Microorganisms

15 pages, 2002 KB

Open AccessArticle

Tissue Expression of NGF in Skin Lesions of HIV-Coinfected and Non-Coinfected Leprosy Patients and Its Relationship with Leprosy Neural Damage

by Marília Brasil Xavier, Lucas dos Santos Fontes, Mariana Garcia Borges do Nascimento, Simone Rodrigues dos Passos, Débora Pinheiro Xavier, Larissa dos Santos Alcantara, Elza Baía de Brito, Cláudia Maria de Castro Gomes and Carlos Eduardo Pereira Corbett

Microorganisms 2025, 13(10), 2271; https://doi.org/10.3390/microorganisms13102271 (registering DOI) - 27 Sep 2025

Abstract

Leprosy remains a significant public health issue, particularly due to its neuropathic consequences, which affect sensory, motor, and autonomic functions, leading to severe disabilities. HIV/AIDS, another major public health concern, overlaps geographically with leprosy and is also associated with peripheral neuropathies, complicating the [...] Read more.

Leprosy remains a significant public health issue, particularly due to its neuropathic consequences, which affect sensory, motor, and autonomic functions, leading to severe disabilities. HIV/AIDS, another major public health concern, overlaps geographically with leprosy and is also associated with peripheral neuropathies, complicating the management of co-infected patients. Understanding how Nerve Growth Factor (NGF) is regulated in leprosy and HIV-leprosy co-infection may contribute to immunomodulatory treatments and neuroimmune response control. A cross-sectional study evaluated NGF tissue expression using immunohistochemistry in 47 HIV/leprosy co-infected patients and 61 leprosy-only patients. The co-infected group had a higher incidence of neuritis (40.4%) and a prevalence of exclusively reversal reactions. However, the occurrence of neuritis was not associated with higher expression of NGF in the tissue. Leprosy reactions were more prevalent in non-co-infected patients with multibacillary forms (50%). Multibacillary forms in both groups of patients showed higher cellular expression of NGF, with a greater tendency for higher NGF expression in non-co-infected multibacillary patients (p = 0.0021), suggesting impairment in the immune response involved in the tissue expression of neurotrophins in the co-infected group. Overall, co-infection with HIV did not influence the increase in NGF in the lesions of leprosy patients compared with patients with leprosy alone. Full article

(This article belongs to the Special Issue Mycobacterium leprae, Mycobacterium lepromatosis and Leprosy Studies)

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25 pages, 1378 KB

Open AccessReview

Microbial Keratinolysis: Eco-Friendly Valorisation of Keratinous Waste into Functional Peptides

by Lindelwa Mpaka, Nonso E. Nnolim and Uchechukwu U. Nwodo

Microorganisms 2025, 13(10), 2270; https://doi.org/10.3390/microorganisms13102270 (registering DOI) - 27 Sep 2025

Abstract

Keratinous wastes, generated from various industries such as poultry processing, slaughterhouses, and salons, accumulate in the environment due to their slow degradation caused by high disulfide cysteine bonds. Traditional methods of managing these wastes, including incineration, composting, open-air burning, and landfilling, have several [...] Read more.

Keratinous wastes, generated from various industries such as poultry processing, slaughterhouses, and salons, accumulate in the environment due to their slow degradation caused by high disulfide cysteine bonds. Traditional methods of managing these wastes, including incineration, composting, open-air burning, and landfilling, have several disadvantages, such as environmental pollution, release of toxic compounds, and breeding of pathogenic and multidrug-resistant microorganisms. Microbial keratinases, produced by bacteria, fungi, and actinomycetes, offer an eco-friendly alternative for valorizing keratinous waste into valuable peptides and amino acids. The biodegradation of keratinous biomass involves four sequential steps: adhesion, colonization, production of keratinolytic enzymes, and breakdown of the keratin substrate. Optimization of culture conditions, such as pH, temperature, substrate concentration, and metal ions, can enhance keratinase production for industrial applications. Keratinases have multifaceted applications in various sectors, including cosmetics, organic fertilizers, leather treatment, animal feed, detergents, and pharmaceuticals. This review highlights the need to explore keratinolytic strains further and improve keratinase yields to develop sustainable solutions for keratinous waste management and generate value-added products, promoting a circular economy. The techno-economic considerations and current limitations in industrial-scale keratinase production are also discussed, emphasizing the importance of future research in this field. Full article

(This article belongs to the Special Issue Microbial Biotechnological Application for Metabolite Bioprocesses)

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20 pages, 9906 KB

Open AccessArticle

It’s a Question at the ‘Root’ of the Problem: Fungal Associations of Dionaea muscipula (Venus’ Flytrap) Roots in Its Native Habitat

by Anna A. Carnaggio and Michelle M. Barthet

Microorganisms 2025, 13(10), 2269; https://doi.org/10.3390/microorganisms13102269 (registering DOI) - 27 Sep 2025

Abstract

Carnivorous plants survive in harsh habitats with limited nutrients and a low pH. Much focus has been placed on carnivorous trap evolution as the primary mechanism to increase nutrient acquisition through insect digestion. Soil microbiome, however, may also play a pertinent role in [...] Read more.

Carnivorous plants survive in harsh habitats with limited nutrients and a low pH. Much focus has been placed on carnivorous trap evolution as the primary mechanism to increase nutrient acquisition through insect digestion. Soil microbiome, however, may also play a pertinent role in nutrient acquisition influencing plant vigor and overall success. Dionaea muscipula, commonly known as the Venus’ flytrap, is endemic to rims of the Carolina Bays located in southeast North Carolina and northeast South Carolina, where D. muscipula survives in nutrient poor soils with a vestigial root system. We utilized a combination of microscopy, plating, and metagenomics, to investigate the presence/absence of fungal partners that may contribute to success and vigor of D. muscipula in its native habitat in order to further conservation of this carnivorous plant. Results support that D. muscipula forms both mycorrhizal and fungal endophytic associations, most likely to aid nutrient uptake from otherwise nutrient-poor soils, as well as aid in stress defense. Several ectomycorrhizal, endophytic, and saprophytic fungal species were identified from the surrounding rhizosphere of D. muscipula roots presenting a first glimpse into fungal communities that may influence D. muscipula physiology and compose the microbiome of the Carolina Bays ecosystem. Full article

(This article belongs to the Section Environmental Microbiology)

14 pages, 1621 KB

Open AccessArticle

Long-Term Sewage Survey of SARS-CoV-2, Influenza A and Respiratory Syncytial Virus (RSV), and Correlation to Human Cases in a City with One Million Inhabitants

by Nathalie Wurtz, Lea Maggiore, Céline Boschi, Alexandre Annessi, Franck Berges, Alexandre Lacoste, Herve Chaudet, Philippe Colson, Bernard La Scola and Sarah Aherfi

Microorganisms 2025, 13(10), 2268; https://doi.org/10.3390/microorganisms13102268 (registering DOI) - 27 Sep 2025

Abstract

Wastewater-based epidemiology is a robust, scalable, cost-effective, and high-performing tool to monitor and predict SARS-CoV-2 trends. We aimed to investigate whether this approach could be applied to influenza A/B viruses and respiratory syncytial virus (RSV) in Marseille, southern France. Wastewater concentrations of SARS-CoV-2, [...] Read more.

Wastewater-based epidemiology is a robust, scalable, cost-effective, and high-performing tool to monitor and predict SARS-CoV-2 trends. We aimed to investigate whether this approach could be applied to influenza A/B viruses and respiratory syncytial virus (RSV) in Marseille, southern France. Wastewater concentrations of SARS-CoV-2, influenza A/B viruses, and RSV in Marseille were monitored by qPCR between January 2021 and October 2024. These concentrations were compared with the diagnosis numbers for the three viruses collected at public hospitals in Marseille, using cross-correlation analyses. The Granger causality test was used to determine whether wastewater concentrations can predict the number of clinical cases. SARS-CoV-2 and influenza virus concentrations in wastewater preceded the rise in the incidence of patient diagnoses by a lag of five days and nine/ten days, respectively. In contrast, for RSV, the rise in incidence of clinical cases preceded that of wastewater concentrations. We conclude that wastewater-based epidemiology is a powerful tool to monitor the level of circulation of these viruses independently of tests carried out on people. It enables earlier alerts than monitoring patients for SARS-CoV-2 and influenza symptoms. However, for RSV, it does not provide an early warning, and clinical data-based surveillance appears to be more suitable. Full article

(This article belongs to the Special Issue Surveillance of SARS-CoV-2 Employing Wastewater)

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9 pages, 358 KB

Open AccessCommunication

Short Communication: Evaluation of MALDI-TOF and Sequencing Technique as Typing Tools for Enterobacteriaceae Bacteria from Raw Milk of Dairy Cows with Subclinical Mastitis

by Ntelekwane George Khasapane

Microorganisms 2025, 13(10), 2267; https://doi.org/10.3390/microorganisms13102267 (registering DOI) - 27 Sep 2025

Abstract

Subclinical mastitis is an udder infection and inflammation in dairy animals that causes no visible changes in the milk or udder, making it hard to detect. Animal welfare and health are negatively impacted by dairy cow mastitis, which also severely impairs the dairy [...] Read more.

Subclinical mastitis is an udder infection and inflammation in dairy animals that causes no visible changes in the milk or udder, making it hard to detect. Animal welfare and health are negatively impacted by dairy cow mastitis, which also severely impairs the dairy industry’s financial standing. This study was carried out in the three local Municipalities of Free State Province, South Africa, sought to determine bacterial contamination of raw milk of cows infected with subclinical mastitis using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA Sanger sequencing. From subclinical mastitic samples, our MALDI-TOF results revealed coliform bacteria such as Pseudomonas oryzihabitans with 25/71 (32.21%) as a dominant species, followed by Pseudomonas aeruginosa, Escherichia coli, Pantoea agglomerans and Enterobacter kobei at 9/71 (12.67%), 8/71 (11.27%), 6/71 (8.45%) and 6/71 (8.45%), respectively. Finally, Enterococcus faecalis, Enterococcus faecium, Micrococcus luteus, Routella ornithinolytica were detected at 3/71 (4.22%) each and 1 sample with mixed species of Routella platicola 1/71 (1.40%) and Routella ornithinolytica at 1/71 (1.40%). The most frequent microbes causing dairy cow mastitis can be identified using MALDI-TOF MS, a technique that is strong, quick, and accurate. With the inclusion of new species, the database can be enhanced and expanded over time. Full article

(This article belongs to the Special Issue Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogenic Microorganisms, 3rd Edition)

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14 pages, 426 KB

Open AccessArticle

Long-Term Safety of Anti-COVID-19 mRNA Vaccines in Patients with Systemic Lupus Erythematosus and Lupus-like Diseases with a Previous History of Myocarditis

by Giovanni Benanti, Marta Secci, Andrea Villatore, Sara Angiulli, Chiara Calabrese, Gabriele Domenico Gallina, Veronica Batani, Giacomo De Luca, Corrado Campochiaro, Giuseppe Pizzetti, Giovanni Peretto, Simone Sala, Enrica P. Bozzolo, Luca Moroni, Marco Matucci-Cerinic, Giuseppe A. Ramirez and Lorenzo Dagna

Microorganisms 2025, 13(10), 2266; https://doi.org/10.3390/microorganisms13102266 - 26 Sep 2025

Abstract

Non-viral myocarditis is rare but relatively more frequent in patients with systemic autoimmune diseases (such as systemic lupus erythematosus, SLE, and allied conditions) than in the general population. In rare cases, mRNA-based vaccines can also trigger non-viral myocarditis. Limited data are available about [...] Read more.

Non-viral myocarditis is rare but relatively more frequent in patients with systemic autoimmune diseases (such as systemic lupus erythematosus, SLE, and allied conditions) than in the general population. In rare cases, mRNA-based vaccines can also trigger non-viral myocarditis. Limited data are available about the cardiac safety of mRNA vaccines in this subset of patients. Here, we report data from a third-level hospital on long-term safety, leveraging on a previously described cohort of 13 consecutive patients with SLE, Undifferentiated (UCTD) and Mixed Connective Tissue disease (MCTD), and a history of myocarditis, who had received anti-COVID-19 vaccination between April 2021 and January 2022. Demographics and clinical data (including validated clinometric for SLE) were collected at baseline, at the first available visit following the primary vaccination cycle, after an additional 12 months, and at the last available follow-up after at least 36 months. Twelve patients, seven females, ten with SLE, one MCTD, and one UCTD, had a median follow-up of 41 (35–45) months. One patient was lost at follow-up. No disease flare or sign of myocarditis recurrence were observed. At last visit, all patients were in a low disease activity state (LLDAS), and all but one were in remission, according to the Definition of Remission in SLE (DORIS) criteria. No significant variations in disease activity or damage accrual nor in markers of inflammation and myocardial injury were observed. Our data suggest that mRNA-based anti-COVID-19 vaccines in patients with previous autoimmune myocarditis in the context of SLE and allied conditions have a good long-term safety profile. Full article

(This article belongs to the Special Issue SARS-CoV-2: Infection, Transmission, and Prevention)

25 pages, 2015 KB

Open AccessArticle

Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam

by Minh Duc Hoang, Pham Thi Lanh, Vu Thi Hien, Cheng-Yen Kao and Dong Van Quyen

Microorganisms 2025, 13(10), 2265; https://doi.org/10.3390/microorganisms13102265 - 26 Sep 2025

Abstract

Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), represents a major threat to poultry production, leading to significant mortality and economic losses. This study aimed to characterize an APEC strain, HPVN24, isolated from diarrheic chickens at a farm in Hai Phong, Vietnam. The [...] Read more.

Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), represents a major threat to poultry production, leading to significant mortality and economic losses. This study aimed to characterize an APEC strain, HPVN24, isolated from diarrheic chickens at a farm in Hai Phong, Vietnam. The strain was investigated through phenotypic assays, antibiotic susceptibility profiling, and whole-genome sequencing using the Illumina platform. HPVN24 exhibited β-hemolytic activity and resistance to trimethoprim, ampicillin, and ciprofloxacin. Whole-genome analysis identified the strain as serotype O78:H9 and sequence type ST23, with a genome size of 5.05 Mb and a GC content of 50.57%. Genome annotation revealed a wide repertoire of genes involved in metabolism, secretion systems, virulence, and biofilm formation. Virulence-associated genes included those related to adhesion, iron acquisition, hemolysin production, and stress response. Analysis predicted multidrug resistance to 18 antibiotic classes, with particularly strong resistance to fluoroquinolones. Phylogenetic comparison demonstrated that HPVN24 clustered closely with O78:H9 strains isolated from poultry in other regions, suggesting potential transmission across populations. These findings indicate that HPVN24 is a multidrug-resistant and highly virulent APEC strain linked to colibacillosis outbreaks in Vietnam and highlight the need for ongoing surveillance, judicious antibiotic usage, and alternative strategies to ensure poultry health and food safety. Full article

(This article belongs to the Special Issue Advancements in Pathogenic Bacteria: Detection, Genomic Analysis, and Antibiotic Resistance)

18 pages, 4846 KB

Open AccessArticle

Niche and Geographic Drivers Shape the Diversity and Composition of Endophytic Bacteria in Salt-Tolerant Peanut

by Xinying Song, Yucheng Chi, Xiaoyuan Chi, Na Chen, Manlin Xu, Xia Zhang, Zhiqing Guo, Kang He, Jing Yu and Ying Li

Microorganisms 2025, 13(10), 2264; https://doi.org/10.3390/microorganisms13102264 - 26 Sep 2025

Abstract

Endophytic bacteria play an important role in the growth, stress tolerance, and metabolic function of salt-tolerant peanuts, yet their community assembly across different saline–alkali soils and plant organs remains poorly characterized. In this study, the V3–V4 variable region of the endophytic bacteria 16S [...] Read more.

Endophytic bacteria play an important role in the growth, stress tolerance, and metabolic function of salt-tolerant peanuts, yet their community assembly across different saline–alkali soils and plant organs remains poorly characterized. In this study, the V3–V4 variable region of the endophytic bacteria 16S rRNA gene in three organs (roots, leaves, and pods) of high-oleic-acid peanut variety Huayu9118 from three saline–alkali locations (Xinjiang, Jilin, and Shandong, China) was analyzed by high-throughput sequencing. A total of 1,360,313 effective sequences yielded 19,449 amplicon sequence variants (ASVs), with Proteobacteria (45.86–84.62%), Bacteroidota (6.52–13.90%), and Actinobacteriota (3.97–10.87%) dominating all samples. Niche strongly influenced microbial diversity: the roots exhibited the highest level of richness (Chao 1/ACE indices), while the leaves showed the greatest diversity (Shannon/Simpson indices) in XJ samples. Significant compositional differences were observed between aerial (leaves) and underground (roots/pods) organs. Geographic location also markedly shaped endophytic communities, with stronger effects in roots and pods than in leaves—a pattern supported by PCoA combined with ANOSIM (R (roots) = 1, R (pods) = 0.874, R (leaves) = 0.336, respectively, p < 0.001). Saline–alkali adaptation led to a marked enrichment of Novosphingobium in roots and pods and of Halomonas in leaves compared to non-saline–alkali-grown peanuts. Furthermore, the endophytic communities within the same organ type varied significantly across the three saline–alkali sites. Redundancy analysis (RDA) identified the key environmental factors shaping bacterial community composition in the root samples from each location: available phosphorus (AP) and sulfate (SO₄²⁻) were the strongest predictors in XJ; available potassium (AK) and chloride (Cl⁻) in DY; and hydrolyzed nitrogen (HN), pH, soil organic matter (SOM), and bicarbonate (HCO₃⁻) in JL. These findings demonstrate that niches and geographical conditions determined the composition and relative abundance of endophytic bacteria in salt-tolerant peanuts, providing new insights into microbial ecological adaptation in saline–alkali ecosystems. Full article

(This article belongs to the Section Plant Microbe Interactions)

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8 pages, 1748 KB

Open AccessCase Report

Not a Dead-End Host: First Confirmed Persistent Microfilaremia in Human Dirofilaria repens Infection

by Martina Perešin Vranjković, Anamarija Vitko Havliček, Martina Kramar, Mirjana Balen Topić, David Beck, Daria Jurković Žilić, Ema Gagović and Relja Beck

Microorganisms 2025, 13(10), 2263; https://doi.org/10.3390/microorganisms13102263 - 26 Sep 2025

Abstract

We report the first confirmed case of persistent microfilaremia in a human host infected with Dirofilaria repens. A 54-year-old woman from an endemic area in Croatia presented with peripheral eosinophilia and dermatological symptoms. Over four months, microfilariae were repeatedly detected in her [...] Read more.

We report the first confirmed case of persistent microfilaremia in a human host infected with Dirofilaria repens. A 54-year-old woman from an endemic area in Croatia presented with peripheral eosinophilia and dermatological symptoms. Over four months, microfilariae were repeatedly detected in her blood using thick smears and Knott’s test, and the diagnosis was molecularly confirmed via COI gene sequencing and detection of Wolbachia endosymbionts. This case provides compelling evidence that D. repens can sustain a complete or near-complete life cycle in humans under specific conditions. Our findings have significant implications for clinical diagnostics, One Health surveillance, and public health interventions. Full article

(This article belongs to the Special Issue One Health Research on Infectious Diseases)

15 pages, 801 KB

Open AccessReview

Vascular Graft Infections Due to Listeria spp.: A Comprehensive Review of the Literature

by Tommaso Lupia, Marco Casarotto, Gianfranco Fonte, Saverio Marena, Francesca Paola Giunta, Fabrizio Buffolo, Silvia Corcione and Francesco Giuseppe De Rosa

Microorganisms 2025, 13(10), 2262; https://doi.org/10.3390/microorganisms13102262 - 26 Sep 2025

Abstract

Vascular graft infections are rare but serious complications of vascular surgery. Listeria monocytogenes represents an exceedingly rare yet potentially life-threatening cause. We present a narrative review according to the Scale for the Assessment of Narrative Review Articles (SANRA) criteria, summarizing the existing literature [...] Read more.

Vascular graft infections are rare but serious complications of vascular surgery. Listeria monocytogenes represents an exceedingly rare yet potentially life-threatening cause. We present a narrative review according to the Scale for the Assessment of Narrative Review Articles (SANRA) criteria, summarizing the existing literature regarding Listeria vascular graft infections. Moreover, we have revised novel potential antibiotics against Listeria spp. A systematic search identified 23 studies involving 39 patients. Most infections affected abdominal aortic grafts (50%), with a median interval of 28 months from graft implantation to infection. Common comorbidities included hypertension (30.8%) and diabetes (18%), with 24% of patients being immunocompromised. Diagnosis was supported by blood cultures (45%) and imaging, particularly computed tomography (CT, 90%) and positron emission tomography CT (PET-CT) in selected cases. Surgical intervention was performed in 55% of patients, while 45% were treated medically. Ampicillin, often combined with an aminoglycoside, was the most common first-line therapy. Median treatment duration was 51 days, with some patients requiring lifelong suppressive antibiotic therapy. Mortality was low (one patient), and no recurrences were reported. This review underscores the diagnostic complexity and evolving management strategies in Listeria spp. vascular graft infections. Full article

(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance: Second Edition)

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9 pages, 2244 KB

Open AccessCommunication

Lactococcus lactis Strain Plasma Uniquely Induces IFN-α Production via Plasmacytoid Dendritic Cell Activation: A Comparative Study of Postbiotic Products

by Shigeru Fujimura, Masato Kawamura and Yurina Tamura

Microorganisms 2025, 13(10), 2261; https://doi.org/10.3390/microorganisms13102261 - 26 Sep 2025

Abstract

Postbiotics are increasingly incorporated into functional foods and supplements due to their potential health benefits, particularly immune modulation. However, the mechanisms by which these products influence antiviral immunity remain incompletely understood. Type I interferons, especially interferon-α (IFN-α), are central mediators of early antiviral [...] Read more.

Postbiotics are increasingly incorporated into functional foods and supplements due to their potential health benefits, particularly immune modulation. However, the mechanisms by which these products influence antiviral immunity remain incompletely understood. Type I interferons, especially interferon-α (IFN-α), are central mediators of early antiviral defense, acting primarily through the activation of plasmacytoid dendritic cells (pDCs). Five commercially available postbiotic products containing heat-killed bacterial strains were evaluated for their ability to stimulate pDCs and induce IFN-α production. Bacterial uptake by pDCs was analyzed using confocal microscopy with Z-stack imaging, and IFN-α levels were quantified by ELISA. Among the tested strains, only Lactococcus lactis strain Plasma (LC-Plasma) demonstrated significant internalization by pDCs and induced measurable IFN-α production (73.8 ± 2.5 pg/mL) at the recommended daily dose. This effect was not observed with other strains, even at higher bacterial loads (up to 1 × 10¹¹ cells). Z-stack imaging confirmed that LC-Plasma was actively phagocytosed by pDCs, whereas other strains, such as L. paracasei MCC1849, adhered to the cell surface without internalization. The pDC concentration used in the assay approximated physiological levels in human blood. Notably, the IFN-α level induced by LC-Plasma exceeded that reported in the serum of hospitalized COVID-19 patients. L. lactis strain Plasma uniquely activates pDCs and induces IFN-α production under physiologically relevant conditions, distinguishing it from other postbiotic strains. These findings suggest that LC-Plasma may serve as a functional postbiotic with the potential to enhance antiviral immunity and mitigate disease severity. Full article

(This article belongs to the Special Issue Clinical Applications and Validation of Probiotics: Exploring Therapeutic and Preventive Potential Across Diverse Medical Conditions)

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15 pages, 1336 KB

Open AccessArticle

Oenological Potential of Lachancea thermotolerans and Hanseniaspora uvarum from High-Sugar Musts: Impacts on Fermentation and Wine Volatilome

by María Trinidad Alcalá-Jiménez, Juan Carlos García-García, Juan Carlos Mauricio, Juan Moreno, Rafael A. Peinado and Teresa García-Martínez

Microorganisms 2025, 13(10), 2260; https://doi.org/10.3390/microorganisms13102260 - 26 Sep 2025

Abstract

Currently, there is little scientific data to support the importance of selecting non-Saccharomyces yeasts from different wineries in the Protected Designation of Origin (PDO) in Andalusia, southern Spain, and how this group of yeasts can affect the sensory properties of wine. Therefore, [...] Read more.

Currently, there is little scientific data to support the importance of selecting non-Saccharomyces yeasts from different wineries in the Protected Designation of Origin (PDO) in Andalusia, southern Spain, and how this group of yeasts can affect the sensory properties of wine. Therefore, this research aimed to study some specific microbiological properties and the metabolites they could produce in order to evaluate the oenological potential of two non-Saccharomyces yeast strains isolated from a region of Andalusia (Córdoba, Spain), Hanseniaspora uvarum TJ-27 and Lachancea thermotolerans T-9, isolated from musts with high sugar content. Of 80 yeast isolates selected, these two strains were chosen for their notable β-glucosidase activity (observed in up to 40% of isolates), cellulase activity (present in 24%), and killer phenotype (found in 40%). In this study, strains that displayed characteristics associated with aroma release were selected. Fermentation assays using a high-sugar synthetic medium revealed that neither H. uvarum TJ-27 nor L. thermotolerans T-9 was able to complete alcoholic fermentation independently, achieving ethanol yields of only 5–6% v/v, indicating the need for subsequent fermentation by Saccharomyces cerevisiae. The originality of this study provides insight into the metabolites contributed by these strains to the wines produced. The best results were obtained when both strains were inoculated together. Furthermore, volatilome analysis showed elevated levels of key compounds such as isoamyl alcohols and 2,3-butanediol. These findings highlight the practical potential of using selected non-Saccharomyces strains from Andalusia to improve fermentation results and wine quality. The novelty of this study lies mainly in confirmation within region-specific isolates. Full article

(This article belongs to the Section Food Microbiology)

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13 pages, 1955 KB

Open AccessArticle

Microbiological Safety of Donor Human Milk: Comparing Culture-Based Methods for Enterobacterales Detection

by Lena Dawczynski, Nora Helke Leder, Sabine Trommer, Frank Kipp and Claudia Stein

Microorganisms 2025, 13(10), 2259; https://doi.org/10.3390/microorganisms13102259 - 26 Sep 2025

Abstract

In neonatal care, donor human milk (DHM) is used when maternal milk is unavailable or insufficient. In several countries, including Germany, raw (i.e., unpasteurised) DHM is occasionally administered under specific clinical conditions. However, the lack of standardised, evidence-based microbiological testing protocols raises concerns [...] Read more.

In neonatal care, donor human milk (DHM) is used when maternal milk is unavailable or insufficient. In several countries, including Germany, raw (i.e., unpasteurised) DHM is occasionally administered under specific clinical conditions. However, the lack of standardised, evidence-based microbiological testing protocols raises concerns about the reliability of safety assessments for this high-risk patient group. The objective of this study was to assess the performance of four culture-based microbiological methods for detecting Enterobacterales in donor human milk, using both spiked samples and raw milk. We compared the detection limits of four culture-based microbiological methods, with and without enrichment, using spiked DHM samples and 93 raw DHM samples from a single donor (limited generalisation). Artificially inoculated samples contained defined concentrations of E. coli, K. pneumoniae, and S. ureilytica. Detection limits varied by several orders of magnitude (2.86 × 10² CFU/mL to 4.90 × 10⁰ CFU/mL). In real samples, enrichment-based methods detected Gram-negative pathogens in four out of ninety-three samples (three S. ureilytica, one P. juntendi); direct plating detected none. Increasing the sample volume and applying enrichment improved detection sensitivity. Whole-genome sequencing confirmed species identity and showed that the S. ureilytica isolates from a single donor were clonally related, indicating a recurring detection pattern and underscoring the need for longitudinal microbiological monitoring. In view of the new EU SoHO Regulation classifying DHM as a Substance of Human Origin, these findings highlight the urgent need for standardised, sensitive protocols to ensure neonatal safety. Full article

(This article belongs to the Special Issue Advances in Neonatal Pathogen Infection)

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18 pages, 4048 KB

Open AccessArticle

Isolation, Pathogenicity and Genomic Analysis of Mannheimia haemolytica Strain XJCJMh1 in Bovine-Mycoplasma Co-Infection

by Chengzhe Liang, Kashaf Kareem, Lichun Zhang, Yafei Liang, Huiying Wu, Beibei Li and Jinliang Sheng

Microorganisms 2025, 13(10), 2258; https://doi.org/10.3390/microorganisms13102258 - 26 Sep 2025

Abstract

Mixed infections of Mannheimia haemolytica and Mycoplasma bovis are relatively common in bovine respiratory diseases, presenting severe respiratory symptoms and high mortality that severely endanger the cattle industry. In this study, a serotype A1 strain of Mannheimia haemolytica, designated as XJCJMh1, was [...] Read more.

Mixed infections of Mannheimia haemolytica and Mycoplasma bovis are relatively common in bovine respiratory diseases, presenting severe respiratory symptoms and high mortality that severely endanger the cattle industry. In this study, a serotype A1 strain of Mannheimia haemolytica, designated as XJCJMh1, was isolated and identified from the lung tissue of a hybrid Simmental calf infected with Mycoplasma bovis. The pathogenicity of this strain was evaluated using Kunming mice as a model. The results indicated that infection with XJCJMh1 caused pathological manifestations such as pulmonary hemorrhage and edema in mice. Subsequently, the genome of this strain was sequenced and assembled using Illumina sequencing to obtain general genomic features. The genome was annotated and analyzed for gene functions using the Swiss-Prot, NR, GO, COG, KEGG, CAZy, TCDB, and Pfam databases. Additionally, the virulence factors and resistance genes of this strain were annotated using the PHI, VFDB, and CARD databases. The genome of Mannheimia haemolytica XJCJMh1 is 2,595,489 base pairs (bp) in length, with a GC content of 40.93%. Notably, this strain exhibits three distinct genomic islands and contains 98 effectors associated with the type III secretion system (T3SS). The XJCJMh1 strain harbors 74 virulence genes and 45 resistance genes. We annotated the proteins, genes, and associated GO and KEGG pathways of the XJCJMh1 strain; exploring the relationship between these annotations and the strain’s pathogenicity is of considerable value. This study is of great significance for clarifying the pathogenic mechanism and genetic characteristics of the Mannheimia haemolytica strain XJCJMh1 in cattle, and its results provide a scientific reference for analyzing the genomic basis of pathogenicity and drug resistance of Mannheimia haemolytica under co-infection conditions. Full article

(This article belongs to the Section Veterinary Microbiology)

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21 pages, 1658 KB

Open AccessArticle

Vancomycin-Resistant Enterococcus Colonisation in the Patients of a Regional Spinal Cord Injury Unit in Northwest England, United Kingdom: Our Experience with Non-Isolation of VRE Colonised Patients

by Vaidyanathan Subramanian, Bakulesh Madhusudan Soni, Gareth Derick Cummings, Sandra Croston, Kim Lucey, Ruth Hilton and Rachel Hincks

Microorganisms 2025, 13(10), 2257; https://doi.org/10.3390/microorganisms13102257 - 26 Sep 2025

Abstract

We reviewed vancomycin-resistant Enterococcus (VRE) colonisation of inpatients of a spinal cord injury centre. The centre consists of one single occupancy en suite room and ten multi-occupancy rooms where two to six patients stay in a cubicle. These patients share bathroom and toilet [...] Read more.

We reviewed vancomycin-resistant Enterococcus (VRE) colonisation of inpatients of a spinal cord injury centre. The centre consists of one single occupancy en suite room and ten multi-occupancy rooms where two to six patients stay in a cubicle. These patients share bathroom and toilet facilities. Active screening for VRE is performed by taking rectal swabs on admission of patients to the spinal unit. The patients, who are colonised with VRE, are not isolated due to constraints in resources. During a twelve-month period (April 2024 to April 2025), 33 patients tested positive for VRE. In April 2025, 17 of 40 in-patients tested positive for VRE. During the last six 12-month periods from 2019, the number of patients testing positive for VRE has shown an upward trend from 18 during 2019–2020 to 33 during 2024–2025. No patient developed systemic infection with VRE (blood stream infection, endocarditis, meningitis, intra-abdominal sepsis, infection of a spinal implant or baclofen pump) during the study period. Twelve patients underwent implantation of a baclofen pump during 2024–2025. No patient developed VRE infection from the implant. We believe that non-isolation of patients colonised with VRE may be a pragmatic approach in a resource-poor healthcare facility. It is possible that non-isolation could have contributed to an increase in the number of patients who became colonised with VRE. Attention should be paid to infection prevention measures including hand washing and environmental cleaning to prevent the spread of VRE colonisation of inpatients and VRE infection of at-risk patients, e.g., immune-compromised individuals. Full article

(This article belongs to the Special Issue Research on Relevant Clinical Infections: 2nd Edition)

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19 pages, 2101 KB

Open AccessArticle

Infantile Anemia and Iron Treatments Affect the Gut Microbiome of Young Rhesus Monkeys

by Christopher L. Coe, Gabriele R. Lubach, Wellington Z. Amaral, Gregory J. Phillips, Mark Lyte, Michael K. Georgieff, Raghavendra B. Rao and James R. Connor

Microorganisms 2025, 13(10), 2256; https://doi.org/10.3390/microorganisms13102256 - 26 Sep 2025

Abstract

The influence of iron deficiency anemia and iron treatments on the gut microbiome was evaluated in young rhesus monkeys. First, the hindgut bacterial profiles of 12 iron-deficient anemic infants were compared to those of 9 iron-sufficient infants at 6 months of age, a [...] Read more.

The influence of iron deficiency anemia and iron treatments on the gut microbiome was evaluated in young rhesus monkeys. First, the hindgut bacterial profiles of 12 iron-deficient anemic infants were compared to those of 9 iron-sufficient infants at 6 months of age, a time when the risk of anemia is high due to rapid growth. After this screening, the anemic monkeys were treated with either parenteral or enteral iron. Seven monkeys were injected intramuscularly with iron dextran, the typical weekly treatment used in veterinary practice. Four other anemic infants were treated with a novel oral supplement daily: yeast genetically modified to express ferritin. Fecal specimens were analyzed using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Bacterial species richness in anemic infants was not different from that of iron-sufficient infants, but beta diversity and LEfSe analyses of bacterial composition indicated that the microbiota profiles were associated with iron status. Both systemic and oral iron increased alpha and beta diversity metrics. The relative abundance of Ruminococcaceae and other Firmicutes shifted in the direction of an iron-sufficient host, but many different bacteria, including Mollicutes, Tenericutes, and Archaea, were also enriched. Collectively, the findings affirm the important influence of the host’s iron status on commensal bacteria in the gut and concur with clinical concerns about the possibility of adverse consequences after iron supplementation in low-resource settings where children may be carriers of iron-responsive bacterial pathogens. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 3rd Edition)

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18 pages, 8305 KB

Open AccessArticle

Characterization of Two Potential Biocontrol Bacillus Strains Against Maize Stalk Rot

by Zhiwei Feng, Mengyao Qin, Xiaobing Ma, Ruiyun Feng, Huifang Zhao, Yingchao Meng and Chunzhen Cheng

Microorganisms 2025, 13(10), 2255; https://doi.org/10.3390/microorganisms13102255 - 26 Sep 2025

Abstract

Maize stalk rot (MSR) is one of the most devastating fungal diseases affecting maize worldwide. In recent years, biological control agents have emerged as an environmentally friendly and highly attractive strategy for managing MSR. In this study, two Bacillus strains—B. subtilis KP3P9 [...] Read more.

Maize stalk rot (MSR) is one of the most devastating fungal diseases affecting maize worldwide. In recent years, biological control agents have emerged as an environmentally friendly and highly attractive strategy for managing MSR. In this study, two Bacillus strains—B. subtilis KP3P9 and B. siamensis K13C—were shown to effectively inhibit the growth of the MSR pathogen Fusarium graminearum in vitro. Pot experiments showed that inoculation with KP3P9 significantly increased plant height, stem width, above-ground part fresh weight, and total plant fresh weight, whereas K13C significantly improved the stem width and under-ground part fresh weight of maize seedlings (p < 0.05), demonstrating their plant-growth-promoting potential. Moreover, both strains markedly reduced the disease severity indices (DSIs) of maize seedlings, indicating that they can enhance maize resistance to the pathogen. Whole-genome sequencing using Oxford Nanopore (ONT) and Illumina technologies showed that the complete genomes of KP3P9 and K13C contained biosynthetic gene clusters involved in the biosynthesis of antimicrobial secondary metabolites, including fengycin, bacillibactin, subtilin, pulcherriminic acid, subtilosin A, bacilysin, and others. Moreover, both strains exhibited strong antagonistic activity against F. solani (the causal pathogen of apple replant disease), as well as F. oxysporum f. sp. cubense race 1 (Foc1) and tropical race 4 (FocTR4) (pathogens responsible for banana wilt disease), with inhibition rates exceeding 70% in vitro. These results indicate that KP3P9 and K13C are promising biocontrol agents for MSR and other devastating Fusarium diseases. Full article

(This article belongs to the Special Issue Microbial Biocontrol in the Agri-Food Industry, 2nd Edition)

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33 pages, 5582 KB

Open AccessReview

The Role of Oral and Gut Microbiota in Bone Health: Insights from Bacterial Extracellular Vesicles

by Ping Liang, Xuanyu Chen, Zhikang Su, Yunlin Luo, Tao Wang, Jiang Li, Lvhua Guo and Tao Luo

Microorganisms 2025, 13(10), 2254; https://doi.org/10.3390/microorganisms13102254 - 25 Sep 2025

Abstract

Bone health is critically influenced by the oral and gut microbiota, which are among the largest microbial reservoirs in the human body. These microbiota play essential roles in maintaining bone mass through immune modulation, metabolite production, and nutrient resorption. Recent observations have underscored [...] Read more.

Bone health is critically influenced by the oral and gut microbiota, which are among the largest microbial reservoirs in the human body. These microbiota play essential roles in maintaining bone mass through immune modulation, metabolite production, and nutrient resorption. Recent observations have underscored that extracellular vesicles (EVs) derived from oral and gut microbiota may circulate to the brain and bone marrow, suggesting their integral roles in the gut–brain–bone axis and oral–brain–bone axis. This review outlines the current research status of bacterial extracellular vesicles (BEVs), including their biogenesis, classification, structural features, and cargo composition, with emphasis on factors influencing cargo heterogeneity and the consequences of cellular uptake and presentation. Oral-microbiota-derived BEVs and their cargo associated with bone health are highlighted, along with recent evidence linking BEVs to systemic dis-eases and the potential integration into the oral–gut–bone axis. Preclinical animal studies on BEV dosage, routes of administration, and disease models are summarized, together with the limitations of current approaches and strategies for engineering BEVs. Finally, an overview of translational applications and future therapeutic prospects is provided, aiming to advance the understanding of BEVs as innovative tools for the treatment and prevention of bone-related diseases. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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16 pages, 1057 KB

Open AccessCommunication

Toxigenic and Antibiotic-Resistant Bacillus cereus in Raw Cow Milk from Eastern Cape, South Africa: A Potential Public Health Threat

by Ezekiel Green and Abraham Goodness Ogofure

Microorganisms 2025, 13(10), 2253; https://doi.org/10.3390/microorganisms13102253 - 25 Sep 2025

Abstract

Bacillus cereus sensu lato is widespread and causes significant food spoilage that alters the flavour and structure of milk. The present study investigated the prevalence, enterotoxigenic genes, and resistant profiles of B. cereus strains isolated from raw milk of Bos taurus in South [...] Read more.

Bacillus cereus sensu lato is widespread and causes significant food spoilage that alters the flavour and structure of milk. The present study investigated the prevalence, enterotoxigenic genes, and resistant profiles of B. cereus strains isolated from raw milk of Bos taurus in South Africa (the Eastern Cape Province). One thousand four hundred samples were obtained from commercial dairy farms and were evaluated for the presence of B. cereus using B. cereus selective agar, and genomic DNA was isolated from B. cereus colonies with specific characteristics. PCR was used to evaluate the presence of enterotoxigenic genes, and antibacterial susceptibility was carried out using the Kirby-Bauer Disc diffusion method. The result revealed that B. cereus was detected in 250 raw milk samples. In addition, 67.2% of the isolates grew when incubated at 4 °C. Among the enterotoxigenic genes studied, ces showed the highest occurrence (88.8%), but hblABC (0%) did not demonstrate amplification from any isolate. Our analysis found two significant patterns (III and V): nheABC-entFM (27.2% and 24.4%) and the ces gene. Total (100%) sensitivity was observed for six of the twelve antibiotics tested, while organisms showed complete resistance to penicillin and rifampicin. This study marks the initial documentation of B. cereus and its enterotoxigenic genes in Bos taurus raw milk sourced from the Eastern Cape Province, South Africa. Enterotoxin FM should be considered the second most crucial enterotoxin, after non-hemolytic enterotoxin, and should be included in the molecular approach used to classify pathogenic B. cereus in nutrimental products. These findings underscore the urgent need for public health awareness, particularly in rural communities where raw milk consumption is prevalent. The high prevalence of antibiotic resistance and toxigenic strains of B. cereus calls for improved milk pasteurization practices to mitigate the risk of foodborne illness. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Foodborne Pathogens: Surveillance, Mechanisms and Mitigation Strategies)

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24 pages, 6917 KB

Open AccessArticle

Effects of Biofertilizer and Green Manure on Soil Bacterial Community in Korla Fragrant Pear Orchard

by Jie Li, Xing Shen, Bolang Chen, Zhanyi He, Linsen Yan, Lele Yang, Bangxin Ding and Zhongping Chai

Microorganisms 2025, 13(10), 2252; https://doi.org/10.3390/microorganisms13102252 - 25 Sep 2025

Abstract

The sustainability of Korla fragrant pear orchards has been increasingly threatened by prolonged intensive agricultural practices. In response, biofertilizers and green manures have gained attention due to their potential to enhance soil structure, activate microbial functions, and improve nutrient uptake. However, the dynamic [...] Read more.

The sustainability of Korla fragrant pear orchards has been increasingly threatened by prolonged intensive agricultural practices. In response, biofertilizers and green manures have gained attention due to their potential to enhance soil structure, activate microbial functions, and improve nutrient uptake. However, the dynamic changes in soil bacterial communities under such interventions remain inadequately understood. This study was conducted from 2022 to 2023 in 7- to 8-year-old Korla fragrant pear orchards in Bayin’guoleng Mongol Autonomous Prefecture, Xinjiang. The treatments included: conventional fertilization (CK), biofertilizer (JF), oil sunflowers (DK1) with 25 cm row spacing and a seeding rate of 27 kg·ha⁻², oil sunflowers (DK2) with 25 cm row spacing and a seeding rate of 33 kg·ha⁻², sweet clover (CM1) with 20 cm row spacing and a seeding rate of 21 kg·ha⁻², and sweet clover (CM2) with 20 cm row spacing and a seeding rate of 27 kg·ha⁻². During the 2023 pear season, soil samples from the 0–20 cm layer were collected at the fruit setting, expansion, and maturity stages. Their physical and chemical properties were analyzed, and the structure and diversity of the soil bacterial community were examined using 16S rRNA gene high-throughput sequencing. Fruit yield was assessed at the maturity stage. Compared to CK, the relative abundance of Actinobacteria increased by 101.00%, 38.99%, and 50.38% in the JF, DK2, and CM1 treatments, respectively. DK1 and CM1 treatments resulted in a 152.28% and 145.70% increase in the relative abundance of the taxon Subgroup_7, while JF and DK2 treatments enhanced the relative abundance of the taxon Gitt-GS-136 by 318.91% and 324.04%, respectively. The Chao1 index for CM2 was 18.76% higher than CK. LEfSe analysis showed that the DK2 and CM2 treatments had a more significant regulatory effect on bacterial community structure. All treatments led to higher fruit numbers and yield compared to CK, with JF showing the largest yield increase. Fertilizer type, soil nutrients, and bacterial community structure all significantly positively influenced pear yield. In conclusion, high-density oil sunflower planting is the most effective approach for maintaining soil microbial community stability, followed by low-density sweet clover. This study provides a systematic evaluation of the dynamic effects of bio-fertilizers and different green manure planting patterns on soil microbial communities in Korla fragrant pear orchards, presenting practical, microbe-based strategies for sustainable orchard management. Full article

(This article belongs to the Special Issue Interactions of Mycorrhizal Fungi and Other Soil Microorganisms with Plants)

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18 pages, 3840 KB

Open AccessArticle

Screening of a Gossypol-Removing Yeast Strain and Characterization of Its Removal Mechanism

by Yushuo Zhang, Tingyao Lv, Qiuyang Jiang, Xiaotong Zeng, Feng Li and Dayong Xu

Microorganisms 2025, 13(10), 2251; https://doi.org/10.3390/microorganisms13102251 - 25 Sep 2025

Abstract

Gossypol, a polyphenolic naphthalene derivative and yellow polyphenolic pigment found in cotton seed glands, presents notable environmental, animal, and human health hazards. To screen for yeast strains capable of utilizing gossypol and to investigate their removal efficiency and mechanisms. Yeast strains capable of [...] Read more.

Gossypol, a polyphenolic naphthalene derivative and yellow polyphenolic pigment found in cotton seed glands, presents notable environmental, animal, and human health hazards. To screen for yeast strains capable of utilizing gossypol and to investigate their removal efficiency and mechanisms. Yeast strains capable of utilizing gossypol as the exclusive carbon source were isolated from cotton field soil. The identification of these strains involved assessment of colony morphology, physiological and biochemical characteristics, and phylogenetic analysis utilizing 26S rDNA gene sequences. Safety evaluations included hemolytic and antibiotic susceptibility tests. The growth responses of the selected strains to varying temperatures and pH levels were determined. Using cotton meal as the solid fermentation substrate, the effects of single factors on gossypol removal by the strains were determined. The intracellular and extracellular localization as well as the nature of the gossypol-removing active components in the strains were characterized, followed by an investigation into the molecular mechanism of gossypol removal using LC-MS analysis. A total of 17 gossypol-utilizing strains were isolated from cotton field soil samples, with strain ZYS-3 demonstrating superior removal capability. Strain ZYS-3 was identified as Meyerozyma guilliermondii, exhibiting no hemolytic activity and susceptibility to nine commonly used antifungal agents. The optimal growth parameters for this strain were determined to be a temperature of 30 °C and a pH of 5.0. In solid-state fermentation using cotton meal at 30 °C with initial fermentation conditions (10% corn flour added as an external carbon source, 40% moisture content, and 6% inoculum concentration) for 3 days, strain ZYS-3 achieved a gossypol removal rate of 73.57%. Subsequent optimization of the fermentation process, including the addition of 10% corn flour as an external carbon source, adjustment of moisture content to 55%, and inoculum concentration to 10%, resulted in an increased gossypol removal rate of 89.77% after 3 days of fermentation, representing a 16.2% enhancement over the initial conditions. Assessment of gossypol removal activity revealed that strain ZYS-3 predominantly removes gossypol through the secretion of extracellular enzymes targeting specific active groups (phenolic hydroxyl groups and aldehyde groups) within the gossypol molecule. These enzymes facilitate oxidation and elimination reactions, leading to the opening of the naphthalene ring and subsequent removal of gossypol. Full article

(This article belongs to the Section Microbial Biotechnology)

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12 pages, 7146 KB

Open AccessArticle

Host Phylogeny Shapes Gut Microbiota and Predicted Functions in Captive Artiodactyls

by Guolei Sun, Tian Xia, Qinguo Wei, Xibao Wang, Yuehuan Dong, Xiufeng Yang, Lei Zhang, Weilai Sha and Honghai Zhang

Microorganisms 2025, 13(10), 2250; https://doi.org/10.3390/microorganisms13102250 - 25 Sep 2025

Abstract

Host phylogeny can imprint the gut microbiota, but it is often masked by diet and environment. Leveraging the standardized husbandry of a zoological collection, we profiled fecal microbiota from 55 captive artiodactyls representing 12 species in Bovidae, Cervidae, and Camelidae using 16S rRNA [...] Read more.

Host phylogeny can imprint the gut microbiota, but it is often masked by diet and environment. Leveraging the standardized husbandry of a zoological collection, we profiled fecal microbiota from 55 captive artiodactyls representing 12 species in Bovidae, Cervidae, and Camelidae using 16S rRNA amplicon sequencing targeting the V3–V4 region on the Illumina MiSeq platform. Community composition differed significantly among host families (Bray–Curtis PERMANOVA, R² = 0.1075, p = 0.001). A host–microbiota tanglegram, which juxtaposes the host phylogeny with a dendrogram of microbiota similarity, recovered a topology congruent with the host phylogeny, with camelids forming a distinct branch separate from true ruminants in both trees. The linear discriminant analysis effect size (LEfSe; LDA ≥ 3.5) identified family-specific biomarkers, including enrichment of Acinetobacter/Moraxellaceae in Bovidae, Rikenellaceae (the Rikenellaceae_RC9_gut_group) in Cervidae, and Rummeliibacillus together with the Christensenellaceae_R-7_group in Camelidae. Functional inference with PICRUSt2 revealed significant differences in KEGG level-2 pathways (e.g., carbohydrate metabolism and xenobiotics biodegradation), consistent with taxonomic shifts. Altogether, these findings show that—even under uniform captive conditions—host evolutionary history remains a primary determinant of both the structure and the predicted functions of the artiodactyl gut microbiota, refining the scope of phylosymbiosis and providing actionable baselines for veterinary monitoring and conservation management in zoo settings. Full article

(This article belongs to the Section Gut Microbiota)

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27 pages, 3758 KB

Open AccessArticle

Stability and Antimicrobial Efficacy of Reuterin and Bacteriocins (Microcin J25, Nisin Z, and Pediocin PA-1) in Chitosan- and Carboxymethyl-Cellulose-Based Hydrogels

by Samira Soltani, Muriel Subirade, Eric Biron, Christophe Cordella, Gabriel Romondetto and Ismail Fliss

Microorganisms 2025, 13(10), 2249; https://doi.org/10.3390/microorganisms13102249 - 25 Sep 2025

Abstract

Traditional chemical-based sanitizers pose risks to health and the environment, highlighting the need for safer natural alternatives. We developed biocompatible hydrogels from carbohydrate-based biopolymers, chitosan (1.5% and 2.5%), and carboxymethylcellulose (CMC, 3% and 5%), each incorporating one of four antimicrobials: microcin J25, nisin [...] Read more.

Traditional chemical-based sanitizers pose risks to health and the environment, highlighting the need for safer natural alternatives. We developed biocompatible hydrogels from carbohydrate-based biopolymers, chitosan (1.5% and 2.5%), and carboxymethylcellulose (CMC, 3% and 5%), each incorporating one of four antimicrobials: microcin J25, nisin Z, pediocin PA-1, or reuterin. Hydrogels were prepared by dissolving the polymers in aqueous solution and incorporating antimicrobials before gelation. The formulations were characterized using viscosity measurements, antimicrobial assays, and stability testing over 28 days of storage at room temperature (23–25 °C). Chitosan hydrogels with microcin J25 maintained strong activity against Salmonella enterica ATCC 6962, while nisin Z retained activity in gel and solution forms, though with some decline during storage. Pediocin PA-1 remained active in 1.5% and 2.5% chitosan hydrogels against Listeria monocytogenes ATCC 19115, but activity was lost in 3% and 5% CMC hydrogels. Reuterin preserved activity in CMC-based hydrogels throughout storage. In solution, microcin J25 and nisin Z consistently achieved ~7-log reductions, whereas pediocin PA-1 and reuterin reached up to ~5-log reductions. In gels, efficacy decreased at lower concentrations and shorter contact times, likely due to diffusion barriers. Overall, the hydrogels remained stable during storage, and CMC- and chitosan-based matrices with selected antimicrobials show promise as alternatives to chemical sanitizers. Their application should be tailored to specific needs, with formulations requiring longer contact times best suited for surfaces that allow prolonged exposure. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT), Third Edition)

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16 pages, 1791 KB

Open AccessArticle

Pediococcus pentosaceus OL77 Enhances Oat (Avena sativa) Silage Fermentation Under Cold Conditions

by Xin Liu, Guiqin Zhao, Jie Bai, Xinyi Qu, Jikuan Chai and Doudou Lin

Microorganisms 2025, 13(10), 2248; https://doi.org/10.3390/microorganisms13102248 - 25 Sep 2025

Abstract

Ensiling forage under low-temperature conditions often leads to poor fermentation and nutrient losses. This study evaluated the effects of a cold-tolerant Pediococcus pentosaceus OL77 strain on oat silage. Silages were prepared with or without Pediococcus pentosaceus inoculation (1 × 10⁵ cfu/g FM). [...] Read more.

Ensiling forage under low-temperature conditions often leads to poor fermentation and nutrient losses. This study evaluated the effects of a cold-tolerant Pediococcus pentosaceus OL77 strain on oat silage. Silages were prepared with or without Pediococcus pentosaceus inoculation (1 × 10⁵ cfu/g FM). After 90 days, OL77-treated silage showed markedly higher lactic acid (45.83 vs. 30.51 g/kg DM), lower pH (3.88 vs. 4.443), and better preservation of WSC (64.68 vs. 47.60 g/kg DM) and crude protein (89.26 vs. 65.52 g/kg DM) than the control. Microbial analysis revealed accelerated colonization by Pediococcus, reduced bacterial diversity, and faster stabilization of the fermentation process. Functional predictions indicated enhanced carbohydrate and energy metabolism. These findings demonstrate that OL77 can effectively improve fermentation quality and nutrient preservation of oat silage under low-temperature conditions, offering a practical inoculant option for cold regions. Full article

(This article belongs to the Special Issue Microorganisms in Silage)

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52 pages, 1456 KB

Open AccessReview

The Gut Microbiome in Enteric Viral Infections: Underlying Mechanisms and Therapeutic Approaches

by Alejandro Borrego-Ruiz and Juan J. Borrego

Microorganisms 2025, 13(10), 2247; https://doi.org/10.3390/microorganisms13102247 - 25 Sep 2025

Abstract

Despite growing recognition of the role of the gut microbiome in host health and in modulating pathogen activity, the dynamic and reciprocal relationship between enteric viruses and the gut microbial ecosystem remains insufficiently defined and requires further exploration. This comprehensive review examines the [...] Read more.

Despite growing recognition of the role of the gut microbiome in host health and in modulating pathogen activity, the dynamic and reciprocal relationship between enteric viruses and the gut microbial ecosystem remains insufficiently defined and requires further exploration. This comprehensive review examines the bidirectional interplay between the gut microbiome and enteric viral infections by addressing (i) viruses associated with gastrointestinal alterations, (ii) how enteric viral infections alter the composition and function of the gut microbiome, (iii) how the gut microbiome modulates viral infectivity and host susceptibility, and (iv) current microbial-based approaches for preventing or treating enteric viral infections. Gastrointestinal viral infections induce gut microbiome dysbiosis, marked by reductions in beneficial bacteria and increases in potentially pathogenic populations. Specific gut microorganisms can modulate host susceptibility, with certain bacterial genera increasing or decreasing infection risk and disease severity. Pattern recognition receptors in the intestinal epithelium detect microbial signals and trigger antimicrobial peptides, mucus, and interferon responses to control viral replication while maintaining tolerance to commensal bacteria. The gut microbiome can indirectly facilitate viral infections by creating a tolerogenic environment, suppressing antiviral antibody responses, and modulating interferon signaling, or directly enhance viral replication by stabilizing virions, promoting host cell attachment, and facilitating coinfection and viral recombination. In turn, commensal gut bacteria can inhibit viral entry, enhance host antiviral responses, and strengthen mucosal barrier function, contributing to protection against gastrointestinal viral infections. Probiotics and fecal microbiota transplantation constitute potential microbial-based therapeutics that support antiviral defenses, preserve epithelial integrity, and restore microbial balance. In conclusion, the role of the gut microbiome in modulating enteric viral infections represents a promising area of future investigation. Therefore, integrating microbiome insights with virology and immunology could enable predictive and personalized strategies for prevention and treatment. Full article

(This article belongs to the Special Issue Microbiota and Gastrointestinal Diseases)

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20 pages, 5625 KB

Open AccessArticle

Dynamic Changes in Microbial Communities in Oil Reservoirs Under a Long-Term Bio-Chemical Flooding Operation

by Gui-Na Qi, Guo-Jun Li, Yi-Fan Liu, Lei Zhou, Ya-Qing Ge, Jin-Feng Liu, Shi-Zhong Yang, Ji-Dong Gu and Bo-Zhong Mu

Microorganisms 2025, 13(10), 2246; https://doi.org/10.3390/microorganisms13102246 - 25 Sep 2025

Abstract

Huge amounts of water and chemicals have been injected into subsurface oil reservoirs in secondary and tertiary oil recovery processes. Although the effects of injected water and chemicals on microbial communities have been investigated, knowledge about their long-term dynamic changes in oil reservoirs [...] Read more.

Huge amounts of water and chemicals have been injected into subsurface oil reservoirs in secondary and tertiary oil recovery processes. Although the effects of injected water and chemicals on microbial communities have been investigated, knowledge about their long-term dynamic changes in oil reservoirs remains limited. To address this gap, we used 16S rRNA sequencing from cDNA and chemical analysis to track the dynamic changes in microbial communities in oil reservoirs under a long-term flooding operation over three years and five months using bio-chemical flooding in the Daqing Oilfield, China. Researchers observed dynamic changes in microbial composition and diversity during the flooding process. Long-term bio-chemical drainage leads to alterations in dominant bacterial community structure, with a decrease in methanogenic archaeal abundance. Bacterial metabolic functions remained stable, but archaeal functions changed notably. Our results indicate that the microbial community and its functions in the oil reservoirs have experienced significant dynamic changes under the long-term flooding intervention of bio-chemical flooding, which opens up a new window for further understanding the impact of injected water and chemicals on microbial community in oil reservoirs and expands our knowledge about the role of microbial community changes in reservoirs under the flooding process. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 3271 KB

Open AccessArticle

Mycobacterium Transcriptional Factor BlaI Regulates Cell Division and Growth and Potentiates β-Lactam Antibiotic Efficacy Against Mycobacteria

by Junqi Xu, Mingjun Zhang, Fuling Xie, Junfeng Zhen, Yuerigu Abuliken, Chaoyun Gao, Yongdong Dai, Zhiyong Jiang, Peibo Li and Jianping Xie

Microorganisms 2025, 13(10), 2245; https://doi.org/10.3390/microorganisms13102245 - 25 Sep 2025

Abstract

Cell division is critical for the survival, growth, pathogenesis, and antibiotic susceptibility of Mycobacterium tuberculosis (Mtb). However, the regulatory networks governing the transcription of genes involved in cell growth and division in Mtb remain poorly understood. This study aimed to investigate the impact [...] Read more.

Cell division is critical for the survival, growth, pathogenesis, and antibiotic susceptibility of Mycobacterium tuberculosis (Mtb). However, the regulatory networks governing the transcription of genes involved in cell growth and division in Mtb remain poorly understood. This study aimed to investigate the impact of BlaI overexpression on cell division and growth in Mtb and elucidate the underlying mechanisms. Mycobacterium smegmatis mc²155 was used as the model organism. Recombinant strains overexpressing BlaI were constructed. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), ethidium bromide and Nile red uptake assays, minimum inhibitory concentration (MIC) determination, drug resistance analysis, quantitative real-time PCR (qRT-PCR) assays, and electrophoretic mobility shift assay (EMSA) were employed to assess changes in bacterial morphology, cell wall permeability, antibiotic susceptibility, gene transcription levels, and the interaction between BlaI and its target genes. Overexpression of BlaI disrupted bacterial division in M. smegmatis, leading to growth delay, cell elongation, and formation of multi-septa. It also altered the lipid permeability of the cell wall and enhanced the sensitivity of M. smegmatis to β-lactam antibiotics. BlaI overexpression affected the transcription of cell division-related genes, particularly downregulating ftsQ. Additionally, BlaI negatively regulated the transcription of Rv1303—a gene co-transcribed with ATP synthase-encoding genes—inhibiting ATP synthesis. This impaired the phosphorylation of division complex proteins, ultimately affecting cell division and cell wall synthesis. Overexpression of BlaI in Mtb interferes with bacterial division, slows growth, and alters gene expression. Our findings identify a novel role for BlaI in regulating mycobacterial cell division and β-lactam susceptibility, providing a foundation for future mechanistic studies in M. tuberculosis, with validation required to assess relevance to clinical tuberculosis—though validation in M. tuberculosis and preclinical models is required. Full article

(This article belongs to the Special Issue Mycobacterial Research)

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18 pages, 4139 KB

Open AccessArticle

Comparative Analyses of Pediococcus pentosaceus Strains Isolated from Milk Cattle Reveal New Insights for Screening Food-Protective Cultures

by Sebastian W. Fischer, Nadine Mariani Corea, Anna Euler, Leonie Bertels and Fritz Titgemeyer

Microorganisms 2025, 13(10), 2244; https://doi.org/10.3390/microorganisms13102244 - 25 Sep 2025

Abstract

Pediococcus pentosaceus is a lactic acid bacterium used inter alia for the fermentation of milk, meat, vegetables, fruits, and even for brewing beer. Several health-promoting effects, such as antibacterial and antifungal activities or microphage and immune system stimulation, have been attributed. Apart from [...] Read more.

Pediococcus pentosaceus is a lactic acid bacterium used inter alia for the fermentation of milk, meat, vegetables, fruits, and even for brewing beer. Several health-promoting effects, such as antibacterial and antifungal activities or microphage and immune system stimulation, have been attributed. Apart from refining foods during the fermentation process, P. pentosaceus strains are added to meat and meat products as protective cultures to improve food safety, while leaving the organoleptic properties untouched. Since knowledge on the latter issue is still limited, we investigated 32 isolates from milk samples and teat canal biofilms regarding their antibacterial efficacy as a prerequisite for possible application as protective cultures. P. pentosaceus strains were unequivocally identified by DNA sequencing of the rrnA gene encoding 16S rRNA. Binary matrices obtained from random amplification of polymorphic DNA experiments showed that all isolates differed by more than 5% and thus represented subspecies. The antibacterial profiles against eight food-borne pathogens and food spoilage bacteria were determined. They efficiently combatted, although to various extents, Gram-negative bacteria such as Pseudomonas aeruginosa or Salmonella enterica, and Gram-positive bacteria such as Staphylococcus aureus and Listeria monocytogenes. Interestingly, acid production was dependent on the presence of the challenged pathogen and did not correlate with the extent of inhibition. Bioinformatic analyses of the genomes of the three top-ranked isolates revealed a pronounced genomic plasticity with a core genome of 1460 genes and additional 91, 130, and 161 unique genes, respectively. Each strain included a set of three, five, or six plasmids and was equipped with different genes encoding bacteriocins. The data suggest that multiple strains of P. pentosaceus should be included in order to optimize the selection of a culture for food preservation. The approach could also be applicable to other bacterial species. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

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9 pages, 1120 KB

Open AccessCommunication

Macrolide-Resistant Mycoplasma pneumoniae Among Japanese Children from 2008 to 2024

by Tomohiro Oishi, Tsuyoshi Kenri and Daisuke Yoshioka

Microorganisms 2025, 13(10), 2243; https://doi.org/10.3390/microorganisms13102243 - 25 Sep 2025

Abstract

Mycoplasma pneumoniae (MP), an important pathogen that causes pneumonia among children and young adults, caused an epidemic every four years in Japan until 2016, with the next epidemic occurring eight years later in 2024. This study compared the prevalence of MP infections among [...] Read more.

Mycoplasma pneumoniae (MP), an important pathogen that causes pneumonia among children and young adults, caused an epidemic every four years in Japan until 2016, with the next epidemic occurring eight years later in 2024. This study compared the prevalence of MP infections among Japanese children in 2024 to previous years using real-time polymerase chain reaction (PCR) and the p1 genotype determined using the PCR restriction fragment length polymorphism typing method from nasopharyngeal swab specimens. Of the 133 total isolates collected in 2024, 54.1% were macrolide-resistant MP (MRMP), with 98.0% of those containing an A2063G mutation in the 23S rRNA gene associated with macrolide resistance. This annual rate of MRMP and incidence of the A2063G mutation was similar to those in 2016. However, the dominant p1 genotype among isolates in 2024 was type 1 (93.4%), whereas type 2 was dominant in the previous epidemic. Thus, although the rate of MRMP in 2024 was similar to that in the previous epidemic year, the distribution of p1 genotypes was different. Further, the rate of MRMP was lower than neighboring Asian countries, including China and Korea, but was higher than in European countries. Therefore, it is important to continue monitoring MP infections in Japan. Full article

(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance: Second Edition)

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Open AccessArticle

Remdesivir: Effectiveness and Safety in Hospitalized COVID-19 Patients—Analysis of Retrospectively Collected Data from Daily Practice in the Omicron Variant Era and Comparison with the Pre-Omicron Period

by Nikos Pantazis, Evmorfia Pechlivanidou, Vassiliki Rapti, Dimitra Kavatha, Haralampos Milionis, Ioannis Kalomenidis, Karolina Akinosoglou, Periklis Panagopoulos, Symeon Metallidis, Diamantis Kofteridis, Nikolaos V. Sipsas, Ioannis Katsarolis, Garyfallia Poulakou, Anastasia Antoniadou, Eirini Christaki, Theofani Rimpa, Markos Marangos, Vasileios Petrakis, Olga Tsachouridou, Vasiliki E. Georgakopoulou, Pinelopi Kazakou, Sotirios P. Karagiannis, Eleni Polyzou and Giota Touloumi Show full author list Hide full author list

Microorganisms 2025, 13(10), 2242; https://doi.org/10.3390/microorganisms13102242 - 25 Sep 2025

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has impacted global health. Remdesivir was approved based on clinical trials demonstrating improved outcomes in hospitalized patients. The ReEs-COVID19 study provides real-world evidence on its effectiveness and safety across two periods: Pre-Omicron and Omicron. This retrospective, observational [...] Read more.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has impacted global health. Remdesivir was approved based on clinical trials demonstrating improved outcomes in hospitalized patients. The ReEs-COVID19 study provides real-world evidence on its effectiveness and safety across two periods: Pre-Omicron and Omicron. This retrospective, observational cohort study included 1610 patients hospitalized with COVID-19, treated with remdesivir during Pre-Omicron (September 2020–February 2021; n = 606) and Omicron (June 2022–March 2023; n = 1004) periods. Primary endpoint: time to discharge; Hepatic/renal function abnormalities were also investigated. In the Omicron period patients were older and had more comorbidities but remdesivir was initiated earlier (median: 2 days from symptom onset) compared to the Pre-Omicron period (8 days). ICU admissions rates and direct COVID-19-related deaths were significantly lower, but overall 30-day mortality was higher during the Omicron period. Earlier remdesivir administration was associated with faster discharge. Abnormal liver tests and acute kidney injury were rare across both periods. ReEs-COVID19 confirmed remdesivir’s effectiveness and safety in real-world clinical settings during both periods, underscoring its importance in treatment of hospitalized COVID-19 patients, especially when initiated earlier in the disease course. Further research is needed to evaluate its utility in specific subgroups (e.g., immuno-compromised) and in combination with other treatments. Full article

(This article belongs to the Special Issue Current Challenges in Infectious Diseases Post COVID-19 Pandemic)

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