Journal Description
Microorganisms
Microorganisms
is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with Microorganisms, and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Microbiology) / CiteScore - Q1 (Microbiology (medical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.2 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Testimonials: See what our editors and authors say about Microorganisms.
- Companion journal for Microorganisms include: Applied Microbiology and Bacteria.
Impact Factor:
4.2 (2024);
5-Year Impact Factor:
4.6 (2024)
Latest Articles
Combating Foodborne MRSA: Identification and Silver Nanoparticle-Based Antibacterial Strategies with Antibiotic Synergy and Resistance Evolution Assessment
Microorganisms 2025, 13(10), 2393; https://doi.org/10.3390/microorganisms13102393 (registering DOI) - 18 Oct 2025
Abstract
Ready-to-eat (RTE) foods can carry antimicrobial-resistant pathogens; however, few studies link real-world surveillance to practical interventions. This study addressed this gap by estimating the prevalence of Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) in ready-to-eat foods from Al-Qassim and
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Ready-to-eat (RTE) foods can carry antimicrobial-resistant pathogens; however, few studies link real-world surveillance to practical interventions. This study addressed this gap by estimating the prevalence of Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) in ready-to-eat foods from Al-Qassim and evaluating a rapid, orthogonal confirmation workflow (culture → MALDI-TOF MS → Vitek 2 → mecA/mecC PCR). The in vitro activity of citrate-stabilized silver nanoparticles (AgNPs) against food-derived MRSA was quantified, and synergy with oxacillin (primary) and ciprofloxacin (secondary) was examined. Silver-susceptibility stability was assessed over 20 days of sub-MIC serial passage, with attention to whether β-lactam co-exposure constrained drift. We surveyed 149 RTE products and paired the confirmation workflow with mechanistic tests of AgNPs as antibiotic adjuvants. S. aureus was recovered from 24.2% of products and MRSA from 6.7%, with higher recovery from animal-source matrices and street-vendor outlets. MALDI-TOF MS provided rapid species confirmation and revealed two reproducible low-mass peaks (m/z 3990 and 4125) associated with MRSA, supporting spectral triage pending molecular confirmation. Antimicrobial susceptibility testing showed the expected β-lactam split (MRSA oxacillin/cefoxitin non-susceptible; MSSA oxacillin-susceptible but largely penicillin-resistant), with last-line agents retained. Citrate-stabilized AgNPs displayed consistent potency against food-derived MRSA (MIC 8–32 µg/mL; MIC50 16; MIC90 32) and were predominantly bactericidal (MBC/MIC ≤ 4 in 90%). Checkerboards demonstrated frequent AgNP–oxacillin synergy (median fractional inhibitory concentration index [FICI] 0.37; 4–16-fold oxacillin MIC reductions) and additive-to-synergistic effects with ciprofloxacin (median FICI 0.63), translating time–kill assays into rapid, sustained bactericidal activity without antagonism. During sub-MIC evolution, silver MICs rose modestly (median two-fold) and often regressed off drug; oxacillin co-exposure limited drift. RTE foods therefore represent credible MRSA exposure routes. Integrating MALDI-assisted triage with automated AST enables scalable surveillance, and standardized AgNP formulations emerge as promising β-lactam adjuvants—pending in situ efficacy, safety, and residue evaluation.
Full article
(This article belongs to the Special Issue Antimicrobial Resistance: Challenges and Innovative Solutions, 2nd Edition)
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Open AccessArticle
Helicobacter pylori-Mediated Injury: The Hidden Path to Gastric Hemorrhage and Neoplasia
by
Sabrina-Nicoleta Munteanu, Ana-Maria Filip, Patrick-Lazăr-Dominik Chiciudean, Monica Pantea, Simona Mocan and Anca Elena Negovan
Microorganisms 2025, 13(10), 2392; https://doi.org/10.3390/microorganisms13102392 (registering DOI) - 18 Oct 2025
Abstract
Helicobacter pylori infection represents a well-established risk factor for the development of gastric carcinogenesis, yet reliable clinical or endoscopic predictors of infection remain poorly defined. Identifying non-invasive or endoscopic markers of this infection could improve early detection, which is crucial for effective prevention
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Helicobacter pylori infection represents a well-established risk factor for the development of gastric carcinogenesis, yet reliable clinical or endoscopic predictors of infection remain poorly defined. Identifying non-invasive or endoscopic markers of this infection could improve early detection, which is crucial for effective prevention and clinical management. This single-center study included 737 patients who underwent upper gastrointestinal endoscopy. We compared clinical, laboratory, and endoscopic features between H. pylori-positive and H. pylori-negative individuals. A total of 263 with H. pylori-positive gastric biopsies and 474 with H. pylori-negative biopsies were enrolled in our study. Cerebrovascular disease (9.51% vs. 5.51%, p = 0.04, OR = 1.80), type 2 diabetes mellitus (T2DM—22.05% vs. 15.86%, p = 0.04, OR 1.5), and alcohol consumption (18.96% vs. 9.3%, p = 0.00, OR = 2.28) were significantly more prevalent among H. pylori-positive patients. Heartburn was more commonly reported in H. pylori-negative individuals (23.77% vs. 15.38%, p = 0.01, OR = 0.58). Laboratory parameters showed no significant differences between groups. Regarding endoscopic findings, corporal erythema (26.92% vs. 16.17%, p = 0.00, OR = 1.91), corporal erosions (11.54% vs. 5.32%, p = 0.00, OR = 2.32), and submucosal hemorrhages (20.91% vs. 11.6%, p = 0.00, OR = 2.01) were associated with H. pylori infection. In the multivariate logistic regression models, alcohol consumption and corporal lesions remained independent predictors of H. pylori-associated gastritis, even after adjusting for age, sex, and PPI use. This study identifies alcohol consumption and specific corporal mucosal changes as novel, independent predictors of H. pylori infection. Heartburn was negatively associated with active H. pylori infection, while the rest of the symptoms did not predict infection or mucosal lesions. The laboratory parameters did not differ significantly between groups. These findings underscore the potential of targeted endoscopic evaluation and risk-based screening (particularly among T2DM and alcohol-consuming populations) to enhance early detection and management of H. pylori-associated disease.
Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Bacterial Infection)
Open AccessArticle
Evaluation of Specific Torulaspora Delbrueckii Fractions to Stimulate Malolactic Fermentation in Limiting Conditions
by
Aitor Balmaseda, Paloma Toraño, Benjamin Leroux, José María Heras, Sibylle Krieger-Weber, Nicolas Rozès, Magali Deleris-Bou and Cristina Reguant
Microorganisms 2025, 13(10), 2391; https://doi.org/10.3390/microorganisms13102391 - 17 Oct 2025
Abstract
Malolactic fermentation (MLF) is a bioprocess driven by lactic acid bacteria (LAB), which is desired in red and highly acidic white wines. Among all LAB, Oenococcus oeni is the main species in wine, followed by Lactiplantibacillus plantarum. The harsh conditions found in
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Malolactic fermentation (MLF) is a bioprocess driven by lactic acid bacteria (LAB), which is desired in red and highly acidic white wines. Among all LAB, Oenococcus oeni is the main species in wine, followed by Lactiplantibacillus plantarum. The harsh conditions found in wine—not only due to the low nutrient concentration but also the presence of antimicrobial compounds such as ethanol, high acidity, SO2, and polyphenols—can compromise MLF performance. In recent years, the use of certain non-Saccharomyces yeasts, such as Torulaspora delbrueckii or Metschnikowia pulcherrima, as starter cultures for alcoholic fermentation, has emerged as a promising strategy to improve MLF. In this study, we evaluated the effect of four different fractions from a T. delbrueckii strain on MLF performance. First, the positive impact of this strain as a starter culture on O. oeni growth was confirmed; then, yeast-derived compounds were tested in different wines. Two fractions showed the most promising results in reducing MLF duration: the inactivated yeast fraction and the autolysate fraction. Those enhanced bacterial viability and promoted mannoprotein consumption. These findings highlight the potential of T. delbrueckii-derived compounds as enological tools to support MLF under restrictive wine conditions.
Full article
(This article belongs to the Special Issue Wine Fermentation Microorganisms)
Open AccessArticle
Preliminary Assessment of Mycobiome at Former Quarry Site That Hosts a Diverse and Abundant Orchid Population
by
Viswambharan Sarasan, Dean Williams and Zoe Ringwood
Microorganisms 2025, 13(10), 2390; https://doi.org/10.3390/microorganisms13102390 - 17 Oct 2025
Abstract
Former quarries offer unique opportunities for biodiversity restoration, yet their potential for orchid meadow creation remains underexplored. This study screened soils to study whether these habitats harbour key orchid-compatible fungi essential for orchid colonisation. We conducted comparative analyses of fungal community composition across
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Former quarries offer unique opportunities for biodiversity restoration, yet their potential for orchid meadow creation remains underexplored. This study screened soils to study whether these habitats harbour key orchid-compatible fungi essential for orchid colonisation. We conducted comparative analyses of fungal community composition across restored quarry sites using alpha and beta diversity metrics, NMDS ordinations, and regression models linking orchid abundance with fungal diversity. Using soil metabarcoding across four restored sites, the results showed that orchid abundance strongly correlated with fungal diversity, including mycorrhizal families such as Sebacinaceae and Thelephoraceae. The gorge-based site supported the highest orchid density and richest fungal assemblage. These findings demonstrate that former quarries can sustain the fungal networks required for orchid recruitment, providing a foundation for large-scale restoration strategies. Association analysis revealed that orchid abundance, though on a limited scale, is a strong predictor of fungal diversity, indicating that denser orchid populations support richer fungal communities. Despite its limited scale, this study demonstrates that former quarries can provide both the physical conditions and the fungal networks necessary for orchid establishment, offering a practical model for restoring orchid-rich meadows and enhancing biodiversity in former quarries.
Full article
(This article belongs to the Section Plant Microbe Interactions)
Open AccessArticle
ROS-Mediated Necroptosis Promotes Coxsackievirus B3 Replication and Myocardial Injury
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Junbo Huang, Yanjun Di, Qing Song, Zhiyun Cheng, Hao Wu, Mei Wu, Minjian He, Genrui Zhang, Fucai Wang and Lei Tong
Microorganisms 2025, 13(10), 2389; https://doi.org/10.3390/microorganisms13102389 - 17 Oct 2025
Abstract
Coxsackievirus B3 (CVB3) is a primary causative agent of viral myocarditis (VMC), which can lead to both acute and chronic cardiac inflammation accompanied by progressive heart failure and arrhythmias. Although CVB3 has been implicated in various forms of programmed cell death, whether it
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Coxsackievirus B3 (CVB3) is a primary causative agent of viral myocarditis (VMC), which can lead to both acute and chronic cardiac inflammation accompanied by progressive heart failure and arrhythmias. Although CVB3 has been implicated in various forms of programmed cell death, whether it triggers necroptosis and the underlying mechanisms remains unclear. This study aimed to investigate the role and mechanism of CVB3-induced necroptosis and its effect on viral replication. Using both in vitro and in vivo models, we demonstrated that CVB3 infection significantly upregulates the expression of key necroptotic markers RIP1 and RIP3 in HeLa cells and mouse myocardial tissues. This upregulation was accompanied by elevated intracellular reactive oxygen species (ROS) levels and suppression of the Nrf2/HO-1 antioxidant pathway. Intervention with the necroptosis inhibitor Necrostatin-1 (Nec-1) or the ROS scavenger N-acetylcysteine (NAC) markedly attenuated cell death, suppressed viral replication, and ameliorated myocardial injury and inflammatory responses in infected mice. Mechanistically, CVB3 inhibits the Nrf2/HO-1 pathway, thereby inducing substantial ROS accumulation that promotes necroptosis. This effect can be reversed by NAC treatment. Our study reveals a novel mechanism through which CVB3 induces ROS-dependent necroptosis via the suppression of the Nrf2/HO-1 pathway, providing new insights into the pathogenesis of viral myocarditis and suggesting potential therapeutic strategies.
Full article
(This article belongs to the Special Issue Viral Proteases in Viral Infection and Drug Development)
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Open AccessArticle
Exploratory Temporal and Evolutionary Insights into the Filoviridae Family Through Multiprotein Phylogeny
by
Thiago S. Messias, Kaique C. P. Silva, Narciso A. Vieira, Gislaine A. Querino, Elaine C. Marcos, Mateus J. de C. Stefani, Ana P. R. Battochio, Thaís M. Oliveira, Ivan S. Vieira, Aline S. Ibanes, Taylor E. T. Olivo, Edson C. de Melo, Silvia C. Arantes, Pedro C. R. da Luz, Maria G. R. Mengoa and Simone Soares
Microorganisms 2025, 13(10), 2388; https://doi.org/10.3390/microorganisms13102388 - 17 Oct 2025
Abstract
Filoviruses are among the most lethal viral human pathogens known, with significant relevance to public health, yet their evolutionary history remains poorly resolved. This study applied a multiprotein molecular phylogenetic approach to investigate the evolutionary and temporal dynamics of the family Filoviridae.
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Filoviruses are among the most lethal viral human pathogens known, with significant relevance to public health, yet their evolutionary history remains poorly resolved. This study applied a multiprotein molecular phylogenetic approach to investigate the evolutionary and temporal dynamics of the family Filoviridae. Amino acid sequences from the proteome and seven individual proteins (NP, VP35, VP40, GP, VP30, VP24, L) were analyzed using MEGA 12, with RelTime inference anchored on uniform calibrations, and integration of epidemiological data (cases, fatalities, case fatality). The phylogenetic reconstructions revealed robust topologies for most proteins, though selective pressures on GP, VP30 and VP40 generated more variable patterns. Temporal inferences supported the classification of filoviruses into three groups: an ancestral lineage (>1 MYA, fish- and reptile-associated), an intermediate lineage (BCE–1 MYA, bat-associated), and a contemporary lineage (CE, ebolaviruses and marburgviruses). VP30 and VP40 showed consistent associations with epidemiological outcomes in Orthoebolavirus zairense, suggesting their interplay may underlie enhanced dispersal and virulence. Contrariwise, Orthoebolavirus restonense emerged as a natural counterpoint for comparison with other potential human pathogenic filoviruses. Taken together, these findings highlight that filoviral evolution is intrinsically linked not only to viral biology but also to the ecology and history of their hosts.
Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
Open AccessArticle
Metagenomics and In Vitro Growth-Promoting Experiments Revealed the Potential Roles of Mycorrhizal Fungus Humicolopsis cephalosporioides and Helper Bacteria in Cheilotheca humilis Growth
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Yawei Liu, Yuhao Shang, Xin Wang, Xiao Li, Zhiming Yu, Zhanghui Zeng, Zhehao Chen, Lilin Wang, Taihe Xiang and Xiaoping Huang
Microorganisms 2025, 13(10), 2387; https://doi.org/10.3390/microorganisms13102387 - 17 Oct 2025
Abstract
In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the
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In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the promotion of plant growth and nutrient uptake. However, the microbial community and key microbial species that function during the growth of the myco-heterotrophic plant Cheilotheca humilis remain unclear. In this study, we evaluated the microbial community associated with Cheilotheca humilis, which was confirmed via morphological characteristics typical of this plant species. Metagenomic analysis showed that the Afipia carboxidovorans was dominant at species level. Based on the LDA score, Bradyrhizobium ottawaense exhibited the higher abundance in the CH-B group (related to bud) while Afipia carboxidovorans was identified from the CH-F group (related to flower). Microbial co-occurrence networks showed that the Rhizobium genus, Herbaspirillum genus, and Cyanobacteriota were defined as core functional microbial species. To explore the potential microorganisms, metagenome-assembled genomes (MAGs) of the rhizosphere microbiome identified 14 medium- and high-quality MAGs, mainly involved in carbon fixation, nitrogen transformation, and phosphorus metabolism, possibly providing nutrients for the plant. Furthermore, a total of 67 rhizospheric and 66 endophytic microorganisms were isolated and obtained. In vitro experiments showed that the mycorrhizal helper bacteria (MHBs) Rhizobium genus and Pseudomonas genus possessed the ability of nitrogen fixation, phosphate solubilization, and siderophores production. Most importantly, the mycorrhizal fungus Humicolopsis cephalosporioides was obtained, which could potentially produce cellulase to supply carbohydrates for host. The findings suggest the mycorrhizal fungus Humicolopsis cephalosporioides and helper bacteria have great potential in the growth of the myco-heterotrophic plant Cheilotheca humilis.
Full article
(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)
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Open AccessReview
The Influence of Seasonal Variations in Clinical Trials Based on Gut Microbiota Studies
by
Giovanna Cocomazzi, Concetta Panebianco, Annamaria Vallelunga, Daniele De Ruvo, Lino Del Pup, Serena Smeazzetto, Monica Antinori, Valeria Chimienti, Gabriele Maggio, Concetta Finocchiaro, Viviana Contu and Valerio Pazienza
Microorganisms 2025, 13(10), 2386; https://doi.org/10.3390/microorganisms13102386 - 17 Oct 2025
Abstract
Seasonality is a key determinant in shaping the composition and function of the human gut microbiota, exerting its influence through multiple interconnected factors. These include seasonal variations in diet, environmental conditions (such as temperature, humidity, and sunlight exposure), behavioral patterns (physical activity, time
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Seasonality is a key determinant in shaping the composition and function of the human gut microbiota, exerting its influence through multiple interconnected factors. These include seasonal variations in diet, environmental conditions (such as temperature, humidity, and sunlight exposure), behavioral patterns (physical activity, time spent outdoors), and the incidence of seasonal infections. These changes are most visible in certain populations where food availability follows a seasonal pattern. Increasing evidence suggests that gut microbiota composition undergoes seasonal variations, which may have significant implications for human health. In patients with non-communicable chronic diseases (NCDs), where microbiota dysbiosis plays a crucial role in disease progression, understanding the seasonal effects on gut microbiota is essential. These dynamic changes impact the gut microbiota immune system interaction and may contribute to the onset or exacerbation of various diseases, including chronic inflammatory, metabolic, and autoimmune disorders. Most clinical trials on probiotics do not consider seasonality as a confounding variable, which could impact the interpretation of results and therapeutic efficacy, potentially biasing estimates of intervention efficacy or associations with disease. This review examines the current evidence on gut microbiota seasonality, discusses its potential bias, and outlines methodological considerations for future clinical trials.
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(This article belongs to the Section Environmental Microbiology)
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Open AccessArticle
Genome Analysis of Alginate-Degrading Bacterium Vibrio sp. 32415 and Optimization of Alginate Lyase Production
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Yi Zeng, Jia Xu, Zhongran Li, Rujie Wei, Haiyang Zhao, Liqin Sun and Chang Lu
Microorganisms 2025, 13(10), 2385; https://doi.org/10.3390/microorganisms13102385 - 16 Oct 2025
Abstract
Vibrio sp. is one of the main producers of alginate lyase; however, most strains have problems such as low and unstable enzyme production. In this study, the enzyme production conditions of V. sp. 32415, a marine bacterium capable of producing extracellular alginate lyase,
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Vibrio sp. is one of the main producers of alginate lyase; however, most strains have problems such as low and unstable enzyme production. In this study, the enzyme production conditions of V. sp. 32415, a marine bacterium capable of producing extracellular alginate lyase, were optimized through Response Surface Design. The optimized medium was as follows: NaCl 12 g/L, FeSO4·7H2O 0.067 g/L, NH4Cl 7 g/L, alginate 11 g/L, K2HPO4·3H2O 4 g/L, MgSO4·7H2O 1 g/L. Under 28 °C, 160 rpm, 30 mL/300 mL liquid volume, and an initial pH 5.5 culture condition, the extracellular enzyme activity was 51.06 U/mL, which was 2.8 times higher compared with the activity before optimization. The optimal temperature, pH, and NaCl concentration for the extracellular alginate lyase were 37 °C, 8.0, and 0.1 M, respectively. The enzyme remained more than 80% of its original activity at 30 °C for 4 h. 1 mM Fe3+, Ca2+, K+, Mg2+, and Na+ enhance enzyme activity, with a preference for polyG blocks. V. sp. 32415 has two circular chromosomes and one circular plasmid. Chromosome 2 has two polysaccharide utilization loci. It utilizes alginate through the Scatter pathway. The results of this study provide theoretical and data support for understanding the production of extracellular alginate lyase by marine Vibrio and their metabolism and utilization of alginate.
Full article
(This article belongs to the Section Microbial Biotechnology)
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Open AccessArticle
Cross-Kingdom Enzymatic Strategies for Deoxynivalenol Detoxification: Computational Analysis of Structural Mechanisms and Evolutionary Adaptations
by
Francisco J. Enguita and Ana Lúcia Leitão
Microorganisms 2025, 13(10), 2384; https://doi.org/10.3390/microorganisms13102384 - 16 Oct 2025
Abstract
Deoxynivalenol (DON) is a trichothecene mycotoxin produced by Fusarium species that frequently contaminates cereal crops, representing a major threat to food safety, public health, and agricultural productivity. Its remarkable chemical stability during food processing presents significant challenges for effective detoxification. Among the available
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Deoxynivalenol (DON) is a trichothecene mycotoxin produced by Fusarium species that frequently contaminates cereal crops, representing a major threat to food safety, public health, and agricultural productivity. Its remarkable chemical stability during food processing presents significant challenges for effective detoxification. Among the available mitigation strategies, biological approaches have emerged as particularly promising, as they exploit enzymatic systems capable of converting DON into metabolites with substantially reduced toxicity. In this study, we provide a comprehensive analysis of the structural and evolutionary mechanisms underlying DON detoxification across three kingdoms of life. We investigated the fungal glutathione S-transferase Fhb7, the bacterial DepA/DepB epimerization pathway, and the plant SPG glyoxalase using integrative bioinformatics, phylogenetics, molecular modeling, and docking simulations. The selected enzymatic systems employ distinct yet complementary strategies: Fhb7 conjugates DON with glutathione and disrupts its epoxide ring, DepA/DepB converts it into the less toxic 3-epi-DON through stereospecific epimerization, and SPG glyoxalase mediates DON isomerization. Despite their mechanistic differences, these enzymes share key adaptive features that enable efficient DON recognition and detoxification. This work provides an integrative view of cross-kingdom enzymatic strategies for DON degradation, offering insights into their evolution and functional diversity. These findings open avenues for biotechnological applications, including the development of DON-resistant crops and innovative solutions to reduce mycotoxin contamination in the food chain.
Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms, 3rd Edition)
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Open AccessArticle
Electricity Production and Population Dynamics of Microbial Community in a Co-Culture of Iron Mine Soil Biofilm and Shewanella oneidensis MR-1 with Anode as Electron Acceptor
by
Huimei Chi, Jiayi Bai and Man Feng
Microorganisms 2025, 13(10), 2383; https://doi.org/10.3390/microorganisms13102383 - 16 Oct 2025
Abstract
Microbial communities that develop within biofilms on electrodes are necessary for the proper functioning of the microbial electrochemical system. However, the mechanism through which an exogenous exoelectrogen influences the population dynamics and electrochemical performance of biofilms remains unclear. In this study, we explored
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Microbial communities that develop within biofilms on electrodes are necessary for the proper functioning of the microbial electrochemical system. However, the mechanism through which an exogenous exoelectrogen influences the population dynamics and electrochemical performance of biofilms remains unclear. In this study, we explored the community structure dynamics and electrochemical characteristics of iron mine soil biofilm co-cultured with Shewanella oneidensis MR-1, with the anode as the electron acceptor, and compared the results with those of iron mine soil biofilms alone on the anode. Shewanella oneidensis MR-1 improved the electrochemical activity of microbial biofilms, resulting in a higher maximum power density of 195 ± 8 mW/m2 compared with that of iron mine soil (175 ± 7 mW/m2) and Shewanella (88 ± 8 mW/m2) biofilms individually. The co-cultured biofilms could perform near the highest power density for a longer duration than the iron mine soil biofilms could. High-throughput 16S rRNA gene sequencing of the biofilms on the anode indicated that the relative abundance of Pelobacteraceae in the co-culture system was significantly (p = 0.02) increased, while that of Rhodocyclaceae was significantly (p = 0.008) decreased, compared with that in iron mine soil biofilms. After continuing the experiment for two months, the presence of Shewanella oneidensis MR-1 changed the predominant bacteria of the microbial community in the biofilms, and the relative abundance of Shewanella was significantly (p = 0.02) decreased to a level similar to that in iron mine soil. These results demonstrate that Shewanella oneidensis MR-1 could improve the performance of iron mine soil biofilms in electrochemical systems by altering the composition of the functional microbial communities.
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(This article belongs to the Section Biofilm)
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Open AccessArticle
Nitrogen Fertilization Effects on Soil Bacterial Communities, Nitrogen-Cycling Genes, and Wheat Yield Across Different Soil Types in the North China Plain
by
Geng Ma, Xiaoyan Zhang, Xiaojie Han, Juan Kang, Haiyan Zhang, Yanfei Zhang, Hongfang Lu, Yingxin Xie, Dongyun Ma and Chenyang Wang
Microorganisms 2025, 13(10), 2382; https://doi.org/10.3390/microorganisms13102382 - 15 Oct 2025
Abstract
Nitrogen (N) fertilization is known to influence soil microbial communities and crop yield, but how N affects the bacterial community and the link to crop yield across different soil types remains poorly understood. Here, we conducted three 5-year stationary field experiments to explore
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Nitrogen (N) fertilization is known to influence soil microbial communities and crop yield, but how N affects the bacterial community and the link to crop yield across different soil types remains poorly understood. Here, we conducted three 5-year stationary field experiments to explore the effect of N fertilization (0, 180, 240, and 300 kg ha−1; termed N0, N1, N2, and N3, respectively) with different soil types (fluvo-aquic soil, FS; sandy soil, SS; lime concretion black soil, BS) on bacterial communities and the relationships among soil, microbes, and N-cycling functional genes to further investigate the effects on wheat yield. The results showed that the N2 treatment (240 kg ha−1) achieved the highest wheat yield, with significantly lower yields in SS than those in FS and BS. N fertilization significantly altered soil physicochemical properties, with a notable decrease in pH, particularly in SS, and an increase in NO3−-N content. Bacterial α-diversity significantly decreased with N application in SS but not in FS and BS, and NO3−-N played a primary role in shaping beta diversity in FS and BS. There were 43, 62, and 11 bacterial species that changed significantly from phylum to genus in the FS, SS, and BS, respectively. The abundance of nitrification genes increased with N fertilization in FS and SS, and N-cycling genes were significantly associated with soil properties. Partial Least Squares Path Modeling (PLS-PM) revealed that N fertilizer affected soil properties, which in turn regulated bacterial communities, and ultimately influenced wheat yield, explaining 67.4% of the yield variation. This study highlights the soil-specific responses to N application, providing a basis for optimizing N management and enhancing agricultural sustainability.
Full article
(This article belongs to the Section Plant Microbe Interactions)
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Molecular Characterization of ‘Candidatus Liberibacter Asiaticus’ Strains from Commercial Citrus-Growing Regions in Cuba Using Polymorphic Regions
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Camilo Paredes-Tomás, Maritza Luis-Pantoja, Miguel Ramos-Leal, Marialea Melle and Assunta Bertaccini
Microorganisms 2025, 13(10), 2381; https://doi.org/10.3390/microorganisms13102381 - 15 Oct 2025
Abstract
Studies of the genetic diversity of ‘Candidatus Liberibacter asiaticus’ strains based on housekeeping genes have been unsuccessful. The increasing availability of complete genome sequences of several strains from different countries has allowed the identification of regions having greater variability, which have been
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Studies of the genetic diversity of ‘Candidatus Liberibacter asiaticus’ strains based on housekeeping genes have been unsuccessful. The increasing availability of complete genome sequences of several strains from different countries has allowed the identification of regions having greater variability, which have been successfully implemented for the bacterium characterization, including microsatellites, genes of prophage origin, and miniature transposable elements with inverted-repeats (MITEs). In the present work, the genetic structure of 147 ‘Ca. L. asiaticus’ strains from nine provinces of Cuba were investigated using two polymorphic regions, consisting of typing for prophages and MITEs. The results showed an important level of coexistence of type 1 and 2 prophages in the Cuban strains, while the type 3 prophage was not detected. Likewise, a high rate of co-occurrence of both types of MITEs (MCLas-A and -B) was also observed. However, the MITE MCLas-A was detected only in its empty form. The double-locus analysis allowed the identification of eight genotypes. Out of these, seven genotypes were present in the Western region, which constitutes the region with the highest genetic variability. This is the first report of a genetic characterization of Cuban strains of ‘Ca. L. asiaticus’ with polymorphic markers in orchards growing in commercial citrus regions.
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(This article belongs to the Section Molecular Microbiology and Immunology)
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Open AccessArticle
Neurotoxicity and Intestinal Microbiota Dysbiosis in the Chinese Mitten Crab (Eriocheir sinensis) Induced by Anatoxin-a: A Microbiota–Intestine–Brain Axis Perspective
by
Huixia Feng, Shengyu Hu, Zihao Song, Ziqi Lin, Kai Zhang, Xianhui Ning, Cong Zhang and Shaowu Yin
Microorganisms 2025, 13(10), 2380; https://doi.org/10.3390/microorganisms13102380 - 15 Oct 2025
Abstract
Anatoxin-a (ANTX-a), a potent neurotoxin produced by various cyanobacterial species, poses a serious threat to aquatic organisms. This study investigated the neurotoxicity of ANTX-a on juvenile Chinese mitten crab (Eriocheir sinensis). Different from previous studies on vertebrate models or fish liver
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Anatoxin-a (ANTX-a), a potent neurotoxin produced by various cyanobacterial species, poses a serious threat to aquatic organisms. This study investigated the neurotoxicity of ANTX-a on juvenile Chinese mitten crab (Eriocheir sinensis). Different from previous studies on vertebrate models or fish liver toxicity, we focused on the microbiota–intestine–brain axis. Results demonstrated that ANTX-a exposure induced significant neurotoxicity, marked by the upregulation of apoptosis-related genes and disruption of neurotransmitter homeostasis. Transcriptomic analysis of thoracic ganglia revealed significant dysregulation of metabolic pathways, characterized by upregulated histidine metabolism (elevated histidine decarboxylase-like) and downregulated lipid metabolism (suppressed sphingomyelin phosphodiesterase-like). Additionally, increased intestinal histamine levels and elevated serum diamine oxidase activity indicated intestinal barrier damage. Intestinal microbiota analysis revealed that the abundance of nerve-related bacteria Tyzzerella and Clostridium sensu stricto 1 changed significantly. In summary, these findings indicate that ANTX-a induced neurotoxicity by affecting neurotransmitter systems and gut health, implicating the microbiota–intestine–brain axis. The results underscore the role of microbiota–intestine–brain communication in cyanotoxin toxicity within aquatic invertebrates and provide new insights into the ecotoxicological risks of cyanobacterial blooms in aquatic invertebrates.
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(This article belongs to the Section Microbiomes)
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Open AccessArticle
Continuous Circulation of Hepatitis E and A Viruses During COVID-19 Pandemic Lockdowns in Munich, Germany—Experience from Three Years of Wastewater Surveillance
by
Jasmin Javanmardi, Mathias Schemmerer, Karina Wallrafen-Sam, Jessica Neusser, Raquel Rubio-Acero, Michael Hoelscher, Thomas Kletke, Bernhard Boehm, Michael Schneider, Elisabeth Waldeck, Martin Hoch, Merle M. Böhmer, Christof Geldmacher, Jan Hasenauer, Jürgen J. Wenzel and Andreas Wieser
Microorganisms 2025, 13(10), 2379; https://doi.org/10.3390/microorganisms13102379 - 15 Oct 2025
Abstract
The COVID-19 pandemic has increased interest in wastewater-based epidemiology (WBE) as a reliable and cost-effective framework for monitoring the spread of microbes. However, WBE frameworks have rarely been applied to the study of fecal–oral transmissible diseases, except for poliomyelitis. Here, we investigated the
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The COVID-19 pandemic has increased interest in wastewater-based epidemiology (WBE) as a reliable and cost-effective framework for monitoring the spread of microbes. However, WBE frameworks have rarely been applied to the study of fecal–oral transmissible diseases, except for poliomyelitis. Here, we investigated the presence of hepatitis A virus (HAV) and hepatitis E virus (HEV) in wastewater in Munich. We collected wastewater samples between July 2020 and November 2023. A total of 186 samples were processed using centrifugation and analyzed for HAV- and HEV-RNA using RT-qPCR. As a reference, we used notification data from clinically or laboratory-diagnosed hepatitis A and E cases. Lockdown stringency levels were derived from official documentation. Our results show that 87.6% of wastewater samples were positive for HEV at concentrations of 9.0 × 101 to 2.5 × 105 copies/L, while HAV was only detectable in 7.5% of the samples at viral loads of 4.6 × 101 to 2.4 × 103 copies/L. We also detected differences in HEV concentrations but not in case numbers when comparing lockdown and no-lockdown periods. This study covers all but the first lockdowns in Bavaria. We present a unique real-world dataset evaluating the impact of lockdown interventions on hepatitis A and E case numbers, as well as on the concentrations of HAV and HEV in wastewater. Person-to-person spread and eating out appear to have contributed to the transmission of HEV. In addition, the consistently high HEV concentrations in sewage support the findings of serological studies, indicating a substantial burden of undetected subclinical infections.
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(This article belongs to the Special Issue Surveillance of Health-Relevant Pathogens Employing Wastewater)
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Open AccessReview
Preharvest Control of Campylobacter Colonization in Chickens, with a Special Emphasis on Vaccination Strategies
by
Chaitanya Gottapu, Lekshmi K. Edison, Gary D. Butcher and Subhashinie Kariyawasam
Microorganisms 2025, 13(10), 2378; https://doi.org/10.3390/microorganisms13102378 - 15 Oct 2025
Abstract
Campylobacter is a leading cause of human gastroenteritis, with poultry serving as the primary reservoir host. Effective preharvest control strategies are crucial for preventing or reducing Campylobacter contamination on meat surfaces. As concerns grow regarding the use of antimicrobials in animal agriculture, the
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Campylobacter is a leading cause of human gastroenteritis, with poultry serving as the primary reservoir host. Effective preharvest control strategies are crucial for preventing or reducing Campylobacter contamination on meat surfaces. As concerns grow regarding the use of antimicrobials in animal agriculture, the importance of non-antimicrobial preharvest strategies in poultry production has become increasingly significant. This comprehensive review focuses on the biology of Campylobacter, its impact on public health, and current and emerging preharvest strategies, with a special emphasis on vaccination. Preharvest strategies are broadly classified into biosecurity measures, gut microbiota modifications using prebiotics, probiotics, postbiotics, feed additives, and vaccination. While some vaccines have proven to be effective in research settings, no commercial vaccines are currently available. Because no single strategy can effectively combat Campylobacter, integrating multiple approaches, such as improved biosecurity measures, immunization, and dietary modifications, may provide a solution for reducing Campylobacter loads in poultry. Embracing a “One Health” approach, gaining a deeper understanding of Campylobacter pathophysiology, advancing vaccine technology, and implementing holistic farm management practices will be essential for the sustainable control of Campylobacter and for reducing the risk of human campylobacteriosis.
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(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)
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Open AccessArticle
Rumen-Protected Leucine Improved Growth Performance of Fattening Sheep by Changing Rumen Fermentation Patterns
by
Shu Li, Jiantao Zhao, Peng Zhang, Shaoyang Pang, Mingyu Ma, Yifan Nie, Zhenzi Xu, Sijin Li, Yuanyuan Li and Wenju Zhang
Microorganisms 2025, 13(10), 2377; https://doi.org/10.3390/microorganisms13102377 - 15 Oct 2025
Abstract
This experiment investigated the effects of rumen-protected leucine (RP-Leu) supplementation on growth performance, rumen fermentation parameters, and rumen microbiota of fattening sheep. Forty fattening sheep (19.03 ± 0.38 kg) were randomly divided into four groups. The four groups were fed the basal diet
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This experiment investigated the effects of rumen-protected leucine (RP-Leu) supplementation on growth performance, rumen fermentation parameters, and rumen microbiota of fattening sheep. Forty fattening sheep (19.03 ± 0.38 kg) were randomly divided into four groups. The four groups were fed the basal diet supplemented with RP-Leu at 0 (L-0), 0.5 (L-0.5), 1.0 (L-1.0), or 1.5 (L-1.5) g/d. The experimental period lasted 67 d. The results demonstrated that compared with the L-0 group, the L-1.0 and L-1.5 groups significantly increased the average daily gain (ADG) by 22.2% and 18.0%, respectively (p < 0.05), and reduced the feed-to-gain ratio (F:G ratio) by 20.0% and 13.4% (p < 0.05); the L-1.5 group significantly increased the concentrations of propionate and isovalerate (p < 0.05) and significantly decreased the acetate to propionate ratio (A:P) by 25.7% (p < 0.05); and the L-1.0 group significantly decreased the concentrations of free branched-chain amino acids (BCAAs) in rumen (p < 0.05). A microbiota analysis showed that RP-Leu enriched the abundance of fiber-degrading bacteria. A correlation analysis showed that acetic acid and A:P were positively correlated with norank_f_F082 and norank_f_UCG-011 (p < 0.05). Phenylalanine, isoleucine, valine, and leucine were negatively correlated with norank_o_Bacteroidales (p < 0.05). In conclusion, RP-Leu improved the growth performance of fattening sheep by changing the rumen fermentation parameters and patterns; the optimal supplementation level is 1.0 g/d.
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(This article belongs to the Section Gut Microbiota)
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Open AccessReview
History and Evolution of the Hypervirulent Clostridioides difficile Ribotype 027 Lineage
by
Isabella A. Tickler, Richard V. Goering and Fred C. Tenover
Microorganisms 2025, 13(10), 2376; https://doi.org/10.3390/microorganisms13102376 - 15 Oct 2025
Abstract
Clostridioides difficile was first identified in 1935 and subsequently emerged over the next several decades as the predominant bacterial cause of healthcare-associated gastrointestinal infections, placing a significant burden on healthcare systems worldwide. A major driver of the rapid rise in the incidence of
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Clostridioides difficile was first identified in 1935 and subsequently emerged over the next several decades as the predominant bacterial cause of healthcare-associated gastrointestinal infections, placing a significant burden on healthcare systems worldwide. A major driver of the rapid rise in the incidence of C. difficile infection (CDI) was the emergence and spread of a hypervirulent strain, which became known as PCR ribotype 027 (RT027). The C. difficile RT027 strain produced not just the typical toxin A and toxin B virulence factors but also expressed a third toxin called binary toxin that enhanced pathogenicity. Interestingly, the C. difficile RT027 strain apparently emerged at least twice in geographically distinct areas. The two lineages can be differentiated by their resistance or susceptibility to fluoroquinolones. Other ribotypes of C. difficile that also express binary toxin have emerged recently, some of which are highly related genetically to RT027. The aim of this study is to integrate genomic data and published literature to clarify the emergence, divergence, and apparent decline of C. difficile RT027.
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(This article belongs to the Section Antimicrobial Agents and Resistance)
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Open AccessArticle
Sodium Butyrate Supplementation in Whole Milk Modulates the Gastrointestinal Microbiota Without Altering the Resistome and Virulome in Preweaned Calves
by
Liwen Xing, Song Niu, Donglin Wu, Zhanghe Zhang and Ming Xu
Microorganisms 2025, 13(10), 2375; https://doi.org/10.3390/microorganisms13102375 - 15 Oct 2025
Abstract
This study investigated the effects of supplementing whole milk (WM) with sodium butyrate (SB) on the gastrointestinal microbiota of preweaned calves. Twelve newborn Holstein calves (4 days old, 39.21 ± 1.45 kg) were randomly assigned into one of two dietary treatments: (1) WM
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This study investigated the effects of supplementing whole milk (WM) with sodium butyrate (SB) on the gastrointestinal microbiota of preweaned calves. Twelve newborn Holstein calves (4 days old, 39.21 ± 1.45 kg) were randomly assigned into one of two dietary treatments: (1) WM without SB (CON) and (2) WM supplemented with SB (8.8 g/d; SB). At 74 days of age, all calves were slaughtered to collect ruminal and cecal digesta. Metagenomic analysis was used to characterize the microbial composition, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs). SB supplementation altered the ruminal microbial composition and increased the abundance of beneficial bacteria, including Actinobacteria, Bifidobacterium, and Olsenella (p < 0.05). Although SB did not significantly affect the overall microbial composition or diversity in the cecum (p > 0.05), it promoted the growth of beneficial genera such as Flavonifractor and Subdoligranulum (p < 0.05). Furthermore, SB supplementation did not significantly alter the composition of VFGs or ARGs in either the rumen or the cecum (p > 0.05). However, significant differences in VFGs and ARGs were observed between the rumen and the cecum, with a greater diversity of both VFGs and ARGs detected in the cecum compared to that in the rumen (p < 0.05). In summary, supplementing whole milk with sodium butyrate modulates gastrointestinal health in preweaned calves by favorably shaping the microbial community without significantly altering the antibiotic resistome or virulome.
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(This article belongs to the Section Gut Microbiota)
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Open AccessReview
Role of IFN-γ from Different Immune Cells in Chlamydia Infection
by
Xuan Chen, Wenjing Yang, Yuchen Hu, Yang Zhou and Zhou Zhou
Microorganisms 2025, 13(10), 2374; https://doi.org/10.3390/microorganisms13102374 - 15 Oct 2025
Abstract
Chlamydia invades multiple mucosal tissues in humans and animals. The body’s first line of defense against chlamydial infection is provided by innate immunity, whereas adaptive immunity plays a crucial role in managing the infection’s progression and preparing the immune system to combat reinfection.
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Chlamydia invades multiple mucosal tissues in humans and animals. The body’s first line of defense against chlamydial infection is provided by innate immunity, whereas adaptive immunity plays a crucial role in managing the infection’s progression and preparing the immune system to combat reinfection. Host resistance to chlamydial infection necessitates a coordinated effort between innate and adaptive immune cells. Numerous cell types are capable of producing interferon gamma (IFN-γ) as a defense mechanism against chlamydial infection, thereby effectively mediating the clearance of infection. However, the distinct roles of various immune cell populations in responding to chlamydial infection, as well as their functions during infection progression, remain poorly understood. Therefore, we will discuss the various roles of IFN-γ released by different immune cells in chlamydial infection, focusing primarily on experimental animal models and a review of available data from in vivo cellular immunological studies in humans.
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(This article belongs to the Section Molecular Microbiology and Immunology)
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