Microbiology Research

23 pages, 5810 KiB

Open AccessArticle

Oral Intake of Klebsiella oxytoca Disrupts Murine Intestinal Bacteriota and Anti-K. oxytoca Compound Baicalin by In Silico and In Vitro Analysis

by Yuming Ma, Xinchi Qin, Yongjie Wang, Lu Xie and Lanming Chen

Microbiol. Res. 2025, 16(8), 189; https://doi.org/10.3390/microbiolres16080189 - 14 Aug 2025

Abstract

Klebsiella oxytoca originating from shellfish Scapharca subcrenata contains a number of virulence-related genes. In this study, we investigated its pathogenicity using a murine intestinal infection model and predicted its antibacterial compounds and targets via molecular docking analysis. The results revealed that the intake [...] Read more.

Klebsiella oxytoca originating from shellfish Scapharca subcrenata contains a number of virulence-related genes. In this study, we investigated its pathogenicity using a murine intestinal infection model and predicted its antibacterial compounds and targets via molecular docking analysis. The results revealed that the intake of K. oxytoca 8-2-11 strain (10⁹ CFU/day) via oral gavage for 7 days reduced the average body weight of the mice. The bacterium was present in fecal samples but absent from blood, lung, and liver samples from the mice. The intake of K. oxytoca 8-2-11 significantly altered colon bacteriota, with reduced abundance of Firmicutes, Lachnospiraceae, Lactobacillaceae, Lactobacillus, and Lactobacillus murinus, and increased in Bacteroidota, Muribaculaceae, and Alistipes (p < 0.05). Forty-four bioactive compounds in Scutellaria baicalensis and Forsythia suspensa were screened for docking with 117 potential virulence factors (VFs) in K. oxytoca 8-2-11. The compound baicalin displayed higher binding affinity toward these VFs, with the lowest mean binding energy (−8.4 kcal/mol). Baicalin was able to bind to key VFs in biofilm formation and adherence/motility (e.g., Mrks and EcpA) via forming stable hydrogen bonds, π-stacking, and π-cation interaction. In vitro, baicalin inhibited the bacterial growth and biofilm formation. This study establishes the first murine infection model using aquatic animal-derived K. oxytoca, and it provides candidate antibacterial compounds and targets for control of K. oxytoca infections. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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16 pages, 2407 KiB

Open AccessArticle

Mechanisms of Cultivation Chronosequence on Distribution Characteristics of Arbuscular Mycorrhizal Fungi in Tea Plantations, South Henan, China

by Xiangchao Cui, Dongmeng Xu, Shuping Huang, Wei Wei, Ge Ma, Mengdi Li and Junhui Yan

Microbiol. Res. 2025, 16(8), 188; https://doi.org/10.3390/microbiolres16080188 - 12 Aug 2025

Abstract

The vital role of arbuscular mycorrhizal (AM) fungi in tea plant growth is well established; however, the mechanisms underlying how increasing cultivation chronosequence (CC) influences AM fungal distribution remain unclear. An investigation was conducted to investigate the temporal dynamics of AM fungal indices [...] Read more.

The vital role of arbuscular mycorrhizal (AM) fungi in tea plant growth is well established; however, the mechanisms underlying how increasing cultivation chronosequence (CC) influences AM fungal distribution remain unclear. An investigation was conducted to investigate the temporal dynamics of AM fungal indices and soil properties across a 100-year tea CC (10-, 30-, 60-, and 100-year CC) in Xinyang Maojian tea (Camellia sinensis L.) plantations (Xinyang, Henan Province, China). Principal coordinate analysis was conducted to reveal the significant reorganization of AM fungal indices during early-to-mid stages (PCoA1: 89.2%, p < 0.05), with triphasic development. Mycorrhizal colonization (MC), hypha biomass (hypha), and spore density (SD) surged by 100% during 10–30 years; SD peaked at 60 years (164 spores g⁻¹) before declining, while glomalin-related soil protein (GRSP) accumulated significantly only at 100 years (p < 0.05). Concurrently, soil acidification (pH decreased from 6.37 to 4.84) and phosphorus depletion (AP from 119.6 mg kg⁻¹ to 32 mg kg⁻¹) intensified by 60 years, contrasting with the significant accumulations of soil organic organisms (SOM) (from 10.6 g kg⁻¹ to 36.4 g kg⁻¹), electrical conductivity (EC) (from 0.019 to 0.050 mS·cm⁻¹), and microaggregate accumulation (MAR) (from 25.8% to 40.3%) during the period. The linear regression model was performed to validate the significant effects (p < 0.05) of CC on the AM indices (MC, SD, hypha, and GRSP) and soil physiochemical characteristics (EC, moisture, and SOM). Variance partitioning attributed 97.4% of the total variation, while interactions among cultivation ages, nutrient characteristics (SOM and AP), and non-nutrient characteristics (pH, EC, moisture, and aggregates) accounted for 23.0%. To identify the driving factors of AM fungi indices, Pearson correlation and redundancy analysis (RDA) were performed, and EC (26.5%) and pH (20.9%) were identified as the paramount regulators of hyphal integrity and colonization efficiency. It was found that 60 years worked as a critical transition point for targeted interventions (e.g., organic amendments and pH buffering) to mitigate rhizosphere dysfunction and optimize mycorrhizal services in perennial monocultures. Full article

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19 pages, 6210 KiB

Open AccessArticle

Novel Reoviruses of Waterfowl Origin in Northern Vietnam: A Laboratory Investigation

by Thi-Ngoc Vu, Van-Truong Le, Thi-Bich-Phuong Cao, Van-Giap Nguyen and Thi-My-Le Huynh

Microbiol. Res. 2025, 16(8), 187; https://doi.org/10.3390/microbiolres16080187 - 12 Aug 2025

Abstract

Novel waterfowl reoviruses (nWRVs) have been reported in several countries, but their circulation and genetic characteristics in Vietnam remain poorly understood. In this study, we investigated nWRVs in northern Vietnam through molecular detection, virus isolation, experimental infection in ducklings, and molecular analysis of [...] Read more.

Novel waterfowl reoviruses (nWRVs) have been reported in several countries, but their circulation and genetic characteristics in Vietnam remain poorly understood. In this study, we investigated nWRVs in northern Vietnam through molecular detection, virus isolation, experimental infection in ducklings, and molecular analysis of the sigma C-encoding (sC) gene. We also applied immunoinformatic tools to explore the antigenic and structural features of the sC protein. nWRVs were detected in 15.6% of tested samples across ten provinces. Three isolates were successfully recovered, all showing a characteristic cytopathic effect—syncytium formation—in Vero cells. When tested in ducklings (n = 72), the isolates caused disease of varying severity, but all induced characteristic gross and microscopic lesions, particularly ecchymotic hemorrhages and large necrotic foci in the liver and spleen. Phylogenetic analysis based on sC sequences placed the Vietnamese isolates (n = 14) within the nWRV clade, with evidence of two genetically distinct groups. Our immunoinformatic analysis identified four predicted B-cell epitopes located in the head and body domains of the sC protein, with little variation. Full article

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15 pages, 1392 KiB

Open AccessArticle

Evaluation of Antibiotic Resistance in Escherichia coli Isolated from a Watershed Section of Ameca River in Mexico

by Mariana Díaz-Zaragoza, Sergio Yair Rodriguez-Preciado, Lizeth Hernández-Ventura, Alejandro Ortiz-Covarrubias, Gustavo Castellanos-García, Sonia Sifuentes-Franco, Ana Laura Pereira-Suárez, José Francisco Muñoz-Valle, Margarita Montoya-Buelna and Jose Macias-Barragan

Microbiol. Res. 2025, 16(8), 186; https://doi.org/10.3390/microbiolres16080186 - 12 Aug 2025

Abstract

Antibiotic resistance (AR) in environmental Escherichia coli represents a growing public health challenge. This study evaluated the prevalence of AR among E. coli isolates recovered from surface water bodies within the Ameca River basin in Jalisco, Mexico, and examined associations with anthropogenic influence [...] Read more.

Antibiotic resistance (AR) in environmental Escherichia coli represents a growing public health challenge. This study evaluated the prevalence of AR among E. coli isolates recovered from surface water bodies within the Ameca River basin in Jalisco, Mexico, and examined associations with anthropogenic influence and seasonal variation. Over a 1-year period, water samples were collected monthly from 16 sites, including tributaries, wetlands, and main river channels with differing degrees of urban impact. E. coli isolates were confirmed by malB gene PCR and tested for susceptibility to six antibiotics using the Kirby–Bauer disk diffusion method. High resistance frequencies were observed for ampicillin (93.9%), tetracycline (92.4%), and streptomycin (89.6%), while gentamicin exhibited the lowest resistance rate (48.1%). Resistance prevalence was significantly higher at sites adjacent to urban settlements and during the rainy season (p < 0.05). These findings underscore the influence of land use and seasonal dynamics on AR dissemination in aquatic environments and highlight the need for improved wastewater management strategies to mitigate the spread of resistant bacteria. Full article

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13 pages, 1098 KiB

Open AccessArticle

Risk Factors and Seroprevalence of Infection by Corynebacterium pseudotuberculosis in Goats from Espírito Santo State, Southeastern Brazil

by Letícia Pereira Pedrini Vicentini, Thiago Doria Barral, Marcus Alexandre Vaillant Beltrame, Luiz Filippe Simão Soares, Ricardo Wagner Portela and Blima Fux

Microbiol. Res. 2025, 16(8), 185; https://doi.org/10.3390/microbiolres16080185 - 8 Aug 2025

Abstract

Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis, a significant infectious disease that affects small ruminants and poses economic challenges to livestock production. This study aimed to assess the seroprevalence of C. pseudotuberculosis in goats from Espírito Santo state, Brazil, and identify [...] Read more.

Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis, a significant infectious disease that affects small ruminants and poses economic challenges to livestock production. This study aimed to assess the seroprevalence of C. pseudotuberculosis in goats from Espírito Santo state, Brazil, and identify risk factors associated with infection by the bacterium. Serum samples from 145 goats were analyzed using an indirect enzyme-linked immunosorbent assay (ELISA). The overall seroprevalence was found to be 34.5%. The risk factors significantly associated with infection included the presence of abscesses and the absence of veterinary assistance on farms. The findings emphasize the need for improved management practices and veterinary oversight to mitigate caseous lymphadenitis transmission. This research provides critical insights into the epidemiology of caseous lymphadenitis in goats from Espírito Santo, informing effective disease control strategies. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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18 pages, 7277 KiB

Open AccessArticle

Comprehensive Analysis of the Molecular Epidemiological Characteristics of Duck-Derived Salmonella in Certain Regions of China

by Jiawen Chen, Xiangdi Li, Yanling Liu, Wenjia Rong, Laiyu Fu, Shuhua Wang, Yan Li, Xiaoxiao Duan, Yongda Zhao and Lili Guo

Microbiol. Res. 2025, 16(8), 184; https://doi.org/10.3390/microbiolres16080184 - 7 Aug 2025

Abstract

Salmonella is a major foodborne pathogen, yet real-time data on duck-derived strains in China remain scarce. This study investigated the epidemiology, antimicrobial resistance (AMR), gene profiles, and PFGE patterns of 114 Salmonella isolates recovered from 397 deceased ducks (2021–2024) across nine provinces (isolation [...] Read more.

Salmonella is a major foodborne pathogen, yet real-time data on duck-derived strains in China remain scarce. This study investigated the epidemiology, antimicrobial resistance (AMR), gene profiles, and PFGE patterns of 114 Salmonella isolates recovered from 397 deceased ducks (2021–2024) across nine provinces (isolation rate: 28.72%). Fourteen serotypes were identified, with S. Typhimurium (23.68%), S. Indiana (21.93%), S. Kentucky (18.42%), and S. Enteritidis (12.28%) being predominant. Most isolates showed high resistance to β-lactams, tetracyclines, quinolones, and sulfonamides, with extensive multidrug resistance (MDR) observed—especially in S. Indiana, S. Typhimurium, and S. Kentucky. Among the 23 detected resistance genes, tet(B) had the highest prevalence (75.44%), particularly in S. Indiana. Biofilm formation was observed in 99.12% of isolates, with 84.21% demonstrating moderate to strong capacity. Eighteen virulence genes were detected; S. Enteritidis carried more spvB/C, sipB, and sodC1, while S. Indiana had higher cdtB carriage. PFGE revealed substantial genetic diversity among strains. This comprehensive analysis highlights the high AMR and biofilm potential of duck-derived Salmonella in China, emphasizing the urgent need for enhanced surveillance and control measures to mitigate public health risks. Full article

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24 pages, 957 KiB

Open AccessReview

Biofilm and Antimicrobial Resistance: Mechanisms, Implications, and Emerging Solutions

by Bharmjeet Singh, Manju Dahiya, Vikram Kumar, Archana Ayyagari, Deepti N. Chaudhari and Jayesh J. Ahire

Microbiol. Res. 2025, 16(8), 183; https://doi.org/10.3390/microbiolres16080183 - 6 Aug 2025

Abstract

Biofilms are a spontaneously formed slimy matrix of extracellular polymeric substances (EPS) enveloping miniature bacterial colonies, which aid in pathogen colonization, shielding the bacteria from antibiotics, as well as imparting them resistance towards the same. Biofilms employ a robust communication mechanism called quorum [...] Read more.

Biofilms are a spontaneously formed slimy matrix of extracellular polymeric substances (EPS) enveloping miniature bacterial colonies, which aid in pathogen colonization, shielding the bacteria from antibiotics, as well as imparting them resistance towards the same. Biofilms employ a robust communication mechanism called quorum sensing that serves to keep their population density constant. What is most significant about biofilms is that they contribute to the development of bacterial virulence by providing protection to pathogenic species, allowing them to colonize the host, and also inhibiting the activities of antimicrobials on them. They grow on animate surfaces (such as on teeth and intestinal mucosa, etc.) and inanimate objects (like catheters, contact lenses, pacemakers, endotracheal devices, intrauterine devices, and stents, etc.) alike. It has been reported that as much as 80% of human infections involve biofilms. Serious implications of biofilms include the necessity of greater concentrations of antibiotics to treat common human infections, even contributing to antimicrobial resistance (AMR), since bacteria embedded within biofilms are protected from the action of potential antibiotics. This review explores various contemporary strategies for controlling biofilms, focusing on their modes of action, mechanisms of drug resistance, and innovative approaches to find a solution in this regard. This review interestingly targets the extracellular polymeric matrix as a highly effective strategy to counteract the potential harm of biofilms since it plays a critical role in biofilm formation and significantly contributes to antimicrobial resistance. Full article

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20 pages, 3465 KiB

Open AccessArticle

Inhibitory Effects of Selected Chemical Substances on the Growth of Filamentous Fungi Occurring in Cellar Management

by Karolina Kostelnikova, Romana Heralecka, Anna Krpatova, Filip Matousek, Jiri Sochor and Mojmir Baron

Microbiol. Res. 2025, 16(8), 182; https://doi.org/10.3390/microbiolres16080182 - 4 Aug 2025

Abstract

This study evaluated the inhibitory efficacy of sulphur dioxide, hydrogen peroxide, copper sulphate pentahydrate, chlorine-based formulations, a chlorine-free formulation, ethanol, and acetic acid against Cladosporium cladosporioides, Aspergillus niger, and Penicillium expansum. An in vitro inhibition test was employed to investigate [...] Read more.

This study evaluated the inhibitory efficacy of sulphur dioxide, hydrogen peroxide, copper sulphate pentahydrate, chlorine-based formulations, a chlorine-free formulation, ethanol, and acetic acid against Cladosporium cladosporioides, Aspergillus niger, and Penicillium expansum. An in vitro inhibition test was employed to investigate the inhibitory properties. The results demonstrated different sensitivities of filamentous fungi to the inhibitors. All tested substances displayed fungicidal properties. Sulphur dioxide (40% NH₄HSO₃ solution) inhibited growth at a 4% v/v concentration. No minimum effective concentration was established for H₂O₂; only a 30% w/v solution inhibited P. expansum. CuSO₄·5H₂O completely inhibited fungal growth at 5% w/v solution, with 2.5% w/v also proving effective. For the chlorine-based product, 40% w/v solution (48 g∙L⁻¹ active chlorine) had the most substantial effect, though it only slowed growth, and NaClO solution completely inhibited growth at 2.35 g NaClO per 100 g of product (50% w/v solution). FungiSAN demonstrated fungicidal effects; however, the recommended dose was insufficient for complete inhibition. Ethanol exhibited the lowest efficacy, while the inhibitory threshold for CH₃COOH was found to be a 5% v/v solution. The findings of this study may serve as a basis for informed decision-making when selecting the most suitable product, depending on specific application conditions. Full article

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11 pages, 593 KiB

Open AccessArticle

Burden of Streptococcus pyogenes and emm12 Type in Severe Otitis Media Among Children

by Alexandra S. Alexandrova, Adile A. Muhtarova, Vasil S. Boyanov and Raina T. Gergova

Microbiol. Res. 2025, 16(8), 181; https://doi.org/10.3390/microbiolres16080181 - 3 Aug 2025

Abstract

Streptococcus pyogenes (GAS) is a leading cause of acute otitis media (AOM) and its complications. This study aimed to evaluate the antimicrobial resistance of all isolated bacterial agents recovered from children with AOM and to perform the emm typing of GAS isolates. Antibiotic [...] Read more.

Streptococcus pyogenes (GAS) is a leading cause of acute otitis media (AOM) and its complications. This study aimed to evaluate the antimicrobial resistance of all isolated bacterial agents recovered from children with AOM and to perform the emm typing of GAS isolates. Antibiotic susceptibility testing was evaluated according to EUCAST criteria. Phenotyping and genotyping were performed for the macrolide-resistant GAS isolates. All GAS isolates were subjected to emm typing. Among the 103 AOM cases considered, we identified GAS isolates (39.4%), Staphylococcus aureus (26.6%), Haemophilus influenzae (13.8%), Streptococcus pneumoniae (11.7%), Moraxella catarrhalis (7.4%), and Serratia marcescens (1.1%). GAS exhibited 32.4% macrolide resistance and 10.8% clindamycin resistance. The M phenotype and mefE gene (18.9%) were the most common, followed by cMLSB (10.8% with ermB), a combination of mefA and ermB (8.1%), and iMLSB (2.7% with ermA). The most prevalent emm types were emm12 (27.0%), emm1 (21.6%), and emm3 (16.2%). The most common GAS emm types identified among AOM patients in this study are found worldwide and are associated with invasive infections in various countries. This may influence the virulence and invasive potential of these strains. Full article

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16 pages, 1226 KiB

Open AccessArticle

Occurrence and Transfer by Conjugation of Linezolid-Resistance Among Non-Enterococcus faecalis and Enterococcus faecium in Intensive Pig Farms

by Giorgia Piccioni, Andrea Di Cesare, Raffaella Sabatino, Gianluca Corno, Gianmarco Mangiaterra, Daniela Marchis and Barbara Citterio

Microbiol. Res. 2025, 16(8), 180; https://doi.org/10.3390/microbiolres16080180 - 2 Aug 2025

Abstract

Enterococcus spp. are opportunistic and nosocomial pathogens. Intensive pig farms have been recently described as important hotspots for antibiotic resistance and reservoirs of potentially pathogenic enterococci, including other species than the most known E. faecalis and E. faecium. Here, we identified Linezolid-resistant [...] Read more.

Enterococcus spp. are opportunistic and nosocomial pathogens. Intensive pig farms have been recently described as important hotspots for antibiotic resistance and reservoirs of potentially pathogenic enterococci, including other species than the most known E. faecalis and E. faecium. Here, we identified Linezolid-resistant non-E. faecalis and E. faecium (NFF) Enterococcus strains isolated from different production stages (suckling piglets, weaning pigs, and fatteners) across six intensive pig farms. The transferability of the linezolid-resistance determinants was assessed by bacterial conjugation and strains were also characterized for biofilm production, hemolytic and gelatinase activity. Among 64 identified NFF Enterococcus strains, 27 were resistant to at least three different antibiotic classes and 8/27 specifically to Linezolid. E. gallinarum and E. casseliflavus both transferred their Linezolid resistance determinants to the main pathogenic species E. faecium. Remarkably, this is the first report of the optrA gene transfer from E. casseliflavus to E. faecium by conjugation, which can greatly contribute to the spread of antibiotic resistance genes among pathogenic enterococcal species. The “weaning pigs” stage exhibited a significantly higher number of antibiotic-resistant enterococci than the “fatteners”. These findings highlight the importance of monitoring pig farms as hotspots for the spread of antibiotic-resistant enterococci, especially in the early stages of production. Furthermore, they underscore the significant role of NFF Enterococcus species as carriers of antibiotic resistance genes, even to last-resort antibiotics, which may be transferable to the major enterococcal species. Full article

(This article belongs to the Special Issue Zoonotic Bacteria: Infection, Pathogenesis and Drugs—Second Edition)

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20 pages, 1876 KiB

Open AccessArticle

Evaluation of Clean-Label Additives to Inhibit Molds and Extend the Shelf Life of Preservative-Free Bread

by Ricardo H. Hernández-Figueroa, Aurelio López-Malo, Beatriz Mejía-Garibay, Nelly Ramírez-Corona and Emma Mani-López

Microbiol. Res. 2025, 16(8), 179; https://doi.org/10.3390/microbiolres16080179 - 1 Aug 2025

Abstract

This study evaluates the efficacy of commercial clean-label additives, specifically fermentates, in inhibiting mold growth in vitro and extending the shelf life of preservative-free bread. The mold growth on selected bread was modeled using the time-to-growth approach. The pH, a_w, and [...] Read more.

This study evaluates the efficacy of commercial clean-label additives, specifically fermentates, in inhibiting mold growth in vitro and extending the shelf life of preservative-free bread. The mold growth on selected bread was modeled using the time-to-growth approach. The pH, a_w, and moisture content of fresh bread were determined. In addition, selected fermentates were characterized physicochemically. Fermentates, defined as liquid or powdered preparations containing microorganisms, their metabolites, and culture supernatants, were tested at varying concentrations (1% to 12%) to assess their antimicrobial performance and impact on bread quality parameters, including moisture content, water activity, and pH. The results showed significant differences in fermentate efficacy, with Product A as the best mold growth inhibitor in vitro and a clear dose-dependent response. For Penicillium corylophilum, inhibition increased from 51.90% at 1% to 62.60% at 4%, while P. chrysogenum had an inhibition ranging from 32.26% to 34.49%. Product F exhibited moderate activity on both molds at 4%, inhibiting between 28.48% and 46.27%. The two molds exhibited differing sensitivities to the fermentates, with P. corylophilum consistently more susceptible to inhibition. Product A displayed a low pH (2.61) and high levels of lactic acid (1053.6 mmol/L) and acetic acid (1061.3 mmol/L). Product F presented a similar pH but lower levels of lactic and acetic acid. A time-to-growth model, validated by significant coefficients (p < 0.05) and high predictive accuracy (R² > 0.95), was employed to predict the appearance of mold on bread loaves. The model revealed that higher concentrations of fermentates A and F delayed mold growth, with fermentate A demonstrating superior efficacy. At 2% concentration, fermentate A delayed mold growth for 8 days, compared to 6 days for fermentate F. At 8% concentration, fermentate A prevented mold growth for over 25 days, significantly outperforming the control (4 days). Additionally, fermentates influenced bread quality parameters, with fermentate A improving crust moisture retention and reducing water activity at higher concentrations. These findings highlight the potential of fermentates as sustainable, consumer-friendly alternatives to synthetic preservatives, offering a viable solution to the challenge of bread spoilage while maintaining product quality. Full article

(This article belongs to the Collection Microbiology and Technology of Fermented Foods)

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18 pages, 2714 KiB

Open AccessArticle

Assessing the Efficacy of Chemical and Green-Synthesized CuO Nanoparticles in Combatting Clinical Candida Species: A Comparative Study

by Hiba Younis Khalaf, Ferid Ben Nasr, Bashar Sadeq Noomi, Sami Mnif and Sami Aifa

Microbiol. Res. 2025, 16(8), 178; https://doi.org/10.3390/microbiolres16080178 - 1 Aug 2025

Abstract

The most prevalent growth of Candida cells is based on biofilm development, which causes the intensification of antifungal resistance against a large range of chemicals. Nanoparticles can be synthesized using green methods via various biological extracts and reducing agents to control Candida biofilms. [...] Read more.

The most prevalent growth of Candida cells is based on biofilm development, which causes the intensification of antifungal resistance against a large range of chemicals. Nanoparticles can be synthesized using green methods via various biological extracts and reducing agents to control Candida biofilms. This study aims to compare copper oxide nanoparticles (CuONPs) synthesized through chemical methods and those synthesized using Cinnamomum verum-based green methods against Candida infections and their biofilms isolated from Iraqi patients, with the potential to improve treatment outcomes. The physical and chemical properties of these nanoparticles were characterized using Fourier-transform infrared spectroscopy (FT-IR,) scanning electron microscopy (SEM), transmission electron microscopy (TEM), atomic force microscopy (AFM) and X-ray diffraction (XRD). Four strains of Candida were isolated and characterized from Iraqi patients in Tikrit Hospital and selected based on their ability to form biofilm on polystyrene microplates. The activity of green-synthesized CuONPs using cinnamon extract was compared with both undoped and doped (Fe, Sn) chemically synthesized CuONPs. Four pathogenic Candida strains (Candida glabrata, Candida lusitaniae, Candida albicans, and Candida tropicalis) were isolated from Iraqi patients, demonstrating high biofilm formation capabilities. Chemically and green-synthesized CuONPs from Cinnamomum verum showed comparable significant antiplanktonic and antibiofilm activities against all strains. Doped CuONPs with iron or tin demonstrated lower minimum inhibitory concentration (MIC) values, indicating stronger antibacterial activity, but exhibited weaker anti-adhesive properties compared to other nanoparticles. The antiadhesive activity revealed that C. albicans strain seems to produce the most resistant biofilms while C. glabrata strain seems to be more resistant towards the doped CuONPs. Moreover, C. tropicalis was the most sensitive to all the CuONPs. Remarkably, at a concentration of 100 µg/mL, all CuONPs were effective in eradicating preformed biofilms by 47–66%. The findings suggest that CuONPs could be effective in controlling biofilm formation by Candida species resistant to treatment in healthcare settings. Full article

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22 pages, 7580 KiB

Open AccessArticle

Bacterial and Physicochemical Dynamics During the Vermicomposting of Bovine Manure: A Comparative Analysis of the Eisenia fetida Gut and Compost Matrix

by Tania Elizabeth Velásquez-Chávez, Jorge Sáenz-Mata, Jesús Josafath Quezada-Rivera, Rubén Palacio-Rodríguez, Gisela Muro-Pérez, Alan Joel Servín-Prieto, Mónica Hernández-López, Pablo Preciado-Rangel, María Teresa Salazar-Ramírez, Juan Carlos Ontiveros-Chacón and Cristina García-De la Peña

Microbiol. Res. 2025, 16(8), 177; https://doi.org/10.3390/microbiolres16080177 - 1 Aug 2025

Abstract

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition [...] Read more.

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article

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13 pages, 1123 KiB

Open AccessArticle

Protective Effects of Grape Seed Extract on Lipopolysaccharide Exposure and Radiation-Induced Intestinal Mucosal Damage: Insights from an In Vitro Study

by Annamaria Altomare, Michele Fiore, Elena Imperia, Gabriele D’Ercole, Ludovica Spagnuolo, Laura De Gara, Gabriella Pasqua, Michele Cicala, Sara Ramella and Michele Pier Luca Guarino

Microbiol. Res. 2025, 16(8), 176; https://doi.org/10.3390/microbiolres16080176 - 1 Aug 2025

Abstract

Backgrounds and aim: Protective effects of natural compounds have been suggested in the prevention and treatment of radiation-induced mucositis or bacterial infections. In this study, the protective effects of proanthocyanidin-rich grape seed extract (GSE) on bacterial Lipopolysaccharide (LPS) and radiation-induced epithelial barrier damage [...] Read more.

Backgrounds and aim: Protective effects of natural compounds have been suggested in the prevention and treatment of radiation-induced mucositis or bacterial infections. In this study, the protective effects of proanthocyanidin-rich grape seed extract (GSE) on bacterial Lipopolysaccharide (LPS) and radiation-induced epithelial barrier damage and Reactive Oxygen Species (ROS) production were investigated in an in vitro model. Methods: Human intestinal epithelial cells Caco-2, previously treated with LPS, GSE, or LPS + GSE, were irradiated with 10 Gy divided into five daily treatments. Epithelial barrier integrity and ROS production were measured before and after each treatment. Results: Irradiation, at different doses, significantly increased intestinal permeability and ROS production; pretreatment with GSE was able to significantly prevent the increased intestinal permeability (4.63 ± 0.76 vs. 15.04 ± 1.5; p < 0.05) and ROS production (12.9 ± 1.08 vs. 1048 ± 0.5; p < 0.0001) induced by irradiation treatment. When the cells were pretreated with LPS, the same results were observed: GSE cotreatment was responsible for preventing permeability alterations (5.36 ± 0.16 vs. 49.26 ± 0.82; p < 0.05) and ROS production (349 ± 1 vs. 7897.67 ± 1.53; p < 0.0001) induced by LPS exposure when added to the irradiation treatment. Conclusions: The results of the present investigation demonstrated, in an in vitro model, that GSE prevents the damage to intestinal permeability and the production of ROS that are induced by LPS and ionizing radiation, suggesting a potential protective effect of this extract on the intestinal mucosa during irradiation treatment. Full article

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32 pages, 4311 KiB

Open AccessArticle

Proteomics-Based Prediction of Candidate Effectors in the Interaction Secretome of Trichoderma harzianum and Pseudocercospora fijiensis

by Jewel Nicole Anna Todd, Karla Gisel Carreón-Anguiano, Gabriel Iturriaga, Roberto Vázquez-Euán, Ignacio Islas-Flores, Miguel Tzec-Simá, Miguel Ángel Canseco-Pérez, César De Los Santos-Briones and Blondy Canto-Canché

Microbiol. Res. 2025, 16(8), 175; https://doi.org/10.3390/microbiolres16080175 - 1 Aug 2025

Abstract

Microbe–microbe interactions have been explored at the molecular level to a lesser degree than plant–pathogen interactions, primarily due to the economic impact of crop losses caused by pathogenic microorganisms. Effector proteins are well known for their role in disease development in many plant–pathogen [...] Read more.

Microbe–microbe interactions have been explored at the molecular level to a lesser degree than plant–pathogen interactions, primarily due to the economic impact of crop losses caused by pathogenic microorganisms. Effector proteins are well known for their role in disease development in many plant–pathogen pleinteractions, but there is increasing evidence showing their involvement in other types of interaction, including microbe–microbe interactions. Through the use of LC-MS/MS sequencing, effector candidates were identified in the in vitro interaction between a banana pathogen, Pseudocercospora fijiensis and a biological control agent, Trichoderma harzianum. The diverse interaction secretome revealed various glycoside hydrolase families, proteases and oxidoreductases. T. harzianum secreted more proteins in the microbial interaction compared to P. fijiensis, but its presence induced the secretion of more P. fijiensis proteins that were exclusive to the interaction secretome. The interaction secretome, containing 256 proteins, was screened for effector candidates using the algorithms EffHunter and WideEffHunter. Candidates with common fungal effector motifs and domains such as LysM, Cerato-platanin, NPP1 and CFEM, among others, were identified. Homologs of true effectors and virulence factors were found in the interaction secretome of T. harzianum and P. fijiensis. Further characterization revealed a potential novel effector of T. harzianum. Full article

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13 pages, 1801 KiB

Open AccessReview

Lactobacillus acidophilus in Aquaculture: A Review

by Lu Zhang, Jian Zhou, Zhipeng Huang, Han Zhao, Zhongmeng Zhao, Chengyan Mou, Yang Feng, Huadong Li, Qiang Li and Yuanliang Duan

Microbiol. Res. 2025, 16(8), 174; https://doi.org/10.3390/microbiolres16080174 - 1 Aug 2025

Abstract

Microbial feed additives can effectively promote the healthy development of aquaculture, and Lactobacillus acidophilus can be utilized to mitigate disease risks and enhance productivity while minimizing antibiotic use. This article summarizes research on the application of L. acidophilus in aquaculture, focusing on growth [...] Read more.

Microbial feed additives can effectively promote the healthy development of aquaculture, and Lactobacillus acidophilus can be utilized to mitigate disease risks and enhance productivity while minimizing antibiotic use. This article summarizes research on the application of L. acidophilus in aquaculture, focusing on growth and nutrient utilization, intestinal structure and microbial communities, disease prevention and control in aquatic organisms, and the regulation of water quality. This review holds significant implications for the development of compound feed additives and environmental regulators involving L. acidophilus, as well as for future aquatic food safety. Full article

(This article belongs to the Topic The Role of Microorganisms in Waste Treatment)

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15 pages, 1894 KiB

Open AccessArticle

Microbial Communities’ Composition of Supralittoral and Intertidal Sediments in Two East African Beaches (Djibouti Republic)

by Sonia Renzi, Alessandro Russo, Aldo D’Alessandro, Samuele Ciattini, Saida Chideh Soliman, Annamaria Nistri, Carlo Pretti, Duccio Cavalieri and Alberto Ugolini

Microbiol. Res. 2025, 16(8), 173; https://doi.org/10.3390/microbiolres16080173 - 1 Aug 2025

Abstract

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial [...] Read more.

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial communities inhabiting supralittoral–intertidal sediments of two contrasting sandy beaches in the Tadjoura Gulf (Djibouti Republic): Sagallou-Kalaf (SK, rural, siliceous sand) and Siesta Plage (SP, urban, calcareous sand). Sand samples were collected at low tide along 10 m transects perpendicular to the shoreline. Bacterial communities differed significantly between sites and along the sea-to-land gradient, suggesting an influence from both anthropogenic activity and sediment granulometry. SK was dominated by Escherichia-Shigella, Staphylococcus, and Bifidobacterium, associated with human and agricultural sources. SP showed higher richness, with enriched marine-associated genera such as Hoeflea, Xanthomarina, and Marinobacter, also linked to hydrocarbon degradation. Fungal diversity was less variable, but showed significant shifts along transects. SK communities were dominated by Kluyveromyces and Candida, while SP hosted a broader fungal assemblage, including Pichia, Rhodotorula, and Aureobasidium. The higher richness at SP suggests that calcium-rich sands, possibly due to their buffering capacity and greater moisture retention, offer more favorable conditions for microbial colonization. Full article

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12 pages, 1161 KiB

Open AccessArticle

Power Ultrasound and Organic Acid-Based Hurdle Technology to Reduce Listeria monocytogenes and Salmonella enterica on Fresh Produce

by Megan L. Fay, Priya Biswas, Xinyi Zhou, Bashayer A. Khouja, Diana S. Stewart, Catherine W. Y. Wong, Wei Zhang and Joelle K. Salazar

Microbiol. Res. 2025, 16(8), 172; https://doi.org/10.3390/microbiolres16080172 - 1 Aug 2025

Abstract

The increasing demand for fresh fruits and vegetables has been accompanied by a rise in foodborne illness outbreaks linked to fresh produce. Traditional antimicrobial washing treatments, such as chlorine and peroxyacetic acid, have limitations in efficacy and pose environmental and worker health concerns. [...] Read more.

The increasing demand for fresh fruits and vegetables has been accompanied by a rise in foodborne illness outbreaks linked to fresh produce. Traditional antimicrobial washing treatments, such as chlorine and peroxyacetic acid, have limitations in efficacy and pose environmental and worker health concerns. This study evaluated the effectiveness of organic acids (citric, malic, and lactic acid) and power ultrasound, individually and in combination, for the reduction in Salmonella enterica and Listeria monocytogenes on four fresh produce types: romaine lettuce, cucumber, tomato, and strawberry. Produce samples were inoculated with bacterial cocktails at 8–9 log CFU/unit and treated with organic acids at 2 or 5% for 2 or 5 min, with or without power ultrasound (40 kHz). Results showed that pathogen reductions varied based on the produce matrix with smoother surfaces such as tomato, exhibiting greater reductions than rougher surfaces (e.g., romaine lettuce and strawberry). Lactic and malic acids were the most effective treatments, with 5% lactic acid achieving a reduction of >5 log CFU/unit for S. enterica and 4.53 ± 0.71 log CFU/unit for L. monocytogenes on tomatoes. The combination of organic acids and power ultrasound demonstrated synergistic effects, further enhancing pathogen reduction by <1.87 log CFU/unit. For example, S. enterica on cucumbers was reduced by an additional 1.87 log CFU/unit when treated with 2% malic acid and power ultrasound for 2 min compared to malic acid alone. Similarly, L. monocytogenes on strawberries was further reduced by 1.84 log CFU/unit when treated with 5% malic acid and power ultrasound for 2 min. These findings suggest that organic acids, particularly malic and lactic acids, combined with power ultrasound, may serve as an effective hurdle technology for enhancing the microbial safety of fresh produce. Future research can include validating these treatments in an industrial processing environment. Full article

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8 pages, 890 KiB

Open AccessCommunication

Single-Cell Protein Using an Indigenously Isolated Methanotroph Methylomagnum ishizawai, Using Biogas

by Jyoti A. Mohite, Kajal Pardhi and Monali C. Rahalkar

Microbiol. Res. 2025, 16(8), 171; https://doi.org/10.3390/microbiolres16080171 - 1 Aug 2025

Abstract

The use of methane as a carbon source for producing bacterial single-cell protein (SCP) has been one of the most interesting developments in recent years. Most of these upcoming industries are using a methanotroph, Methylococcus capsulatus Bath, for SCP production using natural gas [...] Read more.

The use of methane as a carbon source for producing bacterial single-cell protein (SCP) has been one of the most interesting developments in recent years. Most of these upcoming industries are using a methanotroph, Methylococcus capsulatus Bath, for SCP production using natural gas as the substrate. In the present study, we have explored the possibility of using an indigenously isolated methanotroph from a rice field in India, Methylomagnum ishizawai strain KRF4, for producing SCP from biogas [derived from cow dung]. The process was eco-friendly, required minimal instruments and chemicals, and was carried out under semi-sterile conditions in a tabletop fish tank. As the name suggests, Methylomagnum is a genus of large methanotrophs, and the strain KRF4 had elliptical to rectangular size and dimensions of ~4–5 µm × 1–2 µm. In static cultures, when biogas and air were supplied in the upper part of the growing tank, the culture grew as a thick pellicle/biofilm that could be easily scooped. The grown culture was mostly pure, from the microscopic observations where the large size of the cells, with rectangular-shaped cells and dark granules, could easily help identify any smaller contaminants. Additionally, the large cell size could be advantageous for separating biomass during downstream processing. The amino acid composition of the lyophilized biomass was analyzed using HPLC, and it was seen that the amino acid composition was comparable to commercial fish meal, soymeal, Pruteen, and the methanotroph-derived SCP-UniProtein^®. The only difference was that a slightly lower percentage of lysine, tryptophan, and methionine was observed in Methylomagnum-derived SCP. Methylomagnum ishizawai could be looked at as an alternative for SCP derived from methane or biogas due to the comparable SCP produced, on the qualitative level. Further intensive research is needed to develop a continuous, sustainable, and economical process to maximize biomass production and downstream processing. Full article

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