardines Alma Elizabeth Cruz-Guerrero

Sweet whey can be valorized through fermentation and subsequent production of Requeson, a fresh whey cheese obtained by heat-induced protein precipitation. This study evaluated the physicochemical (moisture, water activity, protein, ash, chloride, and EPS content), textural (hardness, cohesiveness, adhesiveness, springiness, chewiness, and fracturability), sensory (overall liking and JAR saltiness), and in vitro bioactive characteristics of Requeson produced from sweet whey fermented with exopolysaccharide (EPS)-producing Lactobacillus delbrueckii subsp. bulgaricus NCFB 2772 and Streptococcus thermophilus SY-102, individually or in co-culture. Unfermented, citric-acid-acidified whey served as the control. The co-culture (FC) showed the highest EPS content (3.5 mg/g), higher moisture, lower hardness and fracturability, and greater springiness than the control. Consumer evaluation (n = 130) showed favorable acceptance of FC. Among FC formulations containing 0.5–1.5% NaCl, 0.5% NaCl yielded the highest overall liking, although it did not differ significantly from 1.0%. FC showed the highest DPPH radical-scavenging (22.76%) and ACE-I inhibitory (31.00%) activities. Overall, co-culture fermentation represents a potential strategy for producing value-added Requeson with modified technological and sensory properties and measurable in vitro bioactivities.

Fermentation doi: 10.3390/fermentation12100469

Authors: Mehmet Mükerrem Rençber Zijing Zhou Jingrui Deng Rutao Liu Qigui Niu

Single-stage dark fermentation offers a promising route to convert lignocellulosic green waste into biohythane, a mixture of biohydrogen (H2) and biomethane (CH4), but conditions maximizing hydrogen selectivity may increase inputs, with unclear economic consequences. This study examines the effect of food-to-microorganism (F/M) ratio, pH, agitation, and NaOH pretreatment on biohythane yield and evaluates the resulting process economics at campus, district, and city scales. The most H2-selective condition (F/M 0.5, pH 6.0, no agitation) produced 50.3 mL H2/g volatile solids (VS) and 245.9 mL CH4/g VS; alkaline operation with agitation and NaOH raised biodegradability to 81.1% of theoretical maximum but suppressed H2 to near zero. Techno-economic analysis showed the acidic, non-agitated condition achieved the highest net present value at district scale under two independent capital-cost methods (NPV = US$19.6 million and US$10.7 million; internal rate of return (IRR) = 55%): its CH4 revenue gain (+US$290,000/yr) was outweighed 3-fold by higher costs (+US$966,000/yr). This ranking held across scales and under H2-purification and tax-incentive scenarios. A low-input strategy therefore achieves superior returns by preserving CH4 revenue while avoiding agitation and pretreatment costs, with H2 better viewed as a co-benefit than the primary target, challenging the assumption that maximizing total biogas output is economically preferable within a scale-sensitive techno-economic framework.

Fermentation doi: 10.3390/fermentation12100470

Authors: Saisai Su Yuxuan Wang Longjun Shi Zuoliang Chen Xiaoyan Yu Yanqing Duan Zhihong Liu

Recovering volatile fatty acids (VFAs) from anaerobic fermentation broth as preferred carbon sources is often hindered by the poor recoverability of powdered adsorbents and the slow mass transfer within conventional hydrogel beads. Herein, we report a MgAl-layered double hydroxide (LDH) and sodium alginate (SA) composite ink tailored for extrusion-based 3D printing, followed by Ca2+ crosslinking and freeze-drying to fabricate monolithic adsorbents. Rheological tests show that the ink exhibits shear-thinning behavior and elastic-dominated viscoelasticity (G′ > G″), ensuring smooth extrusion and high shape fidelity during printing. Under optimized conditions (25 °C, 3.0 g/L, 120 min, pH 7.0), the 3D-printed monolith removed 55.74% of total VFAs. Kinetic analysis reveals that the adsorption follows the pseudo-second-order model (R2 = 0.915), consistent with a chemically controlled adsorption contribution and yielding a calculated equilibrium capacity of 286.5 mg/g. Notably, the adsorbent exhibits a pronounced selectivity toward acetic acid, which accounts for 62% of the total adsorbed VFAs. These findings demonstrate that 3D printing offers a viable strategy to overcome the intrinsic limitations of LDH-based adsorbents, namely, difficult separation and limited internal diffusion, thereby enabling efficient and selective VFA recovery from complex fermentation streams.

Fermentation doi: 10.3390/fermentation12100468

Authors: Lucía M. Mendoza Emilse Bentencourt Guillermo A. Vega-López Silvina Fadda

Oenococcus oeni is the main lactic acid bacterium responsible for malolactic fermentation (MLF) during winemaking, a critical step for obtaining high-quality wines. However, the harsh wine environment, characterized by low pH, ethanol, sulfur dioxide, and inhibitory yeast metabolites, can compromise bacterial growth and MLF performance. To investigate the mechanisms underlying wine stress tolerance, O. oeni CRL 1947 was grown in unfermented and fermented grape juice media and analyzed using a proteomic (two-dimensional electrophoresis) and RT-qPCR. A total of 38 proteins displayed significant differential expression under all conditions, with 23 up-regulated and 15 down-regulated. One protein spot (fructokinase) was exclusively detected in fermented medium, whereas aspartate carbamoyltransferase was completely inhibited. Proteins related to carbohydrate, lipid, nucleotide, and amino acid metabolism, as well as stress-response chaperones and peptidases, were over-expressed in fermented grape juice medium. In contrast, enzymes involved in lipid biosynthesis, glycolysis, amino acid metabolism, hydrolase, and dehydrogenase activities were down-regulated. Differential expression of genes associated with malic acid and citrate metabolism as well as in stress response was also observed. These findings provide further insights into the molecular adaptations of O. oeni to wine-stressful conditions and support the selection of the best adapted starter cultures for efficient MLF during winemaking.

Fermentation doi: 10.3390/fermentation12100467

Authors: Anthony Jose Balcazar-Sinailin Melanie Ashley Ochoa-Ocampo Leslie Galeny Cordero-Castillo Juan A. Castillo-Garit Patricio J. Espinoza-Montero Carlos Méndez-Durazno Noroska G. S. Mogollón Karel Diéguez-Santana

Trametes polyzona is a white-rot fungus whose laccase, manganese peroxidase, and lignin peroxidase system supports fermentation-based bioprocesses: pollutant bioremediation, effluent treatment, and enzyme production under solid-state and submerged fermentation. Its extracts also show antioxidant, antimicrobial, and cytotoxic activity. How this field is structured, and how far it has moved toward application, has not been examined. We analyzed 64 publications indexed in Scopus and Web of Science (1991–2025) with Bibliometrix R-Tool (v4.3.2) and VOSviewer (v1.6.20). Output has grown steadily since 2005, led by Thailand, Belgium, and South Africa. Keyword co-occurrence (119 terms, 3253 links) resolved five clusters: laccase catalysis and immobilization (39 terms); ligninolytic enzyme systems and strain characterization (27); comparative white-rot mycology and effluent treatment (23); dye decolorization with toxicity assessment (21); and enzyme purification and characterization (9). The strategic diagram placed laccase-mediated phenol oxidation and dye biodegradation among the motor themes, whereas bioactivity research remained a niche theme. The field has moved from enzymatic description toward immobilization and reactor-based treatment, but within the 64 records analyzed, species-specific reactor evidence rests on a single laboratory airlift study and no volumetric productivity, oxygen-transfer, or economic data are reported. Genomic and metabolomic resources remain scarce, defining clear priorities for fermentation-oriented research.

Fermentation doi: 10.3390/fermentation12100466

Authors: Emilse Bentencourt Florencia Mohamed Miguel Fernández de Ullivarri Lucía M. Mendoza

Bioinformatics has become an important tool for characterizing the properties of potential starter cultures such as Oenococcus oeni, providing insights into metabolism, wine adaptation, and genetic diversity. This study aimed to characterize the genomes of three native O. oeni strains (X2L, ST, and Sb10) isolated from the wine-producing region of Northwestern Argentina and to compare them with strains from other wine-related environments. The analyzed genomes showed features consistent with the species, including genome sizes of approximately 1.7 Mb and GC contents close to 38%. Most coding sequences were related to carbohydrate and amino acid metabolism. No genes associated with biogenic amine production or antibiotic resistance were detected, supporting their potential suitability as starter cultures for winemaking. ANI values above 97% supported their classification as O. oeni. Despite this high genomic similarity, differences were observed among strains. X2L and Sb10 exhibited an ANI of 99.99% and no SNP differences, suggesting that these isolates may represent clonal variants. In contrast, X2L and ST showed lower genomic similarity and belonged to different phylogroups, despite sharing the same origin. Strain ST exhibited greater genomic similarity to several reference strains, highlighting the genetic diversity and evolutionary complexity of O. oeni populations.

Fermentation doi: 10.3390/fermentation12100465

Authors: Gulmira T. Kassenova Zhanara K. Tulemissova Sagyman Zhadyra Zubaira Kozhakhmetova Aigerim Tuganbay Talgat Ikombayev Akkenzhe Omarova Ayaulym E. Muratbekova Botagoz Kulzhanova Per E. J. Saris

Traditional Suzbe is a fermented dairy product widely prepared at the household level in Kazakhstan, but the composition and functional potential of its microbiota remain poorly characterized. In this study, shotgun metagenomic sequencing was used to investigate the microbial communities of 20 traditional Suzbe samples collected from five geographically distinct regions of Kazakhstan. Lactic acid bacteria dominated the microbial communities, with annotations assigned to Lactococcus lactis, Lactococcus cremoris, and Streptococcus thermophilus present in all samples. Alpha diversity did not differ significantly among the five regions, and PERMANOVA did not detect statistically significant regional differences in overall microbial community composition (R2 = 0.253, p = 0.216). Nevertheless, LEfSe analysis identified several region-associated taxa, mainly among less abundant members of the microbiota. Functional annotation using the KEGG database showed that carbohydrate metabolism, amino acid metabolism, energy metabolism, cofactor and vitamin metabolism, and membrane transport were among the major functional categories. Functional PERMANOVA did not detect statistically significant regional differences in overall functional composition (R2 = 0.249, p = 0.276), although several metabolic pathways differed in relative abundance. Overall, the sampled Suzbe microbiomes were dominated by lactic acid bacteria, with several species detected in all samples and major functional categories detected across regions. Region-associated differences were identified among specific taxa and metabolic pathways; the nonsignificant PERMANOVA results do not establish taxonomic or functional conservation. This study provides new metagenomic data on traditional Suzbe and contributes to a better understanding of fermented dairy microbiota in Central Asia.

Fermentation doi: 10.3390/fermentation12100464

Authors: Yujie Wang Chuyu Zheng Gaoyu Ren Han Zhang Shuna Zhao Guanghui Shen

Production of functional exopolysaccharides (EPS) by lactic acid bacteria (LAB) is a promising strategy for the value-added utilization of beet molasses. This study aimed to isolate high-sucrose-tolerant LAB strains from beet molasses and evaluate their potential for crude EPS production. A total of 13 LAB strains were initially isolated from beet molasses, among which seven isolates were selected as high-sucrose-tolerant candidates based on their growth performance under high-sucrose conditions. Further crude EPS-production screening showed that two isolates, Leuconostoc mesenteroides C4 and Pediococcus pentosaceus T1, produced relatively high crude EPS yields. These two isolates were then identified by 16S rRNA gene sequence analysis. Further, L. mesenteroides C4 was selected as a candidate, and preliminary OFAT screening followed by Box–Behnken response surface methodology (RSM) was employed to optimize the conditions for crude EPS production. The antioxidant activity and antibiofilm activity of the crude EPS-C4 fraction were also evaluated. The RSM-predicted optimal conditions for crude EPS production by L. mesenteroides C4 were 350 g/L of beet molasses, an initial pH of 6.0, a fermentation time of 30 h, a fermentation temperature of 37 °C, an inoculum size of 2.3%, a loading volume of 85%, and a shaking speed of 108 r/min. Under these optimal conditions, a maximum crude EPS yield of 16.99 ± 0.22 g/L was obtained, which was approximately 5.0-fold higher than the yield obtained under the initial fermentation condition (3.40 g/L). Furthermore, crude EPS-C4 exhibited in vitro free-radical-scavenging activity against DPPH and ABTS+ radicals, with scavenging rates of 97.00% and 67.35% at 6.0 mg/mL, respectively. The crude EPS-C4 fraction also inhibited biofilm formation by Escherichia coli and Staphylococcus aureus, with inhibition rates of 60.68% and 68.69% at 8.0 mg/mL, respectively. These findings provide preliminary evidence that beet molasses can be used as a substrate for LAB-EPS production and suggest that crude EPS-C4 is a promising candidate for further purification, structural characterization, safety assessment, and application-oriented evaluation.

Fermentation doi: 10.3390/fermentation12100463

Authors: Jinyu Du Zhenchao Wu Tong Yang Xuan Tang Yu Bai Xinbo Cao Zhiyu Yang Hongzhi Ling Baiyan Cai Jingping Ge

Blue honeysuckle (Lonicera caerulea L.) is a cold-adapted berry rich in bioactive polyphenols. The association of phenolic compounds with the plant cell-wall matrix may limit their extractability. To promote polyphenol release and enhance antioxidant properties, a blue honeysuckle matrix was co-fermented with Lactobacillus rhamnosus 6224 and Saccharomyces cerevisiae W5. Process parameters were optimized using response surface methodology, with total phenolic content (TPC) as the response variable. Under the optimized conditions, TPC reached 1374.79 mg/100 g. Compared with the unfermented control, DPPH radical, ABTS radical, H2O2, and hydroxyl radical scavenging activities increased by 4.27, 15.10, 12.89, and 12.63 percentage points, respectively. LC-MS profiling showed that co-fermentation markedly altered the phenolic profile of the blue honeysuckle matrix and increased the relative abundances of several putatively annotated phenolic compounds, including quercetin, protocatechuic acid, catechin, and caffeic acid. These findings indicate that the optimized co-fermentation process increased TPC, altered phenolic composition, and enhanced in vitro antioxidant activity, offering a potential approach to the value-added processing of blue honeysuckle.

Fermentation doi: 10.3390/fermentation12100462

Authors: Yajing Yin Zhemin Yuan Meng Zhao Weiting Li Jingqi Wang Yueru Zhao

Polyunsaturated fatty acids (PUFAs) play critical physiological roles in maintaining cardiovascular health, neurodevelopment, and immune regulation, with continuously growing market demand. Traditional supply chains based on fish oil and plant oils face severe challenges including resource depletion, environmental pollution, and sustainability concerns. Single cell oil production via fermentation using filamentous fungi has emerged as a sustainable and economically viable alternative. This review provides a comprehensive overview of research progress on PUFA synthesis by filamentous fungi, covering strain resources, biosynthetic pathways, regulatory mechanisms, major product development, and industrialization prospects. Filamentous fungi have formed a complete spectrum from native high-yielding strains (e.g., Mortierella alpina, Mucor circinelloides, Umbelopsis isabelline, Thamnidium elegans, Cunninghamella echinulata) to genetically tractable chassis cells (e.g., Aspergillus oryzae). In addition, the oleaginous yeast Yarrowia lipolytica also plays a non-negligible role in the heterologous synthesis of polyunsaturated fatty acids. Starting from acetyl-CoA, filamentous fungi synthesize saturated fatty acids via the fatty acid synthase system and subsequently convert them to important PUFAs such as arachidonic acid (ARA), γ-linolenic acid (GLA), and eicosapentaenoic acid (EPA) through the sequential catalysis of Δ9-, Δ12-, Δ6-, and Δ5-desaturases and elongases. The SNF1 energy sensor, the nitrogen metabolism regulator AreA, and environmental factors constitute a complex multi-layer regulatory network that coordinately modulates fatty acid unsaturation and yield. The 2A peptide-based multigene co-expression platform, cofactor engineering, competitive pathway blockade, and fermentation process optimization have synergistically enabled the targeted accumulation of specific PUFAs. Nevertheless, industrialization of filamentous fungal PUFA production still faces major bottlenecks. We also provide a perspective on the industrial potential of filamentous fungi as “lipid cell factories” for the production of polyunsaturated fatty acids (PUFAs). This review aims to provide a comprehensive knowledge framework for researchers in related fields and to inform future fundamental research and industrial translation.

Fermentation doi: 10.3390/fermentation12100461

Authors: Kristin Rang Wolfgang Büscher Yurui Sun Jessica Paßmann Gerd-Christian Maack

As temperatures rise worldwide, the effects of ensiling and storage temperature on silage need to be elucidated. In this paper, we aim to illuminate the effect the storage temperature has on the aerobic stability of whole-plant maize silage. The study was designed to identify the effect that temperatures of 23 °C and 33 °C have on untreated or maize silage inoculated with a biological additive. Furthermore, the study elucidates how temperature affects the ensiling phase of untreated maize silage. The silage was incorporated into the novel nine-sample live measuring system, which enables us to constantly measure the temperature pH and oxygen content 10 cm behind the silo face. The second experiment proved that silage that was fermented and stored at 23 °C remained aerobically stable longer than silage fermented at 33 °C. Switching the variant from 33 °C during fermentation to 23 °C during storage resulted in aerobic stability matching that of silage continuously stored at 33 °C, with both differing significantly from the variant continuously stored at 23 °C. In the first experiment, it was demonstrated that the biological additive used in this study improved several indicators of aerobic stability independent of fermentation temperature.

Fermentation doi: 10.3390/fermentation12100460

Authors: Jia Li Panpan Wang Ziwen Qu Ying Xu Wenrui Li Yuhan Shan Yuping Quan

This study examined how targeted mutations in two pyruvate-associated genes, d-ldh and budA, affected adaptive phenotypes and fermented milk quality in Companilactobacillus crustorum MN047. Premature stop codons were introduced into d-ldh and budA by CRISPR-assisted base editing and verified by Sanger sequencing. The resulting nonsense mutants, designated ΔbudA and Δd-ldh, retained growth comparable to the wild-type strain (wt) but showed contrasting phenotypes. At 24 h, auto-aggregation was 4.44-fold the wt value in Δd-ldh and 0.71-fold the wt value in ΔbudA, whereas ΔbudA showed lower aggregation and stress survival. Viable counts remained 7.2–7.7 log10 CFU/mL, although titratable acidity and textural properties differed among fermented milk groups. ΔbudA produced higher firmness and consistency, whereas Δd-ldh showed lower values for both parameters. Electronic nose PCA clearly separated the three groups, while GC-MS identified strain-dependent differences in selected relative volatile compounds. These findings show that the two pyruvate-associated mutations affected bacterial robustness and fermented milk quality in distinct ways.

Fermentation doi: 10.3390/fermentation12100459

Authors: Julia Kruyeniski Carolina Mónica Mendieta Fernando Esteban Felissia María Cristina Area

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Fermentation doi: 10.3390/fermentation12100458

Authors: Leqi Tang Yujue Wang Jianghua Chen Qiang Wang Yan He Miaomiao Zeng Xian Zhang Hailing Zhang

The growing global demand for flavor stability and terroir expression in the specialty coffee industry has positioned postharvest fermentation as a core driver of coffee quality upgrading, second in importance only to cultivar genetic improvement. Coffee fermentation is shifting from an empirical spontaneous pectin-removal process to a precision biotechnological approach for targeted flavor regulation, with microbial communities acting as core mediators of biochemical transformation. This review compiles key research progress in coffee fermentation from 2018 to 2026, spanning processing paradigms, microbial ecology, flavor metabolic mechanisms, sensory safety, and industrial iteration. It compares the microenvironmental characteristics and microbial succession of four mainstream processing modes; clarifies functional divergence and terroir effects of the core microbiota; dissects the multi-stage cascade flavor metabolic network; and explains how fermentation precursors transfer to roasted coffee flavor. Importantly, most microbiota–flavor associations in current studies remain correlative rather than experimentally proven causal relationships. Evidence indicates that inoculated fermentation can improve cupping quality, reduce batch-to-batch variation, and mitigate biosafety risks. Several proposed precision fermentation approaches remain at the laboratory and pilot-scale stage and are not yet widely deployed industrially. Current field bottlenecks include poor regional adaptability of commercial starters, limited real-time monitoring tools, and ambiguous microbiota–flavor causal mechanisms. Future research will focus on terroir-adapted synthetic consortia, AI-driven precision fermentation, and multi-omics integrated studies, to advance coffee processing from empirical craft to precision biomanufacturing.

Fermentation doi: 10.3390/fermentation12100457

Authors: Sasiprapa Kullachonphuri Nuttapon Khongdee Suwimon Wicharuck Yupa Chromkaew Yun-Hsin Lin Kuan-Chen Cheng

Drought stress is one of the most damaging abiotic stressors impacting global agricultural productivity and soil ecosystem integrity, especially in the semi-arid and arid areas. Drought results in a cascade of physiological and biochemical disturbances in plants, such as inhibition of photosynthesis, loss of turgor pressure, and impairment of osmoregulation, while also causing a degradation of soil health through losses in organic carbon, nutrient availability, and microbial community structure. This calls for integrated soil management approaches that can restore soil health and support plant resilience simultaneously under water-limited conditions. Biochar, generated through the thermal decomposition of agro-waste materials under oxygen-limited conditions, represents a promising circular bioeconomy strategy for valorizing agricultural residues into high-value soil amendments. Biochar is widely known to enhance the physicochemical properties of soils, including water retention, cation exchange capacity, and microbial habitat provision. Plant growth-promoting rhizobacteria (PGPR) have been established as an environmentally friendly means of enhancing plant growth through phytohormone production, ACC deaminase activity, and antioxidant enzyme activation under stressed conditions. The combined application of biochar and PGPR has garnered considerable scientific attention due to their complementary modes of action and, in some cases, beneficial combined effects. Several studies reported significant improvement in plant water status, photosynthetic efficiency, osmoregulation, soil enzyme activity, and nutrient retention. This article summarizes the present research on the soil and physiological effects of drought stress before exploring the basic mechanisms of biochar–PGPR interaction and their combined efficacy under drought conditions. Furthermore, the review calls attention to the future research priorities, such as field-scale validation, region-specific formulation development, and omics-based mechanistic investigations to maximize the full potential of PGPR and biochar combined as a sustainable approach for alleviating drought stress.

Fermentation doi: 10.3390/fermentation12100456

Authors: Juan Fernando Campaña-Perez Sascha Bernard Lokman Alpsoy Marta Mollerach Thomas Brandstetter Betiana Lerner Maximiliano Sebastian Perez Jürgen Rühe

This study addresses some limitations of standard cell encapsulation methods by producing hydrogel beads via UV-induced C,H-insertion crosslinking (CHic) in a microfluidic setup and the simultaneous encapsulation of yeast cells. It describes a simple one-step production of monodisperse beads with consistent dimensions of ~1000 × 500 µm and the encapsulation of Saccharomyces cerevisiae within these beads. Glucose consumption profiles show that the encapsulated yeast consumes glucose at rates comparable to free yeast, indicating that encapsulation does not impair metabolic activity. The encapsulated cells maintain high retained metabolic activity for up to 15 days at 4 °C and even at 30 °C, whereas free yeast stored at this temperature suffers a significant loss of activity. This highlights the potential of the platform for storing cells without refrigeration. Another advantage is that the fermentation solutions remain clear with minimal turbidity, and the beads can be easily separated from the solution by simple sieving, thus avoiding the need to filter the solution after fermentation. The results obtained suggest that the platform is robust and versatile for use in fermentation bioreactors and cell storage.

Fermentation doi: 10.3390/fermentation12100455

Authors: Emma P. Fukuda Emily C. Fowler Merritt L. Drewery

Previous research has established distinctions between microbial communities that associate with either the solid or liquid rumen microenvironments utilizing 16S rRNA sequencing. Whole genome metagenomic sequencing (WGS) facilitates comprehensive analysis of a microorganism’s entire genome, producing strain level data and providing insights into microbial functionality. The objective of our study was to utilize WGS to characterize microbial species and enzyme profiles associated with the liquid versus solid rumen microenvironments in beef steers consuming forage. Four steers consuming forage were utilized in a 4 × 4 Latin Square experiment; on d 14 of each period, rumen contents were separated into solid and liquid samples and DNA was extracted then sequenced using WGS. Alpha and beta diversity measures revealed differences between solid and liquid microenvironments. There were also differences in enzyme profiles: carbohydrate-active enzyme classes were different across microenvironments, except glycosyl transferase. Further, the solid microenvironment was enriched in enzymes related to energy production/conversion and nutrient transport and metabolism, while the liquid microenvironment was enriched in coenzyme transport and metabolism enzymes. Species associated with cellulolytic activities were generally more abundant in the solid microenvironment while those associated with amylolytic activity were more abundant in the liquid. Genes related to methanogenesis were also different across microenvironments. Our findings offer valuable insights into the stratification of microorganisms across rumen microenvironments, expanding on existing literature with findings from next-generation sequencing and application to forage-based beef systems.

Fermentation doi: 10.3390/fermentation12100454

Authors: Tuba Buyuksirit-Bedir

The occurrence of pesticide residues in vegetables remains an important food safety concern, while their behavior during traditional fermentation is less well characterized. This study evaluated changes in pesticide residues during 35 days of spontaneous pepper fermentation. Ten commercial pepper samples were fermented using a traditional household-scale procedure, and pesticide residues and microbial populations were monitored throughout fermentation. A total of 120 pesticides were analyzed by liquid chromatography-tandem mass spectrometry, and processing factors (PFs) were calculated. Four pesticides, acetamiprid, boscalid, cypermethrin, and metalaxyl, were detected in seven of the ten fresh pepper samples. The concentrations of all detected pesticides decreased during spontaneous fermentation, although the magnitude of reduction varied considerably among compounds. Cypermethrin showed the greatest reduction, reaching 92.4% by day 21 (PF = 0.076), whereas acetamiprid and metalaxyl decreased by 56.6% (PF = 0.434) and 49.7% (PF = 0.503), respectively, by day 35. Boscalid showed comparatively greater persistence, with a 20% reduction (PF = 0.800) on day 35. Exploratory correlation analysis showed predominantly negative associations between pesticide concentrations and microbial counts. However, these findings should not be interpreted as evidence of a causal relationship with pesticide dissipation. The magnitude of dissipation varied among the detected pesticides and may also have been influenced by sample- and matrix-specific factors.

Fermentation doi: 10.3390/fermentation12100453

Authors: Aris Melloni Michal Dabros Helena Mylise Copeland Yoann Fink Keith D. Rochfort Brian Freeland

This study presents the development of an advanced control system for regulating the specific growth rate of Lactobacillus rhamnosus in fed-batch cultures using an advanced soft sensor approach. A predictive Artificial Neural Network (ANN) model was developed to estimate growth rate in real time, utilizing input variables including total cell density, oxygen uptake rate, carbon evolution rate, dissolved oxygen, and bioreactor volume. The ANN model demonstrated high accuracy, with a validation-subset RMSE of 0.073 h−1 and an R2 of 0.99. To improve control stability, the predicted growth rate was integrated into a closed-loop Proportional-Integral (PI) controller that dynamically adjusted the substrate feed rate. The controller parameters were optimized using the Ziegler-Nichols method, achieving a mean control error of 18.2% ± 5.26% across different growth rate setpoints. The implementation reduced process variability and enhanced control precision compared to traditional control methods. These findings highlight the potential of ANN-based predictive models for improving bioprocess automation, indicating the potential of ANN-based predictive models for bioprocess automation, subject to validation under industrial conditions.

Fermentation doi: 10.3390/fermentation12100452

Authors: Romana Heralecka Karolina Kostelnikova Mojmir Baron Jiri Sochor

Climate change accelerates grape ripening, intensifies malic acid degradation, and promotes potassium accumulation, which results in lower acidity and increased pH in musts and wines. This review summarizes the mechanisms underlying these changes and critically evaluates the available approaches to compensate for them. Traditional chemical and physical acidification methods are associated with several technological, sensory, and economic limitations. Biological acidification is a promising alternative, particularly through the use of Lachancea thermotolerans for lactic acid production and selected Saccharomyces cerevisiae strains capable of producing malic acid. The potential of targeted selection and genetic modification is also discussed. Biotechnological approaches therefore represent a promising tool to maintain acid–base balance and wine quality in a warming climate.

Fermentation doi: 10.3390/fermentation12100451

Authors: Anastasia Thanou Anna Ofrydopoulou Vasileios D. Prokopiou Katie Shiels Alexandros Tsoupras

Commercially available caprine dairy matrices are rich sources of lipid-associated bioactive constituents; however, comparative evaluations of their polarity-separated fractions remain limited. This study aimed to characterize and compare the chemical composition, antioxidant capacity, and inhibitory effects on thrombo-inflammatory agonist-induced platelet aggregation of amphiphilic (total amphiphilic content, TAC) and lipophilic (total lipophilic content, TLC) fractions isolated from three independently produced commercial goat milk and three independently produced commercial kefir-based goat yogurt-type fermented products, with different LOT numbers. Total lipid (lipophilic and amphiphilic) extracts were obtained by Bligh and Dyer extraction and then fractionated to TAC and TLC by counter-current separation using a green hexane/ethanol–water solvent system. Analytical determinations included spectrophotometric quantification of total carotenoid and phenolic contents, attenuated total reflectance Fourier-transform infrared (ATR–FTIR) structural profiling, and liquid chromatography–mass spectrometry (LC–MS) relative fatty-acid profiling. Antioxidant capacity was assessed using DPPH and ABTS radical-scavenging assays, while ex vivo light-transmission aggregometry in human platelet-rich plasma, obtained from six independent healthy donors (n = 6) for each fraction, was employed to evaluate potential inhibitory effects against platelet-activating factor (PAF) and adenosine diphosphate (ADP). Across both matrices, TAC fractions exhibited markedly higher radical-scavenging responses than the corresponding TLC fractions, particularly in the ABTS assay. In platelet aggregometry, TAC fractions showed significantly stronger inhibition of both PAF- and ADP-induced aggregation than their corresponding TLC fractions. Specifically, the TAC fraction from the kefir-based yogurt product exhibited the lowest IC50 value against PAF-induced aggregation, whereas the two TAC fractions showed comparable inhibitory potency against ADP-induced aggregation. ATR–FTIR spectroscopy revealed spectral features consistent with lipid-associated, hydroxyl-containing, and phosphate-containing amphiphilic structures, while LC–MS profiling identified palmitic, stearic, oleic, and α-linolenic acids among the predominant fatty acids in the free and esterified fatty-acid pools. Overall, the TAC fractions exhibited substantial in vitro radical-scavenging activity and ex vivo inhibition of agonist-induced platelet aggregation, suggesting potential anti-inflammatory and antithrombotic relevance for these activities. Further in vivo studies are required to determine their physiological relevance.

Fermentation doi: 10.3390/fermentation12100450

Authors: Ronnie G. Willaert

Microorganisms are, above all, chemists [...]

Fermentation doi: 10.3390/fermentation12100449

Authors: Yaodi Han Yudan Li Yunfei Zhai Xinling Wang Jiaxuan Song Wudong Liu Zhaoyu Han

This study aimed to determine the effects of dietary supplementation with a compound additive containing guanidinoacetic acid (GAA) and cysteamine on rumen metabolism, fermentation, and the microbiota of fattening Holstein bulls. Sixty Holstein dairy bulls (294.33 ± 3.42 kg) were divided into three groups (n = 20). Each treatment comprised three independently fed pens (n = 3 pens per treatment), and one bull was sampled from each pen for the rumen measurements. Group A served as the control group, whereas Groups B and C received a concentrated supplement containing 1 kg/t and 2 kg/t of a compound additive (GAA combined with cysteamine), respectively, over 90 days. Kyoto Encyclopedia of Genes and Genomes identified five key pathways. Specifically, indole-3-acetaldehyde, 2-amino-3-methoxybenzoic acid, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate, and cholesterol glucuronide were upregulated, whereas 4-fumarylacetoacetic acid and pseudouridine 5′-phosphate were downregulated. Compared with those in the control group, acetic acid, butyric acid, total volatile fatty acids (VFAs), propionic acid, and microbial crude protein (MCP) increased, whereas pH, acetic acid/propionic acid (A/P) ratio, and NH3-N did not differ. At the genus level, Weissella abundance increased, Methanobrevibacter abundance decreased, and Xylanibacter and Ruminococcus abundances increased in the low-supplementation group (1 kg/t). Methanobrevibacter correlated negatively with VFAs, MCP, and NH3-N but correlated positively with A/P. Weissella and Ruminococcus showed the opposite trend. Increasing the inclusion level of the compound additive improved rumen metabolism, fermentation, and the microbial environment. This ultimately reduced stress and enhanced rumen health in fattening Holstein bulls.

Fermentation doi: 10.3390/fermentation12100448

Authors: Redife Aslihan Uçar Ömer Şimşek

The cosmetic and dermocosmetic industries are increasingly incorporating fermentation-derived ingredients for their benefits on skin barrier function, hydration, pigmentation, oxidative stress, and microbiome homeostasis. Advances in fermentation biotechnology have enabled the production of bioactive compounds, including organic acids, postbiotics, microbial lysates, bioactive peptides, bacteriocins, and fermentation-enhanced phytochemicals. These bioactives may support skin health through barrier reinforcement, modulation of melanogenesis, antioxidant activity, and microbiome interactions. Beyond topical applications, fermented functional foods and microbiome-derived metabolites may influence skin physiology through the gut–skin axis, linking microbial metabolism with systemic immune and barrier regulation. Fermentation also offers opportunities for sustainable production of dermocosmetic ingredients from renewable resources and agro-industrial by-products. However, evidence on fermentation-derived cosmetic ingredients, fermented foods, microbiome science, nutritional dermatology, and cosmetic biotechnology remains fragmented across disciplines. This review therefore introduces Fermentocosmetology as an integrative conceptual terminology, rather than a new discipline, to connect these research areas within a unified framework. Attention is given to bacteriocins as fermentation-derived antimicrobial peptides with emerging dermatological relevance, including activity against Cutibacterium acnes and Staphylococcus aureus. Overall, the proposed framework positions fermentation as a versatile platform connecting topical and systemic approaches to skin health while highlighting opportunities for microbiome-oriented, sustainable, and precision dermocosmetic innovation.

Fermentation doi: 10.3390/fermentation12100447

Authors: Tevfik Koçak Tuba Eda Arpa Zemzemoğlu Özlem Baran Elif Melek Avci Aziz Alper Biten Bence Raposa Duygu Ağagündüz

Fermentation is among the oldest food technologies, yet its relevance now extends well beyond preservation. Fermented foods are increasingly viewed as matrix-dependent biological systems whose microbial and chemical composition evolves during fermentation and post-fermentation processing, and whose functional components may undergo further transformation during gastrointestinal digestion and host–microbiome interaction, rather than as passive carriers of single nutrients or microorganisms. This review synthesizes mechanistic, compositional, and clinical evidence on fermented foods as functional foods through three core scientific pillars: (i) the biological and matrix-related determinants of functionality, including microbial genotype and community ecology, enzymatic transformation, matrix restructuring, fermentation and post-fermentation processing, gastrointestinal digestion, and host phenotype; (ii) the principal fermentation-derived bioactive systems, including bioactive peptides, exopolysaccharides, organic acids, microbially synthesized vitamins, bioaccessible minerals, biotransformed phenolics, γ-aminobutyric acid and related amino acid derivatives, bacteriocins, bioactive lipids, and postbiotic components; and (iii) the mechanistic pathways linking these systems to immune, metabolic, endocrine, gastrointestinal, neuroimmune, and aging-related outcomes. Building on these foundations, the review further examines two translational dimensions: precision nutrition, with emphasis on interindividual variability, host–microbiome interactions, responder phenotypes, and product-specific human evidence; and next-generation functional fermented foods, integrating systems-level host–microbiome frameworks, multiomics, emerging predictive technologies, sustainability, safety, and regulatory translation. Microbial–epithelial–immune signaling, short-chain fatty acid receptor activation, regulatory T-cell modulation, intestinal barrier reinforcement, bile acid signaling, and selected fermentation-derived bioactive systems are supported by mechanistic evidence. Strong translational evidence is concentrated in well-characterized product–endpoint combinations, while broad metabolic, endocrine, neurocognitive, neurodegenerative, and healthy-aging claims are heterogeneous, limited, or mostly supported by preclinical and observational evidence. Poor strain-level and process characterization, varied product formulations, limited intervention periods, weak comparators, and extrapolation from isolated microbes or metabolites to whole fermented meals continue to hinder causal interpretation in the literature. Thus, future research should replace generic fermented food categories with reproducible product fingerprints integrating matrix composition, strain-resolved microbial identity, fermentation parameters, viable and non-viable fractions, metabolomic profiles, dose, and host characteristics. To determine which fermented products have clinically meaningful effects, in whom, through which mechanisms, and under what conditions, standardized controlled human interventions, multiomics with causal mediation approaches, precision nutrition frameworks, and integrated safety and regulatory evaluation are needed.

Fermentation doi: 10.3390/fermentation12100446

Authors: Gary Meza-Bone Verónica Andrade-Yucailla Iván González-Puetate Jessica Meza-Bone Marcos Barros-Rodríguez Edison Barros-Rodríguez

Forage scarcity, especially during dry periods, limits feed availability for livestock systems, affecting the productivity and sustainability of animal production. The aim of this investigation was to determine the effect of three harvest ages (8, 10 and 12 days) and five nutrient solution concentrations (0, 25, 50, 75 and 100%) on the morpho-agronomic performance, chemical composition, digestibility, rumen degradation kinetics and mitigation of gas, CH4 and CO2 emissions of hydroponic maize forage. Digestibility, degradation, and the reduction in total gas, CH4, and CO2 emissions were evaluated using in vitro techniques. A completely randomized design in a factorial arrangement (3 × 5) was used (8, 10 and 12 days of harvest) (0, 25, 50, 75 and 100% nutrient solution). Four Brahman bulls weighing 550 ± 30.5 kg were used, each fitted with a ruminal cannula. The animals were kept in separate pens, where they were fed Megathyrsus maximus and had access to water ad libitum. Biomass production demonstrated significant differences (p < 0.0001) for the effect of harvest age (12 days), concentration (100%), and their interaction. Dry matter, crude protein, neutral detergent fiber, and acid detergent fiber indicated significant differences (p < 0.0001) for the effect of harvest age, concentration, and their interaction. Dry matter digestibility yielded an effect of harvest age (8 days), concentration (75% and 100%), and their interaction (p < 0.0001). Rumen dry matter degradation of the soluble fraction, potential degradation, and effective degradation (0.02, 0.05, and 0.08, respectively) indicated an effect of harvest age, concentration, and their interaction (p < 0.0001). Gas, CH4 and CO2 production had an effect on harvest age (8 days) and fertilization concentration (75% and 100%; p < 0.0001). It can be concluded that at early harvest ages (8–10 days) combined with intermediate to high concentrations of nutrient solution (75–100%), the biomass production and chemical composition, and thus the increase in ruminal digestibility and degradability and therefore the mitigation of CH4 and CO2, of hydroponic maize forage are optimized, making it a feeding strategy for sustainable livestock production.

Fermentation doi: 10.3390/fermentation12100445

Authors: Xiaohui Li Jinxiu Yu Ke Tong Jianfeng Mei

This study compared two inoculum preparation protocols for the mixed fermentation of unsterilized soybean meal (SBM) with Aspergillus niger and Candida tropicalis. The mono-culture-derived (MO-C) inoculation protocol involved separately cultivating A. niger and C. tropicalis and subsequently inoculating both cultures into SBM, whereas the co-culture-derived (CO-C) inoculation protocol involved cultivating both microorganisms together in the same medium before inoculating into SBM. Compared with the MO-C treatment, the CO-C treatment resulted in a slightly higher apparent crude protein content and significantly increased the acid-soluble protein and free amino acid contents in fermented soybean meal (FSBM), with increases of 9.22% and 141%, respectively. The CO-C treatment was also associated with greater reductions in β-conglycinin and raffinose-family oligosaccharides (RFOs), as well as higher DPPH and ABTS radical-scavenging activities and ferric-reducing power of FSBM. These findings suggest that the co-culture inoculum protocol provides a simplified approach for preparing mixed inocula and may improve selected nutritional and functional properties of FSBM under the tested conditions.

Fermentation doi: 10.3390/fermentation12090444

Authors: Karine Rabelo Fonseca Roberta Passini Sérgio Botelho de Oliveira Danns Pereira Barbosa Luana Alves Akamine Silvia Robles Reis Duarte

This study evaluated the potential for biogas production from anaerobic digestion of cattle manure using bioaugmentation in batch-type bioreactors. A completely randomized design was adopted, with four treatments and three replications: CM, cattle manure only, as control; CMI, cattle manure plus inoculum; CMI-3, cattle manure plus inoculum and 3 mL of bioremediation additive; and CMI-9, cattle manure plus inoculum and 9 mL of bioremediation additive. The inoculum originated from a UASB (Upflow Anaerobic Sludge Blanket) reactor used in the effluent treatment plant of a food industry. The bioremediation additive was a gel containing environmental bacterial spores composed of different concentrations of Bacillus megaterium, Bacillus mycoides, Bacillus amyloliquefaciens, and Bacillus thermoglucosidasius. Substrates were characterized by pH, dry mass, organic and inorganic dry mass, total organic carbonate/total inorganic carbonate ratio, and nutrient concentration. Biogas volume, gas characteristics, and gas concentrations were assessed. Data were analyzed by ANOVA and F tests, followed by Tukey’s test at 5% significance. Inoculum, alone or combined with bioremediation, improved biogas production, with 9 mL addition of bioremediator resulting in 55.40% methane.

Fermentation doi: 10.3390/fermentation12090443

Authors: Na Jiang Yukun Zhang Manabu Ishikawa Xiaoxiao Zhang

Marine macroalgae and terrestrial halophytes represent a structurally distinct class of feed resources that can be produced without the arable land, fresh water, and synthetic fertilizer inputs required by conventional protein crops. Their direct incorporation into animal diets is, however, constrained by a convergent set of physical and toxicological barriers—viscous polysaccharides, lignocellulosic recalcitrance, anti-nutritional secondary metabolites, and accumulated heavy metals and halogens—that collectively impede practical use. Microbial fermentation can transform some of these barriers into functional resources through enzymatic deconstruction, catabolite conversion, and biosorption—a duality described here as the Barrier–Resource Duality. This critical narrative review synthesizes findings from publications across fermentation microbiology, animal nutrition, food safety, life cycle assessment, and regulatory science. The review analyzes cell-wall architectures of Chlorophyta, Rhodophyta, and Ochrophyta alongside the lignocellulosic matrix of terrestrial halophytes, maps the requisite carbohydrate-active enzyme families and polysaccharide-utilization loci, and evaluates the postbiotic mechanisms—TLR/NF-κB, histone deacetylase inhibition, and metabolite-mediated immunomodulation—by which fermentation-derived compounds may exert host benefit. The evidence base is assessed through a critical narrative synthesis that identifies knowledge gaps across five areas: (i) the absence of co-fermentation studies combining seaweeds and halophytes despite predicted substrate complementarity; (ii) the lack of pilot-scale fermentation data (no study exceeds 500 L); (iii) the single-study dependency of core in vivo efficacy claims; (iv) the absence of validated analytical methods for postbiotic quantification; and (v) the lack of a dedicated regulatory category for fermented marine biomass. It concludes that the field, while mechanistically rich, remains at Technology Readiness Level 2 (technology concept formulated), and that coordinated pilot-scale consortia, multi-institutional replication initiatives, and regulatory pathway design are prerequisites for commercial translation.

Fermentation doi: 10.3390/fermentation12090442

Authors: Hülya Hanoğlu Oral

Essential oils (EOs) have been extensively investigated as feed additives; however, their effects on ruminal degradation kinetics remain inconsistent, particularly for thymol- and carvacrol-rich EOs. This study evaluated the effects of concentrate feed with added thymol- and carvacrol-rich EOs, providing different levels of thymol and carvacrol, on ruminal degradation kinetics and effective degradability of dry matter (DM), organic matter (OM), and crude protein (CP) using an in situ nylon bag technique. Treatments included the concentrate feed (control); the concentrate feed with added carvacrol-rich EO to provide 300 or 100 mg carvacrol/kg concentrate (C300 and C100); the concentrate feed with added thymol-rich EO to provide 300 or 100 mg thymol/kg concentrate (T300 and T100); and the concentrate feed with both EOs added to provide 150 mg carvacrol + 150 mg thymol/kg concentrate (CT300) or 50 mg carvacrol + 50 mg thymol/kg concentrate (CT100). The carvacrol treatments generally maintained DM and OM degradability at levels comparable to the control, whereas the thymol and combined EO treatments showed lower degradability, particularly during the early incubation periods (p < 0.05). Thymol treatments also showed lower CP degradability than the control and carvacrol treatments at several incubation times (p < 0.05). Planned contrasts showed significant differences in DM and OM degradation kinetics between the carvacrol and thymol treatments, with thymol treatments showing lower effective degradability of DM, OM, and CP at all evaluated passage rates (p < 0.05), whereas no differences in CP kinetic parameters were detected. Degradation kinetics and effective degradability were similar between the individual EO treatments providing 300 and 100 mg carvacrol or thymol/kg concentrate. Combined EO treatments showed lower effective degradability of DM and OM than the individual EO treatments (p < 0.05), whereas CP effective degradability did not differ between the combined and individual EO treatments. Overall, these findings highlight the importance of considering EO type and nutrient-specific responses when selecting EOs for targeted use in ruminant nutrition.

Fermentation doi: 10.3390/fermentation12090441

Authors: Qingchun Luo Pengju Zhao Jianghua Li Xi Li Jian Chen Xuejun Lei Yanping Lu Jian Su Dong Zhao Jia Zheng Xinrui Zhao

The quality of Baobaoqu directly determines the flavor quality and yield of baijiu. In this work, metagenomic approaches combined with machine learning, including a multilayer perceptron (MLP) neural network model and the SHapley Additive exPlanations (SHAP) method, were employed to investigate the succession patterns and differential characteristics of microbial communities and potential enzymatic systems between two grades of Baobaoqu during storage. The results showed that Premium Baobaoqu possessed a more diverse microbial community than Normal Baobaoqu: a total of 1764 genera and 6901 species were annotated in Premium Baobaoqu, versus 1656 genera and 6440 species in Normal Baobaoqu. The top five dominant microbial genera, namely Weissella, Staphylococcus, Thermoactinomyces, Limosilactobacillus, and Pediococcus, collectively occupied 46.3–87.1% of the total microbial abundance. Ten microbial taxa were identified as key differential candidate microbial markers—including Weissella confusa, Kluyveromyces marxianus, and Staphylococcus lloydii—eight of which exhibited significantly higher abundance in Premium Baobaoqu. Glycoside hydrolases (GHs) constituted the largest enzyme class, accounting for 40.99% of the total. The top ten potential enzyme families significantly differentiated between them were GH43, GH31, GT9, GH2, CBM50, GH5, GH4, GT4, and GT26, with higher abundance of GH43, GH31, GH5, and CBM50 in Premium Baobaoqu. This study systematically uncovered the distinct microbial and enzymatic profiles of Baobaoqu of different qualities throughout storage. The findings provide theoretical guidance for the optimization of industrial production workflows and storage strategies for Baobaoqu manufacturing.

Fermentation doi: 10.3390/fermentation12090440

Authors: Yaling Zhu Rouf Ahmad Dar Xiaojie Mei Ning Fang Chen Sun Weixing Cao Ronghou Liu Adam Smoliński Le Zhang

The global fish industry is an essential contributor to food security and the economy; however, it produces considerable quantities of fish waste. Depending on species and processing methods, 20–80% of fish biomass is discarded as waste, amounting to almost 64 million tons annually. Conventional disposal methods such as landfilling, incineration, and wastewater discharge cause environmental pollution and greenhouse gas emissions. Therefore, for sustainable development, it is important to valorize fish waste into renewable energy and value-added products. Hence, this review aims to encourage the technical development of fish waste into bioenergy and bioresources by thoroughly studying key technologies for converting it into biogas, biodiesel, fertilizer, animal feed, and biochar. Although several studies have explored these technologies, most remain disjointed and lack a systematic assessment. Therefore, this work attempted to critically evaluate the technological principles, advantages, limitations, and optimization strategies of current valorization approaches. Furthermore, several recommendations have been proposed, including conducting pilot-scale trials, producing higher value-added products within a biorefinery system. Overall, this review provides a holistic outlook on the energy and resource conversion of fish waste, supporting sustainable waste management.

Fermentation doi: 10.3390/fermentation12090439

Authors: Zhicun Sheng Die Zhou Lin Niu Yi Zheng

A static magnetic field (SMF)-assisted liquid-state fermentation strategy using Lacticaseibacillus paracasei (L. paracasei) is proposed to improve the comprehensive utilization value of Ginkgo biloba leaves. Taking total flavonoid extraction yield as the objective, Box-Behnken response surface methodology was adopted to optimize the fermentation process. Meanwhile, the nutritional components and hypoglycemic activity of Ginkgo biloba leaves in vitro before and after fermentation were compared and analyzed. The optimal fermentation conditions were determined as follows: 3-fold-diluted De Man, Rogosa, and Sharpe (MRS) medium, an SMF intensity of 4.2 mT, an SMF duration of 2.9 h, and an inoculum size of 6.5%. Under these conditions, the total flavonoid extraction yield reached (3.41 ± 0.11)%, which was 3.33 times that of unfermented raw material. Analysis of the nutritional components revealed that after SMF-assisted fermentation, crude protein and crude fat contents increased by 59.58% and 13.72%, while ash and crude fiber contents decreased by 24.84% and 35.66%, respectively. SMF application also significantly affected the crude fiber content (p < 0.05). Meanwhile, the contents of phytic acid, tannins, phenolic acids, and ginkgolic acids in the SMF-assisted group declined by 29.56%, 43.10%, 23.42%, and 50.37%, respectively, and the SMF further promoted the degradation of anti-nutritional factors. Hypoglycemic activity analysis indicated that fermentation markedly enhanced the inhibitory effect of Ginkgo biloba leaf-derived flavonoids against α-glucosidase and α-amylase, and that SMF stimulation may also contribute to strengthening this inhibitory activity. This study demonstrates that SMF-coupled probiotic fermentation is an effective and environmentally friendly approach for processing Ginkgo biloba leaves, providing experimental support for high-value utilization of plant-based resources through physical-field-assisted microbial fermentation.

Fermentation doi: 10.3390/fermentation12090438

Authors: Bartłomiej Zieniuk

Non-conventional yeasts (NCYs) are promising microbial platforms for converting agro-industrial residues into value-added enzymes, yet their use for lipase production under solid-state fermentation (SSF) remains fragmented across the literature. This scoping review systematically mapped studies on lipase production by NCYs using agro-industrial residues under SSF. Scopus and Web of Science Core Collection were searched according to a PRISMA-ScR-based protocol, yielding 38 eligible original studies published between 1993 and 2025. Yarrowia lipolytica dominated the evidence base, accounting for 21 studies (55.3%), followed by Candida rugosa with six studies. Oilseed- and vegetable-oil-processing residues were used in 31 studies (81.6%), while cereal brans and fruit-processing by-products were also common substrates. Considerable variation was observed in substrate formulation, moisture, supplementation, fermentation time, optimization strategy, enzyme recovery, lipase assays, and activity units. This methodological heterogeneity precluded meaningful meta-analysis and limited direct comparison of reported lipase activities. Although several studies demonstrated applications in ester synthesis, lipid modification, polymer degradation, detergents, and wastewater treatment, most processes remained at the laboratory scale. Future development should prioritize standardized activity reporting, broader NCY diversity, improved reactor-scale control, and integrated downstream strategies to advance SSF-derived yeast lipases toward industrial application.

Fermentation doi: 10.3390/fermentation12090437

Authors: Yao Yan Xinyi Mao Fen Liu Shan Li

Ursodeoxycholic acid (UDCA) is the first-line therapy for primary biliary cholangitis and an important active constituent of bear bile. Whole-cell microbial conversion of inexpensive lithocholic acid (LCA) offers a promising alternative to conventional chemical synthesis owing to its high regioselectivity and mild reaction conditions, yet the fermentation process of Fusarium equiseti HG18 (CCTCC M2023160), a natural fungal catalyst for LCA 7β-hydroxylation, has not been systematically engineered for scalable production. This study developed a whole-cell process for UDCA production by F. equiseti HG18. Systematic optimization by single-factor experiments, Plackett–Burman design and Box–Behnken response surface methodology raised the shake-flask UDCA titer from 0.19 to 0.59 mg mL−1. Scale-up in a 3 L stirred-tank bioreactor shortened the fermentation time from 144 h in shake-flask cultivation to 96 h in the bioreactor under optimized operating conditions (pH 8.5, aeration 2.5 L min−1, and agitation 200 rpm). Experiments across a range of initial LCA loadings revealed a progressive decline in UDCA molar yield at elevated substrate concentrations, consistent with substrate-related inhibitory effects, and this loading-dependent behavior was used to design a two-stage fed-batch feeding strategy. Under the optimized condition (2.0 mg mL−1 LCA fed at 0 and 48 h), UDCA titer reached 1.71 mg mL−1, corresponding to a volumetric productivity of 17.8 mg L−1 h−1 and a UDCA molar yield of 41%. This study establishes a laboratory-scale whole-cell bioprocess for UDCA production from LCA using a wild-type fungal catalyst, integrating statistical medium optimization, bioreactor process development, and substrate-feeding strategies. The findings provide a practical framework for improving fungal whole-cell steroid biotransformation and highlight the potential of wild-type fungal platforms for scalable biocatalytic production.

Fermentation doi: 10.3390/fermentation12090436

Authors: Guangyao Hu Meng Wang Qingsheng Qi Junhong Yu Hua Yin Shumin Hu

Oxidative stress is a major physiological constraint on industrial lager yeast, compromising fermentation efficiency and flavor quality. Unsaturated fatty acids are known to influence membrane fluidity, but whether exogenous fatty acid supplementation can actively reprogram the yeast defense system, beyond serving as a passive membrane component, remains unclear. Here, we compared the effects of four fatty acids (palmitic, palmitoleic, oleic, and linoleic acid) on oxidative stress tolerance and fermentation performance in industrial lager yeast, under a defined chemical oxidative challenge (2.0 mM H2O2) in 15 °P wort, combining physiological assays with targeted gene-expression and untargeted metabolomic analyses; the dose was selected from a 0–2.0 mM gradient, with an ethanol-vehicle control included throughout. Among the fatty acids tested, palmitoleic acid (POA) most markedly enhanced oxidative stress tolerance, maintaining 91% cell viability, restoring intracellular pH to 6.1 by 24 h after transient acidification, and reducing ROS accumulation by 41.2%. Mechanistically, POA upregulated the antioxidant system, increasing catalase and glutathione peroxidase activities by 35.6% and 85.5%, respectively, and restoring glutathione levels by 35.5%. Metabolic profiling revealed a global reconfiguration, including a 2.6-fold increase in the stress-protectant proline and elevated pantothenate and coenzyme A levels, accompanied by a shift in the volatile profile toward esters, which rose from 26.1% to 60.3% of the total pool, alongside a 52.1% increase in total volatiles that did not reach significance after correction for multiple testing (q = 0.070); sensory evaluation confirmed higher fruity-estery intensity and lower soapy and staling notes in the POA beer. These findings identify POA as an active metabolic modulator, not merely a passive structural lipid, pointing to a non-transgenic nutritional strategy whose industrial value now requires validation under high-gravity, pilot-scale, and serial-repatching conditions.

Fermentation doi: 10.3390/fermentation12090435

Authors: Luca Nerva Walter Chitarra Alessandro Romano Giovanni Mian Lorenzo Lovat Raul Romor Diego Tomasi Tiziana Nardi

Grape-associated microbial communities are key contributors to wine quality and microbial terroir, yet their dynamics during withering, a critical post-harvest stage for premium sweet and fortified wine production, remain poorly characterized. Using high-throughput metabarcoding (16S rRNA and ITS), we monitored bacterial and fungal communities on Corvina grape berries throughout withering under controlled (C) and non-controlled (NC) dehydration conditions, integrating microbiome data with previously determined volatile organic compound (VOC) and stilbene profiles to uncover taxon–metabolite relationships. Microbial communities underwent progressive restructuring during dehydration. Moreover, the two withering conditions exhibited distinct dehydration kinetics, with C reaching 30% weight loss 14 days earlier than NC, with a significant effect on the abundance of several wine-relevant and spoilage-associated taxa. Metschnikowia was significantly more abundant under C conditions at 10% and 20% weight loss, while Botrytis reached 26.5% relative abundance at 30% weight loss under NC compared with 2.4% under C. A correlation network analysis identified significant associations between Lactobacillus, Acinetobacter, Clostridium, and metabolite accumulation, with Metschnikowia showing positive associations with bioactive compounds and negative associations with spoilage fungi. This first joint time-course analysis of mycobiome and bacteriome dynamics alongside metabolome changes during withering highlights significant associations between microbial succession and grape biochemical changes during withering.

Fermentation doi: 10.3390/fermentation12090434

Authors: Ahmed E. Kholif Abdelkader M. Kholif

The rumen is a complex microbial ecosystem in which anaerobic fermentation determines the availability of energy and protein to ruminant hosts and influences feed efficiency, animal productivity, and environmental emissions. This review integrates current knowledge of host–rumen microbiome interactions with particular emphasis on microbial fermentation, nutrient utilization, feed efficiency, methane (CH4) production, and sustainable ruminant production. We examine how dietary factors, including forage-to-concentrate ratio, carbohydrate fermentability, protein degradability, and lipid supplementation, alter microbial community structure, hydrogen metabolism, volatile fatty acid production, microbial protein synthesis, and nitrogen utilization. The review further evaluates microbiome-targeted strategies, including 3-nitrooxypropanol, red seaweeds (Asparagopsis spp.), nitrate, direct-fed microbials, and plant-derived bioactive compounds, with emphasis on their effects on fermentation pathways and methanogenesis; these strategies differ substantially in evidence base and mechanistic specificity, with 3-nitrooxypropanol supported by the most consistent mechanistic and in vivo evidence and several plant-derived compounds and direct-fed microbials showing more variable responses. Evidence from microbiome-wide and genome-wide association studies indicates that host genetics contributes to variation in rumen microbial composition and function, with potential consequences for feed efficiency and CH4 emissions. Host-side determinants of the rumen environment, such as feed intake, digesta passage rate, saliva production, and epithelial and immune function, further shape microbial responses. However, responses to microbiome-targeted interventions remain variable because of microbial functional redundancy, dietary context, adaptation, and host-specific effects. We therefore discuss the major constraints limiting the consistent translation of microbiome research into practical feeding strategies and propose an integrated framework combining functional microbiome indicators, precision nutrition, host–microbiome-informed selection, and real-time monitoring. Understanding and manipulating rumen microbial fermentation through coordinated nutritional and host-based approaches may provide a pathway toward improving ruminant productivity while reducing the environmental footprint of livestock production. Among the strategies reviewed, 3-nitrooxypropanol currently has the strongest and most reproducible evidence base, whereas plant-derived bioactives and several direct-fed microbials remain promising but inconsistent, and validated on-farm microbiome biomarkers remain a major gap.

Fermentation doi: 10.3390/fermentation12090433

Authors: Aleksandar Dolashki Lyudmila Velkova Tsvetan Berovski Maria Todorova Ventseslav Atanasov Maria Gerginova Ekaterina Krumova Nadya Armenova Penka Petrova Kaloyan Petrov Pavlina Dolashka

Bacillus velezensis is a promising candidate for the biocontrol of plant pathogens due to its production of broad-spectrum antimicrobial metabolites. The present study evaluates the antifungal potential and metabolic profile of the non-pathogenic rhizobacterial strain Bacillus velezensis 5RB. Modifying the mineral composition across three different growth media (A, B, and C) resulted in distinct secondary-metabolite profiles of B. velezensis 5RB. Notably, the free-cell supernatant of strain 5RB cultivated in medium A and C demonstrated the most potent antifungal activity against the gray mold pathogen Botrytis cinerea. For the first time, the antimicrobial metabolites produced by B. velezensis 5RB across these three media were comprehensively characterized using ultra-performance liquid chromatography-quantitative time-of-flight mass spectrometry (UHPLC-QTOF-MS). Mass spectrometric analyses (LC-ESI-MS) identified predominantly lipopeptides from the surfactin and fengycin families, alongside three classes of polyketides: macrolactins, difficidins, and bacillaenes. Multiple lipopeptide homologues, including a novel surfactin isoform (B*), were confirmed by tandem mass spectrometry (LC-ESI-MS/MS). Additionally, this study provides the first experimental evidence for subtilosin A production by B. velezensis 5RB. The multicomponent fermentation matrix of 5RB conferred robust biocontrol protection to tomato leaves against B. cinerea and Phytophthora infestans in an in vitro disease model, underscoring its strong potential for sustainable agricultural applications.

Fermentation doi: 10.3390/fermentation12090432

Authors: Esra Orenlili Yaylagul Adem Yavaş Mustafa Dikme Seda Gezgin Ecem Akan

Paraprobiotics offer safer alternatives to live probiotics without requiring cell viability. Here, heat-inactivated bacterial preparations (paraprobiotics) were produced from Lacticaseibacillus paracasei subsp. paracasei 431 (L. casei 431) using thermal treatments (65–121 °C). No viable colonies were detected by conventional plating in any treatment, and flow cytometry indicated that more than 96% of cells were membrane-compromised or dead. The most favorable condition (65 °C, 60 min) was identified using a TOPSIS multi-criteria ranking approach integrating loss of culturability with antimicrobial activity against Enterococcus faecalis and Escherichia coli with inactivation efficiency. This paraprobiotic and the corresponding probiotic were subjected to in vitro gastrointestinal digestion and colonic fermentation, followed by short-chain fatty acid (SCFA) and 16S rRNA-based gut microbiota analysis. The fecal inoculum was pooled from five healthy donors and used to run three replicate fermentation vessels per group. Both probiotic and paraprobiotic supplementation significantly increased acetate, butyrate, and total SCFA concentrations compared with the control, and propionate and valerate concentrations were also significantly higher in the paraprobiotic group than in the control. Both interventions increased Chao1 richness and Simpson diversity (p < 0.05), although Shannon diversity did not differ significantly, and induced significant shifts in beta diversity, alongside marked enrichment of butyrate- and SCFA-producing taxa such as Roseburia, Anaerostipes, and Akkermansia muciniphila. However, not all observed microbial changes were unequivocally beneficial; increases in Bilophila wadsworthia and Collinsella aerofaciens warrant cautious interpretation given their context-dependent associations with host health. Spearman correlation analysis identified positive associations between enriched taxa and SCFA concentrations, which should be interpreted as exploratory rather than evidence of causal metabolic cross-feeding. Under the conditions of this in vitro fermentation model, no statistically significant differences were detected between the viable and heat-inactivated preparations for most measured outcomes, indicating that thermal inactivation did not markedly diminish the capacity of L. casei 431 to influence gut microbial composition and short-chain fatty acid production. The multi-criteria selection strategy offers a practical approach for optimizing paraprobiotic production for functional food applications.

Fermentation doi: 10.3390/fermentation12090431

Authors: Raúl Ricardo Gamba Daniela Sedan Dario Andrinolo Angela León Peláez Marina A. Golowczyc

Aflatoxin B1 (AFB1), a potent carcinogenic metabolite produced by Aspergillus flavus and A. parasiticus, constitutes a significant threat to food safety. Conventional decontamination methods are costly or ineffective. Biological detoxification has emerged as a promising alternative. Kefir, a fermented milk beverage, comprises lactic acid bacteria (LAB) and yeasts with documented antifungal properties. This study evaluated whey permeate (WP) as a fermentation substrate for kefir microorganisms and assessed their AFB1-binding capacity. Kefir microorganisms cultivated in WP supported active fermentation, reaching 8.47 log CFU/mL LAB and 7.57 log CFU/mL yeasts, with concomitant lactose consumption and organic acid production. The ability of 13 individual kefir-derived microorganisms and the total kefir microbial community to bind AFB1 was evaluated under diverse conditions. All microorganisms exhibited AFB1 binding ability, although binding depended on strain, growth medium, pH, microbial concentration, and toxin concentration. The highest binding was observed for the total kefir community grown in WP. Binding remained stable over time for the total kefir community and Lactiplantibacillus plantarum CIDCA 83114 and was independent of viability and hydrophobicity. AFB1 binding by kefir microorganisms significantly reduced AFB1-induced cytotoxicity in HepG2 cells. These findings demonstrate that WP can be valorized into a value-added fermented product containing microorganisms with strong AFB1 binding and cytoprotective properties.

Fermentation doi: 10.3390/fermentation12090430

Authors: Qiting Wu Jiarui Zhao Huirong Zhu Yunle Liu Chaowan Guo Lin Ye

Sea rice harbors a diverse array of bioactive constituents, among which the efficient liberation of phytic acid is pivotal for unlocking its full functional potential. In this study, a co-fermentation system integrating yeast and lactic acid bacteria was established to generate a sea rice fermentation filtrate (SRF) with enhanced phytic acid (PA) content, aiming to broaden its application as a cosmeceutical ingredient and to facilitate the high-value utilization of sea rice. Response surface methodology was employed to optimize the inoculation ratios of the two microbial strains and the fermentation duration, and the PA levels were quantified using a commercial assay kit. The anti-melanogenic activity of SRF was assessed in murine B16 melanoma cells, and the underlying molecular mechanisms were elucidated with particular emphasis on the PI3K/AKT/GSK3β/MITF signaling cascade. Under the optimal conditions, specifically Saccharomyces cerevisiae (SC) inoculation at 4.5% and Lactobacillus plantarum (LP) at 6.0% with a fermentation time of 18 h, the PA concentration reached 576.61 μg/mL. Mechanistically, SRF treatment enhanced GSK3β phosphorylation, which was associated with reduced MITF phosphorylation and diminished the expression of downstream melanogenic enzymes, thereby effectively curtailing melanin synthesis, suggesting that SRF, as a complex fermentation product containing multiple bioactive constituents including PA, exhibits potent whitening efficacy. Collectively, these results provide novel perspectives for the valorization of sea rice and the development of natural skin-lightening agents, while also contributing to the extension of the sea rice industrial value chain.

Fermentation doi: 10.3390/fermentation12090429

Authors: Nathalia Fernandes Alessandra De Cesare Valentina Indio Ursula Gonzales-Barron Vasco Cadavez

Alheira is a traditionally smoked, fermented, non-ready-to-eat meat sausage produced in the Trás-os-Montes region of Portugal, where lactic acid bacteria (LAB) are major determinants of product safety and quality. This study used whole-genome sequencing to characterize 59 LAB isolates collected from artisanal alheira produced in six municipalities. Eight species belonging to six genera were identified, and average nucleotide identity analysis resolved 24 non-redundant strain groups. Functional annotation revealed broad repertoires of carbohydrate-active enzymes, proteases, lipases, transport systems, and genes associated with tolerance to acid, oxidative, bile, heat, and salt stress. Genotype–phenotype inference was performed with a subset of 22 strain groups represented by unflagged genome assemblies. After false-discovery-rate correction, carbon-metabolism, transport, energy-metabolism, total functional-gene, acid-stress, bile-stress, and total-stress counts were positively associated with total pH decline. A mixed-effects model showed a positive association between standardized total functional-gene count and acidification (b=0.137±0.059, p=0.049; marginal R2=0.266, conditional R2=0.582), but within–between decomposition indicated that the association was detectable between species rather than within species. Regularized regression, Random Forest, AICc model comparison, and partial least-squares regression converged on carbon metabolism, transport, energy metabolism, and acid- or bile-stress functions as the principal exploratory signals; however, sparse LASSO regression for variable selection was unstable, and prediction of unobserved species was limited. None of the five targeted pathways: acetaldehyde, citrate, diacetyl, exopolysaccharide, and lactose metabolism, remained significant after multiple-testing correction. These findings provide a genomic and phenotypic basis for selecting native starter-culture candidates while emphasizing the need for independent functional and safety validation.

Fermentation doi: 10.3390/fermentation12090428

Authors: Elisa Aiello Mattia Pia Arena Andrea Pulvirenti Maria Gullo

Non-Saccharomyces yeasts shape the aroma, freshness, and reduced-alcohol profiles of wines, yet their oenological contribution is curtailed by a poor tolerance to ethanol. Because ethanol acts on the plasma membrane, the cell’s selective barrier, this limitation is rooted in the membrane lipidome, whose remodeling has been documented but never integrated into a wine-specific, predictive framework. This review provides that synthesis, keeping the non-Saccharomyces wine yeasts as the subject and Saccharomyces cerevisiae as a reference frame. It first describes how ethanol perturbs the bilayer and how the cell compensates through unsaturated fatty acids, ergosterol, phospholipid-class balance, and membrane fluidity. It then traces the concentration- and time-dependent remodeling of the lipidome, together with the medium-chain fatty-acid, temperature, and oxygen co-stressors accompanying it, and the comparative membrane biology distinguishing these yeasts from S. cerevisiae, including the markedly reduced uptake of exogenous sterols under oxygen limitation. Finally, it weighs the nutritional, process, and non-genetically modified strain-improvement strategies that reinforce them. The same lipid descriptors recur throughout, yet are seldom measured in improved wine strains. We argue that the membrane lipidome can be read as a candidate multivariate predictive signature of ethanol tolerance and of fermentation performance, and outline the validation it still requires.

Fermentation doi: 10.3390/fermentation12090427

Authors: Tekmile Cankurtaran Kömürcü Miguel Angel Alvarez Gonzales İhsan Sarıoğlan Stephen R. Lindemann Yunus Emre Tunçil

This study investigated the effects of yeast-mediated pre-fermentation on the composition and functional characteristics of modern and ancient wheat genotypes, and their subsequent impact on gut microbial fermentation. Whole wheat flours were pre-fermented using Saccharomyces cerevisiae (6%, w/w) at 30 °C for 6 h. Raw and pre-fermented whole wheat samples were subjected to in vitro upper gastrointestinal digestion, followed by monosaccharide composition analysis, in vitro fecal fermentation using a pooled inoculum prepared from three healthy donors, microbial profiling, and short-chain fatty acid (SCFA) quantification. Fermentation increased Folin–Ciocalteu-reactive values and antioxidant capacity, while reducing residual starch and protein after digestion, indicating alterations in the composition of digestion-derived residues. After fermentation by S. cerevisiae, monosaccharide analysis revealed a relative enrichment of glucose, accompanied by decreased proportions of arabinose and xylose. Following in vitro fecal fermentation, pre-fermented wheat samples exhibited significantly (p < 0.001, AMOVA) different microbial community structures compared with their raw counterparts, based on Bray–Curtis dissimilarities, whereas differences in α-diversity were comparatively limited. In addition, taxa associated with carbohydrate fermentation and SCFA production, including Parabacteroides distasonis, Butyrivibrio crossotus, and Kineothrix, showed treatment- and genotype-dependent responses. All wheat samples supported SCFA production, although SCFA accumulation was more gradual than with inulin. Overall, yeast-mediated pre-fermentation was associated with changes in wheat composition and subsequent shifts in fecal microbial community structure and fermentation dynamics, with responses varying among wheat genotypes.

Fermentation doi: 10.3390/fermentation12090426

Authors: Gbeminiyi Olamiti Shonisani Eugenia Ramashia

Processing tubers such as potato, sweet potato, cassava, and yam, as well as legumes such as soybean, pea, chickpea, bean, and lentil, generates substantial quantities of peels, pulps, husks, and press cakes that retain considerable nutritional and functional value despite often being discarded. Microbial fermentation has emerged as a low-cost and scalable approach for valorising these residues into functional ingredients with improved digestibility and enhanced bioactive-compound content. This study synthesises the composition of major tuber and legume by-products, the solid-state and submerged fermentation systems employed for their bioconversion, and the biochemical and functional transformations achieved through fermentation, including improvements in antioxidant activity, prebiotic potential, antihyperglycaemic properties, and protein quality. The emerging applications of these fermented by-products in bakery products, dairy alternatives, snacks, nutraceuticals, and the conceptually related field of gut-microbiome-guided precision nutrition are also examined. Persistent challenges, including compositional variability, safety monitoring, and regulatory classification, are critically evaluated alongside strategies for addressing these limitations. Overall, fermentation-based valorisation of tuber and legume residues represents a scientifically credible and environmentally sustainable strategy for transforming agri-food waste streams into value-added, functional nutrition ingredients.

Fermentation doi: 10.3390/fermentation12090425

Authors: Victoria Kleinjan Melisa González Flores María Eugenia Rodriguez Christian Ariel Lopes

Torulaspora delbrueckii is a promising non-Saccharomyces yeast for beverage diversification, although its diversity and application in cider production remain poorly explored. This study characterized Patagonian T. delbrueckii isolates from wine- and cider-associated environments and evaluated their fermentative potential in apple must. Mitochondrial DNA-RFLP analysis showed that mitochondrial profiles varied according to the isolation source, while physiological characterization revealed differences in temperature, sulfite, and ethanol responses among isolates from different sources. Compared with wine isolates, cider isolates generally exhibited greater tolerance to high temperatures, lower sulfite tolerance, and shorter lag phases under ethanol stress. Eleven representative strains completed apple must microfermentations. Compared with a commercial Saccharomyces cerevisiae strain, T. delbrueckii produced higher glycerol and erythritol concentrations while achieving comparable or higher ethanol levels. Two contrasting strains were further evaluated in sequential mixed fermentations with S. cerevisiae. NPCC1340 enhanced glycerol and erythritol production, whereas NPCC1608 increased malic and succinic acids while maintaining low acetic acid levels. In mixed fermentations, ciders retained the characteristic metabolic profiles of each T. delbrueckii strain, whereas S. cerevisiae improved fermentation performance, producing intermediate fermentation kinetics. These findings reveal phenotypic diversity among Patagonian T. delbrueckii strains and suggest differences associated with their isolation sources, highlighting their potential as starter cultures for producing ciders with distinct chemical characteristics.

Fermentation doi: 10.3390/fermentation12090424

Authors: Aminur Rahman Pottathil Shinu JB Senthil Kumar Md Azizul Haque

Chlorpyrifos (CPF) is the most commonly used organophosphorus insecticide in agriculture globally. This has raised concerns due to its persistence, bioaccumulation, neurotoxicity, and environmental and human health effects. Until 2020, CPF was the most commonly used pesticide in European Union (EU) food production. CPF is also used in other parts of the world, though it has been discontinued in the EU, as national pesticide surveillance programs indicate it is found in soil, water, and food. This type of persistence is potentially harmful to farmers, consumers, and animals because CPF is toxic. Markedly, CPF has the potential to change the microbiota composition of soils, i.e., fungal, bacterial, and actinomycete communities, and inhibit the mineralization of nitrogen. The key CPF activity is associated with the inhibition of acetylcholinesterase (AChE), leading to reproductive, neurotoxic, and genotoxic effects. Microbial degradation, especially when applied by means of bacteria, has become one of the promising alternatives to the traditional physicochemical means since it is inexpensive, does not harm the environment and may possibly be fully detoxified. This review summarizes the latest developments in the study of CPF-degrading bacteria, enzyme pathways, microbial diversity, and the evaluation of the environmental impact of microbial remediation. Recent research findings, genomic research developments, and potential applications of CPF-degrading bacteria are addressed. In addition, this study reveals the current knowledge gaps, presents biotechnological challenges, and suggests future directions in the application of field-scale studies, focusing on the application of microbial solutions in sustainable agriculture.

Fermentation doi: 10.3390/fermentation12090423

Authors: Zhonghao Wang Hongyan Hou Weibing Zhang Wei Zhang Yulong Zhao Lianqing Wei Jie Cheng Yuxuan Jiang Feier Ren Jiajin Sun Qinghong Li Wenjie Zhang

Skatole is a harmful, odorous pollutant in livestock manure. Skatole-degrading strains are mostly harmful Gram-negative bacteria, whereas safe Gram-positive strains demonstrate poor degradation performance, limiting bioremediation applications. To solve this problem, this study was conducted to enhance the skatole degradation capacity of the food-grade strain Lactococcus lactis NZ9000 via heterologous expression of the skatole-degrading Ska enzyme from Acinetobacter piscicola p38. Three gene sequences, designated Ska-Y (original sequence from A. piscicola p38), Ska-D (E. coli codon-optimized), and Ska-R (L. lactis codon-optimized), were separately expressed using constitutive pMG36e and nisin-inducible pNZ8148 plasmids. The constitutive system only transcribed mRNA but produced misfolded, nonfunctional inclusion bodies. By contrast, the codon-optimized pNZ8148-Ska-R strain exhibited prominent skatole degradation ability, even under non-inductive conditions. Under optimal conditions (30 ℃, ultra-low nisin induction), the engineered strain increased the 24 h degradation rate of 50 mg/L skatole from 20% to 88% and completely degraded 25 mg/L skatole. Field tests verified that the strain effectively reduced skatole accumulation in manure compost and lagoon manure. This study achieved efficient functional heterologous expression in Gram-positive bacteria, provides new insights into ultra-low-dose induction and codon optimization, and offers a safe and efficient microbial agent for livestock manure odor remediation.

Fermentation doi: 10.3390/fermentation12090422

Authors: Vicente Barros Maribel Mamani Benjamín Castillo Sara Cuadros-Orellana Nidia Torres-Ponce Cristian Valdés

Native Lactic Acid Bacteria (LAB) isolated from fruits and vegetables in Chile’s Maule Region were identified as Lactiplantibacillus plantarum and L. pentosus. Their growth and lactic acid production were evaluated under furan inhibitor stress (furfural and 5-methylfurfural (5-MF)) relevant to agroindustrial waste valorization. In fruit hydrolysates containing natural furans (11–57 mg/L), LAB grew similarly to inhibitor-free controls and produced 17–25 g/L lactic acid. Under controlled conditions, furfural at 12 g/L reduced bacterial growth by over 80% and decreased lactic acid production to only 2 g/L. In contrast, 5-MF at the same concentration allowed substantially higher tolerance, with up to 7 g/L lactic acid. Benchmarked directly against the commercial reference strain Lactiplantibacillus plantarum PL8014 under identical conditions, the native isolate B1 matched or exceeded PL8014’s lactic acid output in most furfural and 5-MF concentrations tested, including the two most severe 5-MF conditions. Logistic growth and Luedeking–Piret models accurately described both bacterial growth dynamics and lactic acid production kinetics under all inhibitory conditions (R2 > 0.96). Inhibitor concentration proved more critical than inhibitor type, although furfural consistently showed stronger potency. These findings confirm the biotechnological potential of native Maule LAB and provide quantitative kinetic parameters for optimizing lactic acid production from lignocellulosic waste, supporting circular economy strategies.

Fermentation doi: 10.3390/fermentation12090421

Authors: Zekeriya Safa İnanç Mustafa Aslan Battal Yılmaz Deniz Şişman Erhan Çetin Oğuzhan Kahraman Mustafa Selçuk Alataş Huzur Derya Arık

Background: Plant flavonoids are candidate alternatives to ionophores for modulating rumen fermentation, yet the intact glycoside rutin (quercetin-3-O-rutinoside) has received little attention. The objective of this study was to determine whether rutin changes the in vitro ruminal fermentation of total mixed rations (TMR) differing in forage-to-concentrate ratio; monensin was included at a single dose as a reference additive rather than a direct comparator. Methods: In a 2 × 4 factorial batch-culture experiment, a roughage-based (60:40) and a concentrate-based (40:60) TMR were incubated for 24 h without additive (control) or with rutin at 2.5% or 5% of substrate dry matter or monensin at 30 ppm. Results: Rutin did not change the gas production kinetics, ruminal pH, the volatile fatty acid (VFA) profile, or the stoichiometrically estimated methane and carbon dioxide at either dose (p > 0.05), and no dose response was found. Substrate type likewise left the VFA profile and the estimated gases unchanged (p > 0.05). Ammonia nitrogen (NH3-N) responded to the additive group (p = 0.027) and to the substrate × additive interaction (p = 0.022), but Tukey comparisons separated no individual means, so this response is preliminary. Conclusions: Neither rutin nor monensin markedly altered fermentation of these silage-, alfalfa- and cereal-based rations in the 24 h batch system; the substrate-dependent NH3-N signal warrants confirmation, and direct methane measurement is required before any anti-methanogenic potential can be claimed.

Fermentation doi: 10.3390/fermentation12090420

Authors: Şükrüye Selin Koyun Gamze Nur Müjdeci

In this study, the potential of oilseed processing residues, namely plum seed pulp, pumpkin seed pulp, pomegranate seed pulp, wheat germ pulp, and coconut pulp, was evaluated as alternative substrates for pulcherrimin production by indigenous yeast strain Metschnikowia pulcherrima ELM-GS-3. Among the tested substrates, wheat germ pulp supported the highest biomass and pulcherrimin concentrations and was therefore selected for process optimization. The effects of temperature, agitation rate, fermentation time, and initial pH on pulcherrimin concentration were investigated using Response Surface Methodology (RSM) based on a Central Composite Rotatable Design (CCRD). The developed quadratic model was statistically significant (p < 0.0001) with an R2 of 0.9441. The numerically selected conditions were determined as 25 °C, 71 rpm, 12 days, and an initial pH of 2 where pulcherrimin concentration reached 5.5 ± 0.3 g/L, representing a 1.79-fold increase compared with the non-optimized process. Bioprocess performance analysis revealed a volumetric productivity (Qp) of 0.459 g/L/day, a specific productivity (qp) of 0.029 g/g/day, and a product yield coefficient (YP/X) of 0.346 g/g biomass. The experimentally obtained value was in good agreement with the model prediction. To the best of our knowledge, this is the first report evaluating wheat germ pulp as a substrate for pulcherrimin production by M. pulcherrima. The results demonstrate the potential of using wheat germ pulp, an oilseed processing residue, as a substrate for natural pigment production and provide a basis for further studies on process sustainability, scale-up, downstream processing, and economic feasibility.

Fermentation doi: 10.3390/fermentation12090419

Authors: Griselda Méndez-Marcial José Alfredo Carrillo-Salazar Alejandra Miranda-Carrazco Martha Hernández-Rodríguez

Pulque is a traditional Mexican beverage produced by the spontaneous fermentation of “aguamiel”, the sap of several Agave species. Fermentation is driven by adding a previously fermented inoculum, locally known as “semilla”, whose microbial community contributes to the sensory and physicochemical properties of the beverage. The objective of this study was to provide a preliminary characterization of the microbial taxonomic composition and functional potential of pulque inoculant prepared from Agave mapisaga and Agave salmiana using shotgun metagenomic sequencing. Six inoculum samples were sequenced on the DNBSEQ using 150 bp paired-end reads. Metagenomic DNA was extracted using a CTAB-based protocol and analyzed in the Galaxy platform. The workflow included quality filtering, host-sequence removal, taxonomic classification with Kraken2, assembly with MEGAHIT, and functional annotation with eggNOG Mapper. Bacterial communities in inoculum from A. mapisaga and A. salmiana sap were dominated by Acetobacter (68.1% and 58.3%) and Leuconostoc (19.5% and 21.9%). Komagataeibacter was more abundant in A. mapisaga inoculum (3.8%), whereas Zymomonas was more abundant in A. salmiana inoculum (11.7%). The greatest species-level difference was observed for Zymomonas mobilis, whose mean relative abundance was 6.4-fold higher in A. salmiana. Fungal communities were dominated by Saccharomyces (91.4% and 72.7%) and Kluyveromyces (6.6% and 25.5%) in A. mapisaga and A. salmiana, respectively. Across all replicates, the most abundant species were Acetobacter sp. AC2005 (23.9%), Saccharomyces paradoxus (17.0%), and Zymomonas mobilis (12.9%), together accounting for approximately 54% of the total relative abundance. Kluyveromyces marxianus was 3.9-fold more abundant in A. salmiana inoculum, whereas Saccharomyces paradoxus was 1.26-fold more abundant in A. mapisaga inoculum. Alpha-diversity analysis indicated higher bacterial diversity in A. mapisaga inoculum, with a Shannon index of 2.74 and 35 exclusive species, whereas A. salmiana inoculum showed greater fungal diversity, with a Shannon index of 0.68. These differences were not statistically significant (p > 0.05). However, beta-diversity analysis suggested substantial separation between the microbial communities associated with the two Agave species (R2 ≈ 0.92). Functional annotation identified genes potentially associated with carbohydrate metabolism, sucrose degradation, and secondary metabolite biosynthesis. These findings suggest that the agave species used as the sap source may influence the taxonomic composition and functional potential of microbial communities involved in pulque fermentation.