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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)

Imprint Information Journal Flyer Open Access ISSN: 2076-2607

Latest Articles

29 pages, 1870 KB

Open AccessArticle

Identification of Three New Rugose Small Colony Variants from a Pseudomonas aeruginosa Biofilm

by Benjamin K. Smartnick, Eric A. Carlson, Chase N. Morse, Taylor A. Dodson, Nathan C. Wamer, Avery M. Horne and Erin G. Prestwich

Microorganisms 2025, 13(11), 2550; https://doi.org/10.3390/microorganisms13112550 (registering DOI) - 7 Nov 2025

Pseudomonas aeruginosa is a Gram-negative, pathogenic, bacterium that produces biofilms comprising phenotypically distinct cell subpopulations. When separating and characterizing a single P. aeruginosa PA14 biofilm, three novel rugose small colony variants (RSCVs) (denoted RSCV_1, RSCV_2, and RSCV_3) were discovered. Characteristics of these stationary [...] Read more.

Pseudomonas aeruginosa is a Gram-negative, pathogenic, bacterium that produces biofilms comprising phenotypically distinct cell subpopulations. When separating and characterizing a single P. aeruginosa PA14 biofilm, three novel rugose small colony variants (RSCVs) (denoted RSCV_1, RSCV_2, and RSCV_3) were discovered. Characteristics of these stationary phase RSCVs differed between stationary phase wild-type (WT) PA14, between the PA14 biofilm subpopulations, and between the RSCVs themselves. The observed phenotypic changes in the RSCVs included differences in cellular morphology, exopolysaccharide production, biosynthesis of virulence factors, biofilm formation, and antibiotic tolerance. Stationary phase cell surface-associated molecules on the RSCVs were differently ionized as compared to WT PA14 using matrix-assisted laser desorption ionization (MALDI) mass spectrometry. Many RNA transcripts were differentially expressed between the RSCVs and WT PA14 as well as between RSCV_1 and RSCV_3. DNA sequencing revealed single-nucleotide deletions and single-nucleotide polymorphisms (SNPs) among the RSCVs and between the RSCVs and WT PA14. The levels of the intracellular signaling molecule bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (cyclic-di-GMP) were higher in the RSCVs compared to WT PA14 and significantly lower in RSCV_3 as compared to both RSCV_1 and RSCV_2. The detected differences in the RSCVs have significant implications for biofilm production, antibiotic tolerance, and virulence. Full article

(This article belongs to the Special Issue Advances in Microbial Biofilm Formation (2nd Edition))

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17 pages, 4261 KB

Open AccessArticle

Multiscale Patterns of Bacterial and Protist Diversity Across Red Sea Coral Reefs

by Christopher A. Hempel and Larissa Frühe

Microorganisms 2025, 13(11), 2549; https://doi.org/10.3390/microorganisms13112549 - 7 Nov 2025

Coral reef microbial communities play pivotal roles in ecosystem functioning but remain understudied, particularly across spatial gradients and domains. Here, we use environmental DNA (eDNA) metabarcoding of 16S and 18S rRNA genes to profile bacterial and protistan communities in surface sediments from six [...] Read more.

Coral reef microbial communities play pivotal roles in ecosystem functioning but remain understudied, particularly across spatial gradients and domains. Here, we use environmental DNA (eDNA) metabarcoding of 16S and 18S rRNA genes to profile bacterial and protistan communities in surface sediments from six coral reefs along the central Red Sea. At each reef, we sampled both exposed (seaward) and sheltered (shoreward) sites, enabling a multiscale analysis of diversity and community composition. We found significant differences in alpha and beta diversity between reefs and between exposure sites within reefs for both microbial groups. Redundancy analysis (RDA) and PERMANOVA revealed reef identity and exposure category as key structuring factors. Indicator species analysis and Random Forest classification identified microbial taxa predictive of exposure gradients, with several exact sequence variants (ESVs) serving as robust bioindicators in both methods. Bacterial and protistan communities exhibited overlapping but distinct patterns, highlighting their complementary ecological roles. Our results underscore the importance of fine-scale habitat heterogeneity in shaping reef microbial assemblages and support the integration of multi-domain eDNA data into coral reef monitoring frameworks. Full article

(This article belongs to the Special Issue Coral Microbiome and Coral Microbes)

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5 pages, 173 KB

Open AccessEditorial

Editorial for “Microbe–Host Interactions in Human Infections”

by Roberta Gaziano and Terenzio Cosio

Microorganisms 2025, 13(11), 2548; https://doi.org/10.3390/microorganisms13112548 - 7 Nov 2025

Despite remarkable advances achieved over recent decades, infectious diseases remain a formidable threat to global public health [...] Full article

(This article belongs to the Section Medical Microbiology)

15 pages, 812 KB

Open AccessArticle

Epidemiology and Drug Susceptibility of Nontuberculous Mycobacteria in the Province of Pavia (Northern Italy): An Overview

by Mariangela Siciliano, Francesco Amisano, Jessica Bagnarino, Giulia Grassia, Patrizia Cambieri, Fausto Baldanti, Vincenzina Monzillo and Daniela Barbarini

Microorganisms 2025, 13(11), 2547; https://doi.org/10.3390/microorganisms13112547 - 7 Nov 2025

Nontuberculous mycobacteria (NTM) represent a heterogeneous group of environmental opportunistic pathogens that have emerged particularly in immunocompromised individuals and patients with underlying pulmonary disorders. NTM infections primarily affect the lungs, but can also manifest as lymphadenitis, skin and soft tissue infections, and disseminated [...] Read more.

Nontuberculous mycobacteria (NTM) represent a heterogeneous group of environmental opportunistic pathogens that have emerged particularly in immunocompromised individuals and patients with underlying pulmonary disorders. NTM infections primarily affect the lungs, but can also manifest as lymphadenitis, skin and soft tissue infections, and disseminated disease. This retrospective study took into consideration 425 NTM-positive samples collected between May 2011 and December 2023, analyzed by sample type, sex, and age group (0–17, 18–49, 50–65, >65 years). Antimicrobial susceptibility analysis was performed on the 223 NTM strains with greater pathogenic power and most frequently isolated, from 2016 to 2023. Pulmonary NTM disease (NTM-PD) infections were most prevalent in patients over 65 years (52.1%), while extrapulmonary NTM disease (NTM-EPD) occurred most frequently in the 0–17 age group (56.4%). Women were slightly more affected (54.4%) than men (45.6%), with the highest incidence in female individuals over 65 years old. The most frequently isolated NTM species was the Mycobacterium avium complex (MAC) (47% of isolates). Antimicrobial susceptibility testing of 223 isolates from 2016 to 2023 revealed species-specific resistance patterns, with high susceptibility to clarithromycin in MAC (94.7%) and Mycobacterium chelonae (100%), but notable resistance in Mycobacterium abscessus complex (MABC). The increasing incidence of NTM infections underscores the need for improved diagnostic techniques and targeted treatment strategies. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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35 pages, 1347 KB

Open AccessReview

Key Challenges in Plant Microbiome Research in the Next Decade

by Ayomide Emmanuel Fadiji, Adegboyega Adeniji, Adedayo Ayodeji Lanrewaju, Afeez Adesina Adedayo, Chinenyenwa Fortune Chukwuneme, Blessing Chidinma Nwachukwu, Joshua Aderibigbe and Iyabo Olunike Omomowo

Microorganisms 2025, 13(11), 2546; https://doi.org/10.3390/microorganisms13112546 - 7 Nov 2025

The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming [...] Read more.

The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant–microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed. Full article

(This article belongs to the Section Plant Microbe Interactions)

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26 pages, 3189 KB

Open AccessArticle

Integrated Assessment of Benthic Bacterial Community Physiology, Structure, and Function Across C, N, P, and S Gradients in Lake Villarrica Sediments, Chile

by Tay Ruiz-Gil, Sebastián Elgueta, Giovanni Larama, Joaquín-Ignacio Rilling, Anthony Hollenback, Deb P. Jaisi, Diego Valdebenito, Bryan M. Spears and Marco A. Campos

Microorganisms 2025, 13(11), 2544; https://doi.org/10.3390/microorganisms13112544 - 7 Nov 2025

Benthic bacterial communities play a critical role in nutrient cycling and are highly sensitive to environmental pollution. This study aimed to investigate the physiological, compositional and functional responses of bacterial communities across a range of carbon (C), nitrogen (N), phosphorus (P), and sulfur [...] Read more.

Benthic bacterial communities play a critical role in nutrient cycling and are highly sensitive to environmental pollution. This study aimed to investigate the physiological, compositional and functional responses of bacterial communities across a range of carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) gradients in sediments from Lake Villarrica, Chile. Sediment samples were collected from 5 sites representing a gradient of nutrient pressure from the lake basin (NL < PuB < PoP < SL < VB). Nutrient forms (TC, TN, TP, TS, and OM) were chemically quantified. Community function was assessed via community-level physiological profiles (CLPPs) using Biolog^® EcoPlates (C substrates), PM3B (N substrates), and PM4A (P and S substrates). Function and composition were assessed based on total bacterial and functional nutrient-cycling gene abundances (16Sr RNA, chiA, mcrA, nifH, amoA, nosZ, phoD, pqqC, soxB, dsrA) using qPCR and 16S rRNA metabarcoding, respectively. In general, the CLPPs were higher for C substrates, followed by P, S, and N substrates, with metabolism of organic forms of these nutrients preferential, and P-cycling genes were the most abundant in the lake. Spatially, the most nutrient-enriched site (VB) showed a significantly (p ≤ 0.05) higher nutrient content (e.g., 5.4% TC, 0.54% TN, 1302.8 mg kg⁻¹ TP and 854.1 mg kg⁻¹ TS) and total bacterial abundance (2.9 × 10¹¹ gene copy g⁻¹ dw sediment) but displayed lower CLPPs (from 0.63 to 1.02 AWCD) and nutrient-cycling gene abundances (e.g., 9.1 × 10¹, 2.7 × 10³, 3.6 × 10³ and 4.7 × 10³ gene copy g⁻¹ dw sediment for chiaA, nifH, phoD and dsrA, respectively) compared to the less nutrient-enriched sites (e.g., NL). The bacterial community composition shifted accordingly, with Bacillota enriched in VB and Planctomycetota occurring more frequently in less nutrient-exposed sites. Functional prediction analysis revealed enhanced methanotrophy and sulfate respiration in nutrient-rich sediments, whereas nitrification and organic P (P_o) mineralization dominated in less impacted areas. The results demonstrate that nutrient enrichment constrains bacterial functional diversity in Lake Villarrica and, so, may be useful indicators of environmental stress to be considered in pollution monitoring programmes. Full article

(This article belongs to the Special Issue Advances in Microbial Ecology That Drives Biogeochemical Cycles: Environmental Impact)

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19 pages, 1846 KB

Open AccessArticle

Comparison of QIIME1 and QIIME2 for Analyzing Fungal Samples from Various Built Environments

by Kensuke Watanabe and U Yanagi

Microorganisms 2025, 13(11), 2545; https://doi.org/10.3390/microorganisms13112545 - 6 Nov 2025

This study evaluates the differences between bioinformatics pipelines by analyzing samples collected from various built environments. Previous comparative studies of microbial community analysis pipelines have largely focused on bacterial communities, mock communities, or soil fungi, often with small sample sizes, and have not [...] Read more.

This study evaluates the differences between bioinformatics pipelines by analyzing samples collected from various built environments. Previous comparative studies of microbial community analysis pipelines have largely focused on bacterial communities, mock communities, or soil fungi, often with small sample sizes, and have not specifically targeted built environments. Our results highlight key differences between OTU (QIIME1) and ASV (QIIME2) analyses. OTU analysis clusters OTUs at 97% similarity and tends to show higher diversity values in diversity analyses. Regarding abundantly detected fungi, OTU analysis identified more genera than ASV analysis. However, the OTU method has a high rate of false positives and false negatives, indicating low error-removal capability and suggesting that many fungal genera may have been detected. Therefore, a combined approach using OTU analysis combined with ASV analysis allows for both the comprehensive detection of dominant taxa and the inclusion of rare species. Overall, our findings emphasize that the choice of pipeline significantly influences the composition of the observed fungal community in built environments. Careful consideration of both OTU and ASV strategies can enhance the reliability and completeness of fungal metabarcoding studies, particularly when studying complex indoor microbial communities. Full article

(This article belongs to the Section Microbiomes)

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19 pages, 2200 KB

Open AccessArticle

Competition-Exclusion for Manganese Is Involved in Antifungal Activity of Two Lactic Acid Bacteria Against Various Dairy Spoilage Fungi

by Charlène Boulet, Emmanuel Coton, Marie-Laure Rouget, Florence Valence and Jérôme Mounier

Microorganisms 2025, 13(11), 2543; https://doi.org/10.3390/microorganisms13112543 - 6 Nov 2025

Biopreservation using lactic acid bacteria has gained a growing interest as an alternative to chemical preservatives and/or as a complementary tool to prevent fungal spoilage in dairy products. Among the action mechanisms of antifungal LAB, competitionexclusion for trace elements has recently been highlighted. [...] Read more.

Biopreservation using lactic acid bacteria has gained a growing interest as an alternative to chemical preservatives and/or as a complementary tool to prevent fungal spoilage in dairy products. Among the action mechanisms of antifungal LAB, competitionexclusion for trace elements has recently been highlighted. To further investigate this mechanism, two antifungal LAB strains, Lactiplantibacillus plantarum L244 and Lactobacillus rhamnosus CIRM-BIA1759, were studied in a yogurt model. Firstly, the antifungal activity of these strains against four main dairy spoilage fungi (Penicillium biforme, Mucor racemosus, Galactomyces geotrichum and Yarrowia lipolytica) was evaluated with or without trace element (6 metals and 12 vitamins) supplementation. Only manganese supplementation led to a suppression of the antifungal activity of both L. plantarum L244 and L. rhamnosus CIRM-BIA1759 against P. biforme and/or Y. lipolytica. The scavenging of trace elements was then measured using HR-ICP-MS in both cell-free yogurt whey and fungal biomass. HR-ICP-MS results showed a significant scavenging of Mn in L. plantarum L244 and L. rhamnosus CIRM-BIA1759 whey, as well as Cu for L. rhamnosus CIRM-BIA1759. Moreover, element uptake profiles, including metal and non-metal elements, for each of the target fungi were affected by the use of antifungal cultures. Finally, the role of competitionexclusion for manganese in the inhibition of 25 fungal spoilers was evaluated via oCelloScope growth follow-up. Growth inhibition by antifungal LAB strains was suppressed after Mn supplementation in cell-free whey for the 16 (out of 25) fungi initially inhibited without Mn supplementation. The nine other fungi were not inhibited or were poorly inhibited in the different tested conditions. This study confirmed the role of competitionexclusion for Mn in the antifungal activity of L. plantarum L244 and L. rhamnosus CIRM-BIA1759 strains but also revealed that this mechanism is not generic among fungal species, as the growth behavior of several tested species was not impacted by Mn scavenging. Full article

(This article belongs to the Section Food Microbiology)

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10 pages, 741 KB

Open AccessArticle

Comparison of Adjuvant Potency of Alum, AddaVax, and ISA 71 VG on the Seasonal Split Influenza Vaccine in Mice

by Li Wu, Rui Yang, Huimin Wu, Beibei Yang, Xin Zhang, Yingying Tao, Xing Wu, Shaozhen Li, Jianhong Shu, Yulong He and Huapeng Feng

Microorganisms 2025, 13(11), 2542; https://doi.org/10.3390/microorganisms13112542 - 6 Nov 2025

Influenza is a highly contagious disease and is transmitted by the upper respiratory tract. Vaccination is an effective strategy to prevent and control seasonal influenza. The current predominant split-inactivated influenza vaccine presents a high safety profile but has weak immunogenicity. The addition of [...] Read more.

Influenza is a highly contagious disease and is transmitted by the upper respiratory tract. Vaccination is an effective strategy to prevent and control seasonal influenza. The current predominant split-inactivated influenza vaccine presents a high safety profile but has weak immunogenicity. The addition of adjuvants is one method to optimize the immunogenicity of the seasonal influenza vaccine. In this study, we compared the effect of aluminum (Alum), MF59-like adjuvant AddaVax, and ISA71 VG adjuvants for the seasonal split influenza vaccine in a mouse model based on the induction of influenza-virus-specific antibody levels, body weight changes, and survival rates after lethal challenge. Two very low and sub-optimal HA doses, 0.003 µg and 0.01 µg, representing the calculated amount of HA from the A/California/07/2009 (H1N1) strain only per mouse dose, were selected and used in this study. The 0.003 µg antigen (Ag) plus AddaVax showed the best adjuvant effect among these three adjuvants. The 0.01 µg Ag plus ISA 71 VG induced the highest total IgG, IgG1, and IgG2a. Both the 0.003 µg and 0.01 µg Ag plus AddaVax protected all the immunized mice from the lethal challenge, and Alum exhibited the protective potency intermediate between that of the AddaVax and ISA 71VG. The 0.01 µg Ag plus one of these three adjuvants could enhance the efficacy of the split influenza vaccine against lethal challenge. Therefore, AddaVax is the first candidate for the further development of the adjuvanted split seasonal influenza vaccine among these three adjuvants. These initial findings offer valuable guidance for selecting promising adjuvanted influenza vaccine formulations. Full article

(This article belongs to the Topic Advances in Infectious and Parasitic Diseases of Animals)

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11 pages, 850 KB

Open AccessCommunication

Serological Investigations on West Nile Virus in Horses in Kazakhstan

by Dana A. Alibekova, Kainar B. Barakbayev, Zamira D. Omarova, Rashida A. Rystaeva, Kulyaisan T. Sultankulova, Yerbol D. Burashev, Takhmina U. Argimbayeva, Ali B. Tulendibayev, Nurdos A. Aubakir, Tangat T. Yermekbay, Khairulla B. Abeuov, Aslan A. Kerimbayev and Mukhit B. Orynbayev

Microorganisms 2025, 13(11), 2541; https://doi.org/10.3390/microorganisms13112541 - 6 Nov 2025

This study presents the first investigation of West Nile virus (WNV) seroprevalence among farmed horses in Kazakhstan. In 2024, a total of 368 serum samples were collected from horses across 106 settlements in 10 regions of the Republic of Kazakhstan. Using an enzyme-linked [...] Read more.

This study presents the first investigation of West Nile virus (WNV) seroprevalence among farmed horses in Kazakhstan. In 2024, a total of 368 serum samples were collected from horses across 106 settlements in 10 regions of the Republic of Kazakhstan. Using an enzyme-linked immunosorbent assay (ELISA), antibodies to WNV were detected in 32 horses (8.7%; 95% CI: 6.2–12.0%) from six regions. Among the seropositive animals, 26 (81.25%) were females and 6 (18.75%) were males, ranging in age from 1 to 19 years. No statistically significant association between sex and the presence of antibodies to WNV was found in any of the six regions. Significant differences between age groups were observed in Aktobe (χ² = 12.16; p = 0.002) and Turkestan (χ² = 4.20; p = 0.040). In the remaining regions (Almaty, Zhetisu, West Kazakhstan, and Atyrau), no significant age-related differences were recorded (p > 0.05). These findings confirm the circulation of WNV among horse populations in Kazakhstan and highlight the practical value and effectiveness of using horses as sentinel indicators for WNV surveillance. Full article

(This article belongs to the Special Issue Arboviruses and Global Health: Epidemiology, Pathogenesis, and Emerging Challenges)

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15 pages, 4080 KB

Open AccessArticle

ISG20 Restricts BK Polyomavirus Infection and Engages in Reciprocal Regulation with Viral Large T Antigen

by Yumin Hou, Chunlan Hu, Yejing Shi, Xiaohui Zhou, Tongyu Zhu and Nannan Wu

Microorganisms 2025, 13(11), 2540; https://doi.org/10.3390/microorganisms13112540 - 6 Nov 2025

BK polyomavirus (BKPyV) causes severe urinary tract diseases, including BKPyV-associated nephropathy (BKPyVN) and ureteric stenosis, in immunocompromised individuals such as renal transplant recipients. Effective antiviral therapies for BKPyV infection remain an unmet clinical need. While the interferon-stimulated gene 20 (ISG20) exhibits broad-spectrum antiviral [...] Read more.

BK polyomavirus (BKPyV) causes severe urinary tract diseases, including BKPyV-associated nephropathy (BKPyVN) and ureteric stenosis, in immunocompromised individuals such as renal transplant recipients. Effective antiviral therapies for BKPyV infection remain an unmet clinical need. While the interferon-stimulated gene 20 (ISG20) exhibits broad-spectrum antiviral activity against RNA viruses, its role and mechanisms against DNA viruses are poorly defined. This study demonstrates, for the first time, potent antiviral activity of ISG20 against BKPyV. This restriction was observed with both endogenous levels of ISG20 and upon overexpression, and this effect was confirmed by ISG20 knockout and immunofluorescence imaging. We observed that ISG20 expression is dynamically regulated during BKPyV infection: it is upregulated both during early infection and by expression of the viral large T antigen (LT) alone. However, endogenous ISG20 expression becomes significantly suppressed during later stages of infection, coinciding with declining LT levels. The physical interaction between LT and both wild-type and mutant ISG20 suggests a potential viral strategy to sequester this restriction factor. These findings establish ISG20 as a novel host restriction factor against BKPyV and suggest that BKPyV employs LT-mediated mechanisms to evade or counteract ISG20’s antiviral effects. Our results elucidate a complex biphasic interplay between BKPyV and host innate immunity, identifying ISG20 as a potential therapeutic target for BKPyV-associated diseases. Full article

(This article belongs to the Section Virology)

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14 pages, 636 KB

Open AccessReview

Alteration of Gut Microbiota by Ketogenic Diet as an Alternative Therapeutic Target for Drug-Resistant Epilepsy

by Mi Tang, Wei Wang, Jiwen Wang and Yingyan Wang

Microorganisms 2025, 13(11), 2539; https://doi.org/10.3390/microorganisms13112539 - 6 Nov 2025

As one of the most serious and widespread neurological disorders, epilepsy affects nearly 70 million people worldwide. In the development of this disease, significant alterations of gut microbiotas are often observed in the patients. During the treatment of drug-resistant epilepsy, which accounts for [...] Read more.

As one of the most serious and widespread neurological disorders, epilepsy affects nearly 70 million people worldwide. In the development of this disease, significant alterations of gut microbiotas are often observed in the patients. During the treatment of drug-resistant epilepsy, which accounts for ~20–30% of cases, a ketogenic diet (KD), a diet containing high fat, adequate protein, and low carbohydrate, has been widely used and showed promising therapeutic effects. The underlying mechanisms of the neuroprotective effects of a KD have been suggested in recent studies to be connected to the gut microbiota, the composition of which is dramatically influenced by this treatment. In this review, we summarize the recent advances of the relationship between a KD, gut microbiota, and epilepsy, with an emphasis on the gut bacterial changes under KD treatment, hoping to delineate the gut microbiota as a potential therapeutic target in epilepsy. Full article

(This article belongs to the Special Issue Gut Microbiota: Influences and Impacts on Human Health)

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20 pages, 3343 KB

Open AccessArticle

Environmental Heterogeneity and Host Genotype Jointly Shape Endophytic Bacterial Community Composition Associated with an Endemic Chinese Sphagnum Species

by Yan Liu, Xuechun Sun, Hongping Deng and Zhengwu Zhao

Microorganisms 2025, 13(11), 2538; https://doi.org/10.3390/microorganisms13112538 - 5 Nov 2025

Peat mosses of the genus Sphagnum are keystone species in peatland ecosystems and play critical roles in carbon sequestration, nitrogen fixation, and hydrological regulation. Indeed, these ecological functions are largely mediated by endophytic bacteria associated with Sphagnum. Here, five populations of the [...] Read more.

Peat mosses of the genus Sphagnum are keystone species in peatland ecosystems and play critical roles in carbon sequestration, nitrogen fixation, and hydrological regulation. Indeed, these ecological functions are largely mediated by endophytic bacteria associated with Sphagnum. Here, five populations of the endemic Chinese moss species, S. multifibrosum, were sampled across southern China in peatland (PH) and rock habitats (RH). High-throughput sequencing of 16S rRNA and nitrogenase (nifH) genes was applied to characterize overall endophytic bacterial diversity and diazotroph diversity associated with S. multifibrosum, respectively, alongside host microsatellite genotyping. Proteobacteria was the dominant endophytic bacterial phylum. The bacterial communities exhibited significant spatial separation between eastern and western communities and community dissimilarities significantly increased with increasing geographic distances. Environmental heterogeneity and host genetics jointly shaped endophytic bacterial community assemblage. Climate was the most important determinant influencing bacterial composition, followed by host genotype and habitat type. Temperature, precipitation, and nitrogen deposition were the primary environmental factors that influenced composition. Bacterial diversity and composition exhibited no statistically significant differences between the two habitats. Further, the richness and abundances of diazotrophs and methanotrophs from PH communities were higher than in RH communities. Co-occurrence network analysis suggested that RH bacterial networks had lower connectance but were more modularized and exhibited higher complexity than PH networks. These results highlight the ecological functions of peat mosses in carbon and nitrogen cycling and suggest a need to prioritize the conservation of S. multifibrosum in peatland environments under global climate change. The results also provide a framework to help future wetland management and biodiversity conservation efforts in China. Full article

(This article belongs to the Section Environmental Microbiology)

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11 pages, 1841 KB

Open AccessArticle

Pathogenicity Evaluation and Virulence Gene Identification of an Attenuated Duck Enteritis Virus

by Xiaona Shi, Haibin Zhuang, Dun Shuo, Luzhao Li, Shenghui Pan, Zihua Wu, Mei Tang, Wenxia Yang, Qinfang Liu, Chunxiu Yuan, Dawei Yan, Xue Pan, Bangfeng Xu, Zhifei Zhang, Minghao Yan, Qiaoyang Teng and Zejun Li

Microorganisms 2025, 13(11), 2537; https://doi.org/10.3390/microorganisms13112537 - 5 Nov 2025

Duck enteritis virus (DEV), an epornitic pathogen, causes substantial economic losses in the commercial duck industry and poses persistent risks to wild and migratory waterfowl populations. However, due to the large genomic capacity of the DEV, the understanding of the virulence-associated genes of [...] Read more.

Duck enteritis virus (DEV), an epornitic pathogen, causes substantial economic losses in the commercial duck industry and poses persistent risks to wild and migratory waterfowl populations. However, due to the large genomic capacity of the DEV, the understanding of the virulence-associated genes of DEV is still limited. In previous studies, we developed an attenuated strain E74 by serial passage of a virulent strain E1 on primary chicken embryo fibroblasts (CEFs). The bird experiment showed that the mortality rate of E1 on ducks reached 100%, and high-titered viruses were detected in all tested tissue samples. In contrast, the E74 virus has lost its pathogenicity in ducks and can only be detected at a relatively low viral load in the spleen. Furthermore, the E74 stimulated a significant increase in antibodies in the ducks at 7 days post-inoculation. To further investigate the molecular basis of the attenuation of DEV in ducks, the complete genomes of E74 and E1 were sequenced and analyzed. Compared with E1, E74 had a 5152 bp deletion in the UL region, which resulted in the lack of the hypothetical protein, LORF5, UL55 and LORF4 genes. To test the influence of the deletion on the viral pathogenicity, a rescued virus rE1-Δ5152 with the 5152 bp deletion in the UL region was generated on the E1 backbone. Animal experiments showed that the lethality of rE1-Δ5152 in ducks had disappeared. Those findings suggest that the hypothetical protein, LORF5, UL55, and LORF4 genes of DEV are associated with virus virulence, and the flexibility of this region provided excellent insertion sites for exogenous genes when DEV is used as a recombinant vaccine vector. Full article

(This article belongs to the Special Issue Epidemiology, Detection and Control of Avian Infectious Diseases)

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14 pages, 805 KB

Open AccessArticle

Impact of Kefir on the Gut–Brain Axis: Serotonin Metabolism and Signaling in Pediatric Rats

by Mehmet Gazi Boyaci, Ayhan Pektaş, Fadime Topal, Nur Önen and Bilgehan Mehmet Pektaş

Microorganisms 2025, 13(11), 2536; https://doi.org/10.3390/microorganisms13112536 - 5 Nov 2025

Serotonin (5-hydroxytryptamine) is a key neurotransmitter involved in gastrointestinal and central nervous system functions. Given that approximately 90% of serotonin is synthesized in the gut, dietary interventions targeting the gut microbiota have emerged as promising strategies to modulate serotonin homeostasis. Kefir, a fermented [...] Read more.

Serotonin (5-hydroxytryptamine) is a key neurotransmitter involved in gastrointestinal and central nervous system functions. Given that approximately 90% of serotonin is synthesized in the gut, dietary interventions targeting the gut microbiota have emerged as promising strategies to modulate serotonin homeostasis. Kefir, a fermented milk beverage rich in probiotics and bioactive compounds, has been suggested to influence gut–brain axis signaling, yet its effects in the pediatric period remain insufficiently characterized. This study aimed to investigate the impact of kefir supplementation on serotonin biosynthesis, receptor expression, and metabolic pathways in a pediatric rat model, focusing on molecular markers across brain, jejunum, and serum tissues. Sixteen male Wistar rats (four weeks old) were divided into kefir and control groups. The kefir group received daily oral gavage of kefir (1 mL/100 g) for eight weeks, while controls received saline. Gene and protein expression levels of serotonergic markers (5-HT, TPH1, TPH2, SLC6A4, VMAT2, 5-HTR2B, 5-HTR3A, and 5-HTR4) were analyzed using quantitative PCR, ELISA, and Western blotting. Serotonin turnover was assessed via 5-HIAA levels. Kefir supplementation significantly increased 5-HT and TPH1 expression in both brain and jejunum tissues. In the brain, kefir elevated TPH2 and upregulated 5-HTR3A and 5-HTR2B, while reducing 5-HIAA levels, suggesting decreased serotonin degradation. In the jejunum, 5-HTR4 expression was markedly increased. Serum analyses revealed reduced TPH1/TPH2 expression but elevated 5-HTR4 levels, indicating systemic modulation of serotonergic signaling. Kefir exerts multifaceted effects on the serotonergic system in pediatric rats by enhancing serotonin biosynthesis, modulating receptor expression, and reducing serotonin turnover. These findings highlight kefir as a potential psychobiotic capable of influencing the gut–brain axis during early life, with implications for pediatric neurodevelopment and mental health. Further research, including clinical trials, is warranted to confirm its translational potential. Full article

(This article belongs to the Special Issue Role of Dietary Nutrients in the Modulation of Gut Microbiota)

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22 pages, 4772 KB

Open AccessArticle

Effects of Dietary Rapeseed Meal on Growth Performance, Intestinal Structure, Gut Microbiota, and Related Gene Expression of Juvenile Largemouth Bass (Micropterus salmoides)

by Ximing Hou, Haiqing Wu, Rongyan Yue, Xinghua Zhou, Yongjun Chen, Li Luo, Shimei Lin, Hailong Ge and Yuanfa He

Microorganisms 2025, 13(11), 2535; https://doi.org/10.3390/microorganisms13112535 - 5 Nov 2025

This study aimed to explore the effects of dietary rapeseed meal replacing fish meal on growth performance, intestinal structure, gut microbiota, and related gene expression of juvenile largemouth bass (Micropterus salmoides). Five isonitrogenous and isolipidic diets were designed, in which rapeseed [...] Read more.

This study aimed to explore the effects of dietary rapeseed meal replacing fish meal on growth performance, intestinal structure, gut microbiota, and related gene expression of juvenile largemouth bass (Micropterus salmoides). Five isonitrogenous and isolipidic diets were designed, in which rapeseed meal replaced 0% (FM, control), 5% (RM5), 10% (RM10), 15% (RM15), and 25% (RM25) of fish meal. Then, largemouth bass (11.00 ± 0.20 g) were randomly and equally allocated to 15 experimental tanks (25 fish per tank) for an 8-week feeding trial. The results showed that growth performance declined as replacement levels increased to 25%. However, the RM5 group had the highest body crude protein, distal intestinal muscle layer thickness (MLT), and plica height (PH) and width (PW), which were significantly higher than those of the FM group. In addition, compared to the FM group, the RM15 and/or RM25 groups had higher levels of D-lactic acid, diamine oxidase, and lipopolysaccharide. Furthermore, the RM25 group exhibited higher abundances of Lactococcus and Weissella but lower levels of Aeromonas and Staphylococcus compared to the FM group. Intestinal transcriptome analysis revealed that the PI3K-Akt and NF-κB signaling pathways were significantly up-regulated when comparing the RM25 and FM groups. The results demonstrate that the replacement of 5% fish meal with rapeseed meal did not have a negative impact on the physiological status of largemouth bass. However, a replacement level of 25% reduced growth performance and damaged intestinal structure, potentially by altering the abundance of intestinal microbiota and up-regulating the PI3K-Akt and NF-κB signaling pathways. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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1 pages, 134 KB

Open AccessCorrection

Correction: Yang et al. Nutrient-Driven Metabolic Activation and Microbial Restructuring Induced by Endophytic Bacillus in Blight-Affected Forest Soils. Microorganisms 2025, 13, 1454

by Quan Yang, Shimeng Tan, Anqi Niu, Junang Liu and Guoying Zhou

Microorganisms 2025, 13(11), 2534; https://doi.org/10.3390/microorganisms13112534 - 5 Nov 2025

In the original publication [...] Full article

(This article belongs to the Section Plant Microbe Interactions)

16 pages, 3586 KB

Open AccessArticle

Active Factors in the Adult Pig Colon: Microbial Transplantation Versus Supplementation with Metabolites in Weaned Piglets

by Jianhao Cui, Liefa Tang, Zixuan Li, Shuang Wang, Jiayi Zhou, Huichao Yan and Xiaofan Wang

Microorganisms 2025, 13(11), 2533; https://doi.org/10.3390/microorganisms13112533 - 5 Nov 2025

The adult pig intestinal microbiota boosts piglet intestinal and microbiome development, thereby improving growth. However, the functional bacteria, metabolites, and their region-specific intestinal roles remain to be characterized. Administration of adult colon microbiota (CM; devoid of metabolites) to piglets promoted intestinal development post-weaning, [...] Read more.

The adult pig intestinal microbiota boosts piglet intestinal and microbiome development, thereby improving growth. However, the functional bacteria, metabolites, and their region-specific intestinal roles remain to be characterized. Administration of adult colon microbiota (CM; devoid of metabolites) to piglets promoted intestinal development post-weaning, as indicated by increased intestinal mucosal weight, villus-to-crypt ratio of the ileum (p < 0.05), and stimulated mucin secretion (p < 0.05). This effect was potentially mediated by modulating beneficial microbiota, including ASV50_Prevotella 7, ASV52_Prevotella 1, and ASV81_Coprococcus 1. Adult colon-derived microbiota was found to preferentially colonize the piglet colon, supported by significantly higher bacterial loads in colonic contents. Piglets receiving adult colon supernatant (CS; without bacterial cells) showed improved feed efficiency (FE; p < 0.05), with numerically higher body weight (BW) and average daily gain (ADG) compared to the control (CON) group. Additionally, CS transplantation (CST) promoted intestinal development, potentially by modulating abundances of beneficial bacteria species, including ASV95_Turicibacter, and ASV109_Ruminococcaceae, which correlated with increased production of antioxidant and anti-inflammatory chemicals, including protocatechuic acid (PCA, p < 0.01). Adult colon-derived microbiota and metabolites enhanced intestinal development in piglets. CS supplementation improved growth and immunity, mitigating post-weaning stress potentially through enriching growth-linked bacteria (e.g., Turicibacter and Ruminococcaceae) and metabolites production (e.g., prephenate and PCA). These findings highlight these functional microbiota and metabolites as promising direct-fed microbial or metabolite additives for piglet growth and intestinal health post-weaning. Full article

(This article belongs to the Section Gut Microbiota)

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17 pages, 4620 KB

Open AccessArticle

Aerosolization Affects Bacillus globigii Vegetative Cell and Spore Behaviors

by Brooke L. Smith, Meiyi Zhang, Sunil Kumar and Maria D. King

Microorganisms 2025, 13(11), 2532; https://doi.org/10.3390/microorganisms13112532 - 5 Nov 2025

Antimicrobial resistance (AMR) in bacteria is a critical global health threat, yet the impact of environmental stressors such as aerosolization on resistance remains unclear. We previously showed that aerosolization can induce antibiotic resistance in Escherichia coli MG1655, a gram-negative pathogen simulant. Here, we [...] Read more.

Antimicrobial resistance (AMR) in bacteria is a critical global health threat, yet the impact of environmental stressors such as aerosolization on resistance remains unclear. We previously showed that aerosolization can induce antibiotic resistance in Escherichia coli MG1655, a gram-negative pathogen simulant. Here, we investigated Bacillus globigii, a surrogate for the gram-positive pathogen Bacillus anthracis, to assess how aerosolization affects bacterial survival and antibiotic resistance. B. globigii vegetative cells and spores were aerosolized under varying conditions and durations (5, 10, 15, 30, and 45 min) into a sterile, airtight chamber and collected using the wetted wall cyclone (WWC) system. Samples were analyzed via antibiotic susceptibility testing, culture-based assay, and quantitative polymerase chain reaction (qPCR). Vegetative cells exhibited the lowest culturability after 5 and 30 min aerosolization, while spores showed reduced culturability at 15–45 min. Both vegetative cells and spores displayed lowest antibiotic susceptibility profiles after 15 min of aerosolization. Our findings suggest that aerosolization duration and bacterial state (vegetative vs. spores) can influence bacterial survival and development of antibiotic resistance. Understanding these dynamics is essential for designing strategies to mitigate the airborne spread of antibiotic-resistant bacteria. Full article

(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment (Second Edition))

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12 pages, 805 KB

Open AccessArticle

Role of Genomic, Economic, and Demographic Disparities in Mpox Epidemic in Africa: A Retrospective Cross-Country Analysis

by Blondy Kayembe-Mulumba, Anderson Kouabenan N’gattia, Marie Roseline Darnycka Belizaire, Thomas D’Aquin Koyazegbe, Marcel Mbeko Simaleko, Yap Boum II and Pierre Somsé

Microorganisms 2025, 13(11), 2531; https://doi.org/10.3390/microorganisms13112531 - 5 Nov 2025

To investigate the role of epidemic predictors in the mpox outbreak in Africa. This was a retrospective analysis of national-level mpox surveillance data from 20 mpox-affected African countries from January through December 2024. Predictors included viral clades, gross domestic product (GDP) per capita, [...] Read more.

To investigate the role of epidemic predictors in the mpox outbreak in Africa. This was a retrospective analysis of national-level mpox surveillance data from 20 mpox-affected African countries from January through December 2024. Predictors included viral clades, gross domestic product (GDP) per capita, and population density. A negative binomial regression model estimated the incidence rates ratio (IRR) [95% confidence interval] for mpox incidence and mortality. Random forest models assessed the influence of each predictor in the epidemic dynamic. Clade II was associated with lower mpox incidence (IRR = 0.15 [0.02–0.97]) and mortality (IRR = 0.09 [0.01–1.72]) compared to Clade I. GDP per capita was associated with a 95% reduction in cases count per US $1000 (IRR = 0.05 [0.38–0.74]). Population density was not significantly associated with mpox incidence or mortality. Random forest analysis confirmed GDP per capita as the strongest predictor of mpox burden. The 2024 mpox epidemic highlights how countries with low GDP per capita and Clade I face greater outbreak burdens. Strengthening health systems and addressing poverty as a key social determinant of health through a multisectoral approach are essential to ensure equitable outbreak prevention, control, and long-term resilience. Full article

(This article belongs to the Special Issue Prioritizing Diseases for Public Health in Emergency Contexts: A WHO Initiative)

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