Journal Description
Applied Microbiology
Applied Microbiology
is an international, peer-reviewed, open access journal on application of microorganisms published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, EBSCO, and other databases.
- Journal Rank: CiteScore - Q2 (Biochemistry, Genetics and Molecular Biology (miscellaneous))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 13.3 days after submission; acceptance to publication is undertaken in 3.4 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
- Applied Microbiology is a companion journal of Microorganisms.
Latest Articles
Brucella Diagnostics in Endemic Areas: Evaluation of Point-of-Care Kits and the Need for Alternative Diagnostic Tests
Appl. Microbiol. 2025, 5(4), 104; https://doi.org/10.3390/applmicrobiol5040104 - 29 Sep 2025
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Brucellosis is a significant public health challenge in Kenya, particularly in pastoralist communities where the disease is endemic. Reliable and accurate point-of-care diagnostics are essential for timely case identification and effective disease management. The Febrile Brucella Agglutination Test (FBAT) is commonly used for
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Brucellosis is a significant public health challenge in Kenya, particularly in pastoralist communities where the disease is endemic. Reliable and accurate point-of-care diagnostics are essential for timely case identification and effective disease management. The Febrile Brucella Agglutination Test (FBAT) is commonly used for diagnosis of brucellosis in Kenya, but concerns have been noted about its diagnostic accuracy, prompting an independent evaluation. The aim of this study was to compare the diagnostic performance of five FBAT kits with a commercial Enzyme-Linked Immunosorbent Assay (ELISA) as the reference standard, and to build local laboratory capacity for in-house kit validation for the Kajiado County laboratory staff. A total of 200 serum samples (100 ELISA-confirmed positives and 100 negatives) were tested using the FBAT kits. Each kit was evaluated for its ability to detect antibodies to both B. abortus and B. melitensis antigens. Diagnostic performance indicators, including sensitivity, specificity, and Cohen’s Kappa, were calculated, and McNemar’s test was applied to assess concordance with the ELISA results. Overall, none of the FBAT kits proved to have acceptable sensitivity and specificity compared to ELISA. We conclude that FBAT kits are not sufficient for the diagnosis of brucellosis and that alternative diagnostics should be considered.
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Open AccessEditorial
Current Trends in the Applications of Probiotics and Other Beneficial Microbes: Expanding Horizons
by
Sabina Fijan and Tamara Fijan
Appl. Microbiol. 2025, 5(4), 103; https://doi.org/10.3390/applmicrobiol5040103 - 26 Sep 2025
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While pathogenic microbes, such as Yersinia pestis, Mycobacterium tuberculosis, Clostridium tetani, influenza a virus, and many others, have historically been the focus of scientific attention due to their role in causing severe diseases, beneficial microorganisms are being increasingly recognized for
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While pathogenic microbes, such as Yersinia pestis, Mycobacterium tuberculosis, Clostridium tetani, influenza a virus, and many others, have historically been the focus of scientific attention due to their role in causing severe diseases, beneficial microorganisms are being increasingly recognized for their essential contributions to human, animal, and plant health within the One Health framework, as well as their contributions to nutrition and the stability of ecosystems [...]
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(This article belongs to the Special Issue Current Trends in the Applications of Probiotics and Other Beneficial Microbes)
Open AccessArticle
Development and Evaluation of an Exogenous Bioaugmentation Framework Using an Immobilized Mixed Bacterial Consortium for the Remediation of Hydrocarbon-Contaminated Soils
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Emerance Jessica Claire D’Assise Goma-Tchimbakala, Ilaria Pietrini, Alessandro Conte, Neria Costa and Stefano Paolo Corgnati
Appl. Microbiol. 2025, 5(4), 102; https://doi.org/10.3390/applmicrobiol5040102 - 25 Sep 2025
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Improving the quality of oil-contaminated soils remains a critical challenge, and bioaugmentation using allochthonous bacteria offers promising perspectives. This study proposes a framework for exogenous bioaugmentation using a bacterial consortium, composed of strains from diverse climates, immobilized in alginate beads and combined with
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Improving the quality of oil-contaminated soils remains a critical challenge, and bioaugmentation using allochthonous bacteria offers promising perspectives. This study proposes a framework for exogenous bioaugmentation using a bacterial consortium, composed of strains from diverse climates, immobilized in alginate beads and combined with calcium peroxide as an oxygen-releasing compound. Two conditions were tested: freshly prepared beads (BA) and lyophilized beads (LA). Their performance was compared to natural attenuation (NA) and to landfarming coupled with bioaugmentation using a free autochthonous consortium. Hydrocarbon degradation was assessed through total petroleum hydrocarbon (TPH) and alkane depletion (GC-MS), microbial community dynamics (amplicon sequencing), and abundance of the alkB gene (qPCR). In three months, the BA treatment achieved a 44% TPH reduction, outperforming LA (34%) and NA (10% less than BA). However, LA induced a marked increase in alkB gene copies and microbial biomass at the end of the experiment, suggesting greater long-term potential. Dominant genera varied across treatments: Rhodococcus in NA, Gordonia in BA, and Pseudomonas in LA. In parallel, the autochthonous consortium achieved up to 80% oil degradation. This study demonstrates the viability of lyophilized microbial consortia in scalable, ready-to-use formulations and provides an operational methodology for exogenous bioaugmentation as a tool for the remediation of hydrocarbon-contaminated soils.
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Open AccessReview
Streptococcus thermophilus: Metabolic Properties, Functional Features, and Useful Applications
by
Alyaa Zaidan Ghailan and Alaa Kareem Niamah
Appl. Microbiol. 2025, 5(4), 101; https://doi.org/10.3390/applmicrobiol5040101 - 23 Sep 2025
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Streptococcus thermophilus is a Gram-positive, homofermentative lactic acid bacterium classified within the Firmicutes phylum, recognized for its probiotic properties and significant role in promoting human health. This review consolidates existing understanding of its metabolic pathways, functional metabolites, and diverse applications, highlighting evidence-based insights
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Streptococcus thermophilus is a Gram-positive, homofermentative lactic acid bacterium classified within the Firmicutes phylum, recognized for its probiotic properties and significant role in promoting human health. This review consolidates existing understanding of its metabolic pathways, functional metabolites, and diverse applications, highlighting evidence-based insights to enhance scientific integrity. S. thermophilus predominantly ferments lactose through the Embden-Meyerhof-Parnas pathway, resulting in L(+)-lactic acid as the primary end-product, along with secondary metabolites including acetic acid, formic acid, and pyruvate derivatives. Exopolysaccharides (EPS) are composed of repeating units of glucose, galactose, rhamnose, and N-acetylgalactosamine. They display strain-specific molecular weights ranging from 10 to 2000 kDa and contribute to the viscosity of fermented products, while also providing antioxidant and immunomodulatory benefits. Aromatic compounds such as acetaldehyde and phenylacetic acid are products of amino acid catabolism and carbohydrate metabolism, playing a significant role in the sensory characteristics observed in dairy fermentations. Bacteriocins, such as thermophilins (e.g., Thermophilin 13, 110), exhibit extensive antimicrobial efficacy against pathogens including Listeria monocytogenes and Bacillus cereus. Their activity is modulated by quorum-sensing mechanisms that involve the blp gene cluster, and they possess significant stability under heat and pH variations, making them suitable for biopreservation applications. In food applications, S. thermophilus functions as a Generally Recognized as Safe (GRAS) starter culture in the production of yogurt and cheese, working in conjunction with Lactobacillus delbrueckii subsp. bulgaricus to enhance acidification and improve texture. Specific strains have been identified to mitigate lactose intolerance, antibiotic-related diarrhea, and inflammatory bowel diseases through the modulation of gut microbiota, the production of short-chain fatty acids, and the inhibition of Helicobacter pylori. The genome, characterized by a G + C content of approximately 37 mol%, facilitates advancements in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas technology and heterologous protein expression, with applications extending to non-dairy fermentations and the development of postbiotics. This review emphasizes the adaptability of S. thermophilus, showcasing the variability among strains and the necessity for thorough preclinical and clinical validation to fully utilize its potential in health, sustainable agriculture, and innovation. It also addresses challenges such as susceptibility to bacteriophages and limitations in proteolytic activity.
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Open AccessArticle
Characterization of L-Asparaginase Free of L-Glutaminase and Urease Activity Produced by the Marine Paraconiothyrium cyclothyrioides Strain MABIK FU00000820
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Woon-Jong Yu, Ha Young Lee, Yong Min Kwon, Seung Seob Bae, Hyun-Ju Hwang and Dawoon Chung
Appl. Microbiol. 2025, 5(3), 100; https://doi.org/10.3390/applmicrobiol5030100 - 17 Sep 2025
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Asparaginase (ASNase) is an important enzyme used to treat acute lymphoblastic leukemia. However, the clinical use of the currently available ASNases is limited because of their associated side effects. One of the major reasons for these adverse effects is the coactivity of glutaminase
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Asparaginase (ASNase) is an important enzyme used to treat acute lymphoblastic leukemia. However, the clinical use of the currently available ASNases is limited because of their associated side effects. One of the major reasons for these adverse effects is the coactivity of glutaminase (GLNase) with ASNase. Furthermore, the concomitant urease activity may exacerbate the toxicity associated with ASNase treatment. Therefore, identifying novel sources of ASNase with minimal or no glutaminase and urease activities is important. We isolated a marine fungal strain, MABIK FU00000820, which produced ASNase free of GLNase and urease activity. Based on morphological and phylogenetic analyses, this strain was identified as Paraconiothyrium cyclothyrioides. The crude extract of intracellular ASNase exhibited the maximum activity at 37–50 °C, pH 8.5, and 0% (w/v) NaCl. In addition, the enzyme stability assay showed that the P. cyclothyrioides ASNase pre-treated at 4–25 °C for 2 h retained 77% of its activity compared to the untreated control. Based on the available literature, this appears to be the first study to investigate ASNase from P. cyclothyrioides, and it is of particular significance because the enzyme exhibits neither GLNase nor urease activity.
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Open AccessArticle
Dietary Saccharomyces cerevisiae Ameliorates the Adverse Effects of Aflatoxin B1 on Growth Performance, Haematological and Biochemical Parameters in Broiler Chickens
by
Doanh Huy Bui, Vinh Thi Nguyen, Giang Thi Phuong Nguyen, Le Thị Tuyet Nguyen, Yen Thi Dinh, Hai Thai Dang, Tiep Ba Nguyen, Thinh Hoang Nguyen, Majid Shakeri and Hieu Huu Le
Appl. Microbiol. 2025, 5(3), 99; https://doi.org/10.3390/applmicrobiol5030099 - 15 Sep 2025
Abstract
Aflatoxin contamination of animal feeds may impact broiler chicken health and production. The adverse impact of aflatoxin can be ameliorated and detoxified by adding capable binding agents, such as Saccharomyces cerevisiae. A total of 648 mixed gender 1-day-old Ross-308 were assigned to
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Aflatoxin contamination of animal feeds may impact broiler chicken health and production. The adverse impact of aflatoxin can be ameliorated and detoxified by adding capable binding agents, such as Saccharomyces cerevisiae. A total of 648 mixed gender 1-day-old Ross-308 were assigned to a 3 × 2 factorial experiment to investigate the effect of aflatoxin B1 (AF) and Saccharomyces cerevisiae (SAC) on growth performance, blood parameters and carcass characteristics. Chickens were randomly allocated to dietary treatments consisting of three levels of AF at 0, 20 and 60 µg/kg, and with or without SAC (1010 cells/kg) supplementation of 1 g/kg of dried yeast. Results showed that both AF and SAC increased average daily feed intake (both, p < 0.001) and reduced feed efficiency (p < 0.001 and p = 0.035, respectively), while only AF reduced average daily gain (p = 0.009). Supplementation with SAC improved the average daily feed intake in chickens subjected to AF60 (interaction, p < 0.001), suggesting that SAC could improve the appetite of broilers. Chickens fed AF had a lower carcass weight (p = 0.028) and heart weight (p = 0.031), but higher carcass-normalized weight of gizzard (p = 0.038) and liver (p = 0.010). Aflatoxin administration reduced white blood cells (p = 0.030), lymphocytes (p = 0.029) and basophils (p < 0.001), while increasing neutrophils (p = 0.009). SAC reduced neutrophils (p = 0.004) and mean corpuscular haemoglobin (p < 0.001) while increasing lymphocytes (p = 0.003) and basophils (p = 0.015). The haematological results suggest that AF caused a disturbance in the immune system, compromising the health of the chicken, whereas SAC potentially mitigates these alterations. Dietary AF increased the activity of glutamate oxaloacetate transaminase (p = 0.009). These findings suggest a potential use of Saccharomyces cerevisiae as a natural binder to reduce aflatoxicosis in poultry production systems.
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(This article belongs to the Special Issue Current Trends in Exploiting the Influence of Natural Substances, Compounds and Probiotics as Antimicrobial Agents for Food and Health Applications, 2nd Edition)
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Open AccessArticle
Surface Display of Human GM-CSF in Methylotrophic Yeasts
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Olena Dmytruk, Nataliya Finiuk, Rostyslav Stoika, Andriy Sibirny and Kostyantyn Dmytruk
Appl. Microbiol. 2025, 5(3), 98; https://doi.org/10.3390/applmicrobiol5030098 - 15 Sep 2025
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Human granulocyte-macrophage colony-stimulating factor (GM-CSF) is an important therapeutic cytokine. Methylotrophic yeasts such as Komagataella phaffii and Ogataea parapolymorpha are attractive hosts for recombinant protein production. In this study, these yeasts were engineered to produce GM-CSF in both secreted and cell-surface-anchored forms. Secreted
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Human granulocyte-macrophage colony-stimulating factor (GM-CSF) is an important therapeutic cytokine. Methylotrophic yeasts such as Komagataella phaffii and Ogataea parapolymorpha are attractive hosts for recombinant protein production. In this study, these yeasts were engineered to produce GM-CSF in both secreted and cell-surface-anchored forms. Secreted GM-CSF accumulated to tens of milligrams per liter in culture supernatants following induction. Fluorescent antibody labeling confirmed that yeast strains expressing surface-displayed GM-CSF exhibited markedly increased fluorescence compared to parental strains. The highest signal was observed in K. phaffii and further validated by immunofluorescence microscopy. Functional assays demonstrated that K. phaffii cells displaying GM-CSF stimulated TF-1 cell proliferation 1.41-fold compared to control yeast lacking GM-CSF. These results confirm both the successful surface display and preserved biological activity of the cytokine. This work demonstrates the feasibility of engineering K. phaffii to present active human GM-CSF on the cell surface. Surface display was efficient and yielded biologically functional cytokine, as shown by fluorescence-based quantification and TF-1 proliferation assays. The study highlights yeast surface display as a promising platform for delivering therapeutic cytokines without requiring purification steps.
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Open AccessArticle
What Can Contribute to Weakening of Poly(Vinyl Alcohol) Cryogels Used for Cell (Self)Immobilization?
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Olga Senko, Nikolay Stepanov, Olga Maslova and Elena Efremenko
Appl. Microbiol. 2025, 5(3), 97; https://doi.org/10.3390/applmicrobiol5030097 - 12 Sep 2025
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This work was undertaken in order to identify the presence of changes in the characteristics of poly(vinyl alcohol) (PVA) cryogels that can contribute to the degradation of such polymer matrices under the influence of their contact with various microorganisms used in immobilized form
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This work was undertaken in order to identify the presence of changes in the characteristics of poly(vinyl alcohol) (PVA) cryogels that can contribute to the degradation of such polymer matrices under the influence of their contact with various microorganisms used in immobilized form in different biotechnological processes using various complex media and conditions. Immobilized cells of bacteria, yeasts, microalgae, fungi, and microbial consortia were involved in the investigations. It was established that the presence of microorganisms can indirectly (through media transformed by them, in particular, containing lipids) or directly (through high rates of metabolite production, in particular, the fast accumulation of gases in the pores of polymer matrices, or due to the colonization of cryogels (self)immobilization by fungi with the growing mycelium) decrease rheological characteristics of PVA cryogel. Such weakening of PVA cryogels can be expected as a result of the first stage of further degradation of polymer matrices. The values of both the modulus of elasticity and the shear modulus of PVA cryogels confirmed this. The effect of high pressure accumulated in the reactors with PVA cryogel-immobilized cells, as well as their use in flow systems, was not revealed. These factors can be taken into account for the sustainable use of matrices based on PVA cryogels as biocatalysts with microorganisms or soil-structuring elements in artificial or natural environments.
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(This article belongs to the Special Issue Novel Microbiological and Metabolic Approaches Applied to Pollutant Matrices Degradation)
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Open AccessArticle
Composition and Occurrence of Airborne Fungi in Two Urbanized Areas of the City of Sofia, Bulgaria
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Margarita Ivanova, Galina Stoyancheva, Vladislava Dishliyska, Jeny Miteva-Staleva, Radoslav Abrashev, Boryana Spasova, Yana Gocheva, Lyudmila Yovchevska, Galina Satchanska, Maria Angelova and Ekaterina Krumova
Appl. Microbiol. 2025, 5(3), 96; https://doi.org/10.3390/applmicrobiol5030096 - 11 Sep 2025
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Air pollution remains one of the most urgent global challenges, affecting both public health and environmental integrity, with its severity escalating in parallel with industrialization and urban expansion. Defined as the presence of harmful substances in the atmosphere, air pollution poses risks to
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Air pollution remains one of the most urgent global challenges, affecting both public health and environmental integrity, with its severity escalating in parallel with industrialization and urban expansion. Defined as the presence of harmful substances in the atmosphere, air pollution poses risks to human health and disrupts the development of plant and animal life. Urban areas, particularly large cities, frequently exhibit pollutant concentrations that exceed safety thresholds established by the World Health Organization (WHO). This study presents a comprehensive analysis of airborne fungal microbiota in two distinct districts of Sofia, Bulgaria: the highly urbanized city center (Orlov Most) and a less urbanized southwestern area (New Bulgarian University, Ovcha Kupel). Weekly fluctuations in mold spore abundance were monitored, revealing elevated contamination levels on Fridays, likely due to intensified vehicular traffic preceding weekends and public holidays. Taxonomic identification of dominant mold species was conducted using both classical and molecular genetic methods. The isolated fungal strains predominantly belonged to the phylum Ascomycota (80%), with Talaromyces and Alternaria emerging as the most prevalent genera. Additionally, antifungal susceptibility testing indicated that most isolates were sensitive to commonly used antifungal agents, although resistance was observed in two strains of Talaromyces wortmannii. These findings underscore the significance of fungal bioaerosols in urban air quality assessments and highlight the need for targeted monitoring and mitigation strategies.
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Open AccessArticle
Conversion of Komagataella phaffii Biomass Waste to Yeast Extract Supplement
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Laura Murphy and David J. O’Connell
Appl. Microbiol. 2025, 5(3), 95; https://doi.org/10.3390/applmicrobiol5030095 - 4 Sep 2025
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Valorisation of spent yeast biomass post-fermentation requires energy-intensive autolysis or enzymatic hydrolysis that reduces the net benefit. Here, we present a simple and reproducible method for generating functional yeast extract recycled from Komagataella phaffii biomass without a requirement of a pre-treatment process. Spent
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Valorisation of spent yeast biomass post-fermentation requires energy-intensive autolysis or enzymatic hydrolysis that reduces the net benefit. Here, we present a simple and reproducible method for generating functional yeast extract recycled from Komagataella phaffii biomass without a requirement of a pre-treatment process. Spent yeast pellets from fermentations were freeze-dried to produce a fine powder that can be used directly at low concentrations, 0.0015% (w/v), together with 2% peptone (w/v), to formulate complete media ready for secondary fermentations. This media formulation supported growth rates of yeast culture that were statistically indistinguishable (p-value > 0.05) from cultures grown in standard YPD media containing commercial yeast extract, and these cultures produced equivalent titres of recombinant β-glucosidase (0.998 Abs405nm commercial extract vs. 0.899 Abs405nm recycled extract). Additionally, nutrient analyses highlight equivalent levels of sugars (~23 g/L), total proteins, and cell yield per carbon source (~2.17 g) with this recycled yeast extract media formulation when compared to commercial media. This method reduces process complexity and cost and enables the circular reuse of yeast biomass. The protocol is technically straightforward to implement, using freeze drying that is commonly available in research laboratories, representing a broadly applicable and sustainable alternative to conventional media supplementation that achieves a circular approach within the same fermentation system.
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Open AccessArticle
Phyllosphere Antagonistic Bacteria Induce Growth Promotion and Effective Anthracnose Control in Cucumber
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Mst. Habiba Kamrun Nahar, Preangka Saha Briste, Md. Rabiul Islam, Touhidur Rahman Anik, Md. Tanbir Rubayet, Imran Khan, Md. Motaher Hossain and Mohammad Golam Mostofa
Appl. Microbiol. 2025, 5(3), 94; https://doi.org/10.3390/applmicrobiol5030094 - 4 Sep 2025
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The phyllosphere, the aerial part of plants, serves as a crucial habitat for diverse microorganisms. Phyllosphere bacteria can activate protective mechanisms that help plants resist disease. This study focuses on isolating and characterizing phyllosphere bacteria from cucurbits to evaluate their potential in controlling
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The phyllosphere, the aerial part of plants, serves as a crucial habitat for diverse microorganisms. Phyllosphere bacteria can activate protective mechanisms that help plants resist disease. This study focuses on isolating and characterizing phyllosphere bacteria from cucurbits to evaluate their potential in controlling Colletotrichum orbiculare, a pathogen causing anthracnose in cucumbers. Among the 76 bacterial isolates collected, 11 exhibited strong antagonistic effects against C. orbiculare in vitro. Morphological and 16S rRNA analyses identified these isolates as different Bacillus species, including B. vallismortis, B. velezensis, B. amyloliquefaciens, and B. subtilis. These bacteria demonstrated essential plant-growth-promoting and biocontrol traits, such as motility, biofilm formation, phosphate solubilization, nitrogen fixation, and the production of indole acetic acid. Most of the bacterial strains also produced biocontrol compounds such as ammonia, acetoin, siderophores, hydrogen cyanide, chitinase, protease, lipase, and cellulase. The application of these bacteria significantly enhanced cucumber growth in both non-manured and organically manured soils, showing improvements in root and shoot length, chlorophyll content, and biomass accumulation. Additionally, bacterial treatments effectively reduced anthracnose severity, with isolates GL-10 and L-1 showing the highest disease suppression in both soil types. Colonization studies showed that phyllobacteria preferentially colonized healthy leaves over roots and diseased tissues, and they were more effective in manure-amended soils. These results suggest that Bacillus phyllobacteria have strong potential as sustainable bio-stimulants and biocontrol agents, offering an effective approach for enhancing cucumber growth and disease control under both fertilized and unfertilized soil conditions.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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Open AccessArticle
Ruminal Planktonic, Weakly, and Tightly Feed-Adhered Bacterial Community as Affected by Two Trichoderma reesei Enzyme Preparations Fed to Lactating Cattle
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Marjorie A. Killerby, Juan J. Romero, Zhengxin Ma and Adegbola T. Adesogan
Appl. Microbiol. 2025, 5(3), 93; https://doi.org/10.3390/applmicrobiol5030093 - 3 Sep 2025
Abstract
This study evaluates the effects of two Trichoderma reesei exogenous fibrolytic enzyme (EFE) preparations on the taxonomic profile, diversity, relative abundance, and population shifts of three ruminal bacteria fractions of lactating cows: free-floating (LIQ), weakly (AS), and tightly (SOL) feed-adhered. Three lactating cows
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This study evaluates the effects of two Trichoderma reesei exogenous fibrolytic enzyme (EFE) preparations on the taxonomic profile, diversity, relative abundance, and population shifts of three ruminal bacteria fractions of lactating cows: free-floating (LIQ), weakly (AS), and tightly (SOL) feed-adhered. Three lactating cows were fed three EFE treatments in a 3 × 3 Latin square design: one control (CON) without enzymes, a cellulase/xylanase mix (MIX), and a high-xylanase treatment (XYL). Rumen contents were collected, and bacteria were extracted from the three ruminal content fractions for next-generation sequencing analysis. Alpha diversity was higher in XYL compared to CON. However, no EFE effect was observed on beta diversity. The relative abundance (RA) of the family Prevotellaceae increased, while that of Ruminococcaceae and Rikenellaceae decreased in XYL compared to MIX and CON. The bacterial community structure (beta diversity) of LIQ was differentiated from that of SOL and AS (p = 0.03), but no effects of fraction were observed on alpha diversity. Lachnospiraceae RA was greater in SOL, followed by AS, and lower in LIQ (p < 0.001), while Spirochaetaceae RA was greater in SOL and AS compared to LIQ (p = 0.003). The effects of EFE supplementation on rumen bacterial RA were independent of the ruminal content fraction.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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Open AccessReview
Bacterial Cellulose Production in Co-Culture Systems: Opportunities, Challenges, and Future Directions
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Dheanda Absharina, Filemon Jalu Nusantara Putra, Chiaki Ogino, Sándor Kocsubé, Csilla Veres and Csaba Vágvölgyi
Appl. Microbiol. 2025, 5(3), 92; https://doi.org/10.3390/applmicrobiol5030092 - 26 Aug 2025
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Bacterial cellulose (BC), a nanostructured biopolymer produced by Komagateibacter spp., exhibits remarkable mechanical strength, purity, and biocompatibility, making it highly attractive for applications in biomedicine, food, and sustainable materials. Despite its potential, monoculture fermentation suffers from low yield and limited scalability. This review
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Bacterial cellulose (BC), a nanostructured biopolymer produced by Komagateibacter spp., exhibits remarkable mechanical strength, purity, and biocompatibility, making it highly attractive for applications in biomedicine, food, and sustainable materials. Despite its potential, monoculture fermentation suffers from low yield and limited scalability. This review highlights the innovative application of co-culture fermentations as a novel strategy, where Komagataeibacter is paired with complementary microorganisms such as yeasts, lactic acid bacteria, and photosynthetic microbes. This approach has emerged as a promising solution to overcome the limitations of monoculture by enhancing BC productivity, tailoring material properties, and improving sustainability. We explore the synergistic interactions within co-cultures, including metabolic cross-feeding and in situ polymer integration, while also addressing critical challenges such as microbial stability and operational complexity. Unlike previous reviews focused primarily on BC biosynthesis, applications, or genetic engineering, this article emphasizes co-culture fermentation with Komagataeibacter as a novel and underexplored strategy to improve the yield, functionality, and scalability of BC production.
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Open AccessArticle
Biosynthesis of the Siderophore Desferrioxamine E in Rouxiella badensis SER3 and Its Antagonistic Activity Against Fusarium brachygibbosum
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Luzmaria R. Morales-Cedeño, Sergio de los Santos Villalobos, Pedro D. Loeza-Lara, Debasis Mitra, Ajay Kumar, Ma. del Carmen Orozco-Mosqueda and Gustavo Santoyo
Appl. Microbiol. 2025, 5(3), 91; https://doi.org/10.3390/applmicrobiol5030091 - 26 Aug 2025
Abstract
Iron is a limiting factor for plant and microbial growth because, in soil environments, it is predominantly present as oxyhydroxide minerals, rendering it unavailable to plants and microorganisms. Siderophores are chelating agents secreted to solubilize iron and facilitate its uptake. To understand the
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Iron is a limiting factor for plant and microbial growth because, in soil environments, it is predominantly present as oxyhydroxide minerals, rendering it unavailable to plants and microorganisms. Siderophores are chelating agents secreted to solubilize iron and facilitate its uptake. To understand the evolutionary and ecological dynamics of microbial communities, as well as the evolution of pathogens within hosts, it is essential to study the genes shared between microorganisms for environmental adaptation and survival. In this study, we conducted microbiological assays to evaluate the effect of the siderophore produced by Rouxiella badensis strain SER3 on the mycelial growth of fungal pathogens such as Fusarium brachygibbosum 4BF. Using spectrophotometric techniques and bioinformatics tools, we identified desferrioxamine E (nocardamine) in the culture supernatant, and the corresponding biosynthetic gene cluster in the SER3 genome was confirmed through antiSMASH analysis and synteny comparisons. Gene expression analysis by RT-PCR showed differential expression of biosynthetic precursors when strain SER3 was grown alone or in interaction with fungal pathogen. Finally, scanning electron microscopy revealed structural damage to F. brachygibbosum hyphae during co-culture with strain SER3. These results suggest that the production of desferrioxamine E may act as a biocontrol mechanism employed by R. badensis SER3 against F. brachygibbosum.
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(This article belongs to the Topic New Challenges on Plant–Microbe Interactions)
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Open AccessReview
The Microbiome as a Driver of Insect Physiology, Behavior, and Control Strategies
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Hazem Al Darwish, Muqaddasa Tariq, Safiyah Salama, Tia Hart and Jennifer S. Sun
Appl. Microbiol. 2025, 5(3), 90; https://doi.org/10.3390/applmicrobiol5030090 - 26 Aug 2025
Abstract
Insect pests impose major economic, agricultural, and public health burdens, damaging crops and transmitting pathogens such as dengue, malaria, and Zika. Conventional chemical control is increasingly ineffective due to insecticide resistance and environmental concerns, prompting a search for innovative strategies. The insect microbiome—comprising
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Insect pests impose major economic, agricultural, and public health burdens, damaging crops and transmitting pathogens such as dengue, malaria, and Zika. Conventional chemical control is increasingly ineffective due to insecticide resistance and environmental concerns, prompting a search for innovative strategies. The insect microbiome—comprising both obligate symbionts and environmentally acquired microbes—emerges as a key driver of host physiology and behavior. Microbes influence nutrient acquisition, immunity, reproduction, and chemosensory processing, often to promote their own transmission. By modulating olfactory and gustatory pathways, microbiota can alter host-seeking, mate choice, foraging, and oviposition patterns, reshaping ecological interactions and vector dynamics. These effects are shaped by microbial acquisition routes, habitat conditions, and anthropogenic pressures such as pesticide use, pollution, and climate change. Understanding these multi-directional interactions offers opportunities to design highly specific, microbe-based insect control strategies, from deploying microbial metabolites that disrupt host sensory systems to restoring beneficial symbionts in threatened pollinators. Integrating microbiome ecology with insect physiology and behavior not only deepens our understanding of host–microbe coevolution but also enables the development of sustainable, targeted alternatives to chemical insecticides. This review synthesizes current evidence linking microbiomes to insect biology and explores their potential as tools for pest and vector management.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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Open AccessArticle
Investigating the Role of Cytoskeletal Dynamics in Cronobacter Invasion: A Study of Caco-2 and H4 Cell Lines
by
Mahmoud B. Agena, Khaled M. Ibrahim, Abdlrhman M. Alsonosi, Mohamed T. Saad and Bassam A. Elgamoudi
Appl. Microbiol. 2025, 5(3), 89; https://doi.org/10.3390/applmicrobiol5030089 - 24 Aug 2025
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Pathogenic bacteria have developed different ways to cause infections. One strategy involves using components from host cells. This study looks at the role of the cytoskeleton in the human colon adenocarcinoma Caco-2 and neonatal non-transformed epithelial H4 cell lines during bacterial invasion. The
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Pathogenic bacteria have developed different ways to cause infections. One strategy involves using components from host cells. This study looks at the role of the cytoskeleton in the human colon adenocarcinoma Caco-2 and neonatal non-transformed epithelial H4 cell lines during bacterial invasion. The bacteria studied include Cronobacter malonaticus, Cronobacter sakazakii, and E. coli K1, as they are associated with known diseases. Salmonella enteritidis 358 served as a positive control and E. coli K12 as a negative control for the invasion experiments. Before the invasion experiments, cell lines were treated with microfilament inhibitors, specifically Cytochalasin D, and microtubule inhibitors, such as Colchicine, Nocodazole, Vinblastine, and Taxol. The results showed that Cytochalasin D reduced about 60–80% of Cronobacter invasion into H4 cells and 50% of E. coli K1 invasion. In contrast, Colchicine reduced the invasion of some strains to just 2% compared to untreated cells. Meanwhile, Nocodazole and Taxol increased the invasion of C. sakazakii 709 and C. malonaticus 1569 into H4 cells by about 140% and 160%, respectively, while slightly inhibiting other strains. In Caco-2 cells, certain strains exhibited increased invasion due to Cytochalasin D, Vinblastine, and Colchicine treatment. This led to increases of up to 500%, 227%, and 248% compared to untreated cells. However, Nocodazole and Taxol decreased invasion into Caco-2 cells, with only E. coli K1 showing an increase of about 150% in Taxol-treated cells. The findings with eukaryotic cytoskeleton inhibitors on neonatal H4 cells suggest that bacterial invasion mainly relies on microfilaments or microfilament-dependent. No specific dependence on the cytoskeleton was seen in Caco-2 cells. In conclusion, cytoskeletal inhibitors significantly affected bacterial invasion, specifically Cronobacter, compared to untreated cells. This suggests that invasion methods may vary by strain and are influenced by how each inhibitor alters cytoskeleton behavior. Therefore, the invasion process, both with and without cytoskeletal inhibitors, is crucial for understanding how bacteria manipulate cell components during infection.
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Open AccessArticle
Lactic Acid Fermentation Inactivates Salmonella Typhimurium in Contaminated Cattle Manure at Moderate and Low Temperatures
by
Hannah Halm, Sören Woelke, Ines Lehnert, Thorben Schilling, Thorsten Meissner, Charlotte Schröder, Ludwig E. Hoelzle and Hendrik A. Scheinemann
Appl. Microbiol. 2025, 5(3), 88; https://doi.org/10.3390/applmicrobiol5030088 - 22 Aug 2025
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In the case of a notifiable animal disease like salmonellosis, manure is contaminated and must be disinfected. This can be performed using heat measures, chemical disinfectants, or long-term storage. All these measures bring along severe economic, ecological, and logistical problems. The aim of
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In the case of a notifiable animal disease like salmonellosis, manure is contaminated and must be disinfected. This can be performed using heat measures, chemical disinfectants, or long-term storage. All these measures bring along severe economic, ecological, and logistical problems. The aim of this study was to evaluate lactic acid fermentation (LAF) as an alternative disinfection method. Fermentation was started by adding a carbohydrate source to the manure and creating anaerobic conditions. For testing, cattle manure was enriched with different carbohydrate (CHO) sources and spiked with Salmonella Typhimurium (S. Ty.). The samples were incubated at 10 °C and 21 °C for 111 days (Exp1) and at 21 °C for 50 days (Exp2). The microbial shift was determined using cultural methods and MALDI-TOF. Both the change in pH and Enterococcus spp. were tested as suitable indicators. The results showed the different suitability of the selected CHO for hygienization by LAF. Using squeezed oat as an additive, S. Ty was reduced to below the detection limit under both temperature conditions within 21 days and 14 days. Additional saccharose decreased the reduction time. This study showed that LAF is a valuable alternative for disinfecting cattle manure in the case of bovine salmonellosis. Using this method, both manure and feed residues can be treated in one approach and afterwards be used as fertilizer.
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Open AccessArticle
Efficacy of Escherichia coli O157:H7 Phage Φ241 in Model Food Systems
by
Zhongjing Lu
Appl. Microbiol. 2025, 5(3), 87; https://doi.org/10.3390/applmicrobiol5030087 - 21 Aug 2025
Abstract
Escherichia coli O157:H7 has been an important foodborne pathogen causing severe disease in humans worldwide. It is challenging to control E. coli O157:H7 due to its intrinsic acid resistance, ability to survive in various environments, and the emergence of antimicrobial resistance. Recent research
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Escherichia coli O157:H7 has been an important foodborne pathogen causing severe disease in humans worldwide. It is challenging to control E. coli O157:H7 due to its intrinsic acid resistance, ability to survive in various environments, and the emergence of antimicrobial resistance. Recent research showed that phages are promising antibacterial agents. A phage (Φ241) infecting 48 E. coli O157:H7 strains from various sources was previously isolated from an industrial cucumber fermentation at pH 3.7 and 5% NaCl. The efficacy of phage Φ241 infection was evaluated in this study in four representative model food systems (beef broth, cucumber juice, cucumber juice supplemented with NaCl, and apple juice). Pronounced differences in phage effectiveness were found in the tested food systems, and impacted by pH, salinity, and multiplicity of infection. The potential of this phage is evident in beef broth and cucumber juice, where 4- to 6-log reduction in host concentration was achieved within 3 to 5 h. However, apple juice (pH 3.55) completely inhibited host growth and phage infection. Overall, the study shows the high potential of Φ241 as an antibacterial agent to improve food safety. Future research will incorporate a cocktail of phages targeting E. coli O157:H7 to mitigate phage resistance development.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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Open AccessFeature PaperArticle
Functional Characterization of Native Microorganisms from the Pulp of Coffea arabica L. Var. Castillo and Cenicafé 1 for Postharvest Applications and Compost Enhancement
by
Paula A. Figueroa-Varela and Eduardo Duque-Dussán
Appl. Microbiol. 2025, 5(3), 86; https://doi.org/10.3390/applmicrobiol5030086 - 21 Aug 2025
Abstract
Coffee pulp, the primary residue generated during the wet processing of Coffea arabica L., is frequently applied directly to fields as a crude soil amendment. However, this practice often lacks proper microbial stabilization, limiting its agronomic potential and posing risks due to the
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Coffee pulp, the primary residue generated during the wet processing of Coffea arabica L., is frequently applied directly to fields as a crude soil amendment. However, this practice often lacks proper microbial stabilization, limiting its agronomic potential and posing risks due to the presence of phytotoxic compounds. In Colombia, disease-resistant varieties such as Coffea arabica L. var. Castillo and var. Cenicafé 1, developed by the National Coffee Research Center (Cenicafé), are the amongst the most widely cultivated varieties in the country; however, despite their widespread adoption, the microbial ecology of postharvest residues from these varieties remains poorly characterized. This study aimed to isolate and functionally characterize native microbial communities from the pulp of Coffea arabica var. Castillo and var. Cenicafé 1, and to evaluate their role in postharvest processing and organic waste management. Fresh pulp samples were collected from a wet-processing facility located in tropical mid-elevation zones. A total of 53 microbial isolates were recovered using culture-dependent techniques on selective media targeting yeasts, lactic acid bacteria (LAB), and filamentous fungi. Amplicon sequencing of the 16S rRNA gene (V3–V4 region) and ITS1 region was conducted to profile bacterial and fungal communities, revealing diverse microbial consortia dominated by Aspergillus, Lactobacillus, Leuconostoc, Pichia, and Saccharomyces species. Enzymatic screening indicated high pectinolytic and cellulolytic activity. Composting trials using inoculated pulp showed a ~40% reduction in composting time and improved nutrient content. These findings support the use of native microbiota to enhance composting efficiency and postharvest valorization, contributing to more sustainable and circular coffee systems.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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Open AccessArticle
Biocontrol Potential of Fungal and Oomycete Phytopathogens by Myxobacterial Strains
by
Adnan Ismaiel, Dilip K. Lakshman and Patricia Millner
Appl. Microbiol. 2025, 5(3), 85; https://doi.org/10.3390/applmicrobiol5030085 - 20 Aug 2025
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Myxobacteria, a group of swarming, predatory soil bacteria, are of interest because of their biocontrol potential. In this study, the inhibitory effects of 13 strains of myxobacteria were examined against four different phytopathogenic fungi, as follows: two isolates of Rhizoctonia solani from different
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Myxobacteria, a group of swarming, predatory soil bacteria, are of interest because of their biocontrol potential. In this study, the inhibitory effects of 13 strains of myxobacteria were examined against four different phytopathogenic fungi, as follows: two isolates of Rhizoctonia solani from different AG groups and one isolate each from Sclerotinia sclerotiorum and the oomycete Pythium ultimum. Inhibition levels varied among phytopathogens, with slow-growers being more susceptible than fast-growers. Myxococcus xanthus BS 248, M. flavus ATCC 29617, and M. coralloides BS249 were the most inhibitory strains tested. non-contact and contact inhibition on agar media between phytopathogens and myxobacteria were visually discernible. This distinction potentially reflects the activity of low-molecular-weight metabolites and high-molecular-weight lytic enzymes, respectively. In a pot soil study, the inhibitory effect of a mixture of two strains of myxobacteria against two strains of R. solani was apparent from the reduced disease in cucumber seedlings compared to controls without myxobacteria. This is the first report of an in vivo inhibitory effect of myxobacteria against Rhizoctonia. The survival of M. xanthus BS248 in sterile soil amended with rabbit manure (1:1) increased up to five weeks compared to one week in soil without the manure, suggesting that organic amendment could enrich myxobacteria in soil.
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