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Microorganisms, Volume 13, Issue 9 (September 2025) – 184 articles

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33 pages, 483 KB  
Review
Human Microbiome as an Immunoregulatory Axis: Mechanisms, Dysbiosis, and Therapeutic Modulation
by Matías Cortés, Paula Olate, Rodrigo Rodriguez, Rommy Diaz, Ailín Martínez, Genisley Hernández, Nestor Sepulveda, Erwin A. Paz and John Quiñones
Microorganisms 2025, 13(9), 2147; https://doi.org/10.3390/microorganisms13092147 (registering DOI) - 14 Sep 2025
Abstract
The human microbiome plays a central role in modulating the immune system and maintaining immunophysiological homeostasis, contributing to the prevention of immune-mediated diseases. In particular, the gut microbiota is a key ecosystem for immune system maturation, especially in early life. This review aimed [...] Read more.
The human microbiome plays a central role in modulating the immune system and maintaining immunophysiological homeostasis, contributing to the prevention of immune-mediated diseases. In particular, the gut microbiota is a key ecosystem for immune system maturation, especially in early life. This review aimed to analyze the molecular and cellular mechanisms linking the microbiome to immune and neuronal functions, as well as the impact of dysbiosis and emerging therapeutic strategies targeting the microbiome. The analysis was based on scientific databases, prioritizing studies published since 2000, with special emphasis on the past decade. The microbiome influences immune signaling through microorganism-associated molecular patterns (MAMPs) and pattern recognition receptors (PRRs), including Toll-like receptors (TLRs). Additionally, microbial metabolites—such as short-chain fatty acids (SCFAs), tryptophan derivatives, and secondary bile acids—exert significant immunomodulatory effects. The intestinal epithelial barrier is also described as an active immunological interface contributing to systemic regulation. The literature highlights innovative therapies, including fecal microbiota transplantation (FMT), probiotics, and microbiome editing with CRISPR-Cas technologies. These strategies aim to restore microbial balance and improve immune outcomes. The growing body of evidence positions the microbiome as a valuable clinical and diagnostic target, with significant potential for application in personalized medicine. Full article
(This article belongs to the Special Issue Advances in Human Microbiomes)
15 pages, 4918 KB  
Article
Gastrointestinal Parasites, Ectoparasites, and Fungi in Rabbits Attending Clinical Consultations and from Private Owners and Breeders in Portugal
by Carolina Vale, João Lozano, Ana Reisinho, Mariana Louro, Manuela Oliveira, Eva Cunha, Patrícia Lopes, Lídia Gomes and Luís Madeira de Carvalho
Microorganisms 2025, 13(9), 2146; https://doi.org/10.3390/microorganisms13092146 (registering DOI) - 13 Sep 2025
Abstract
Few studies have investigated gastrointestinal (GI) and external parasites, as well as environmental fungi, in rabbits using a One Health approach. Between September 2023—May 2024, fecal, hair and skin scraping samples were collected from 72 rabbits that attended clinical consultations and from private [...] Read more.
Few studies have investigated gastrointestinal (GI) and external parasites, as well as environmental fungi, in rabbits using a One Health approach. Between September 2023—May 2024, fecal, hair and skin scraping samples were collected from 72 rabbits that attended clinical consultations and from private owners and breeders in Portugal. Diagnostic techniques included Mini-FLOTAC, direct immunofluorescence antibody, and the analysis of the virulence profile of fur fungi. A total of 58% of the rabbits were positive for GI parasites, namely Eimeria spp. (45%), Cryptosporidium spp. (32%), Trichostrongylus retortaeformis (17%), Passalurus ambiguus (13%), Graphidium strigosum (13%), and Giardia spp. (9%), with only 12% of the infected animals showing clinical signs (diarrhea). In addition, 10% of the animals were positive for Cheyletiella sp. infestations. Environmental fungi of the genera Penicillium, Rhizopus, and Scopulariopsis were isolated from 7% of these animals, with the Scopulariopsis sp. isolate S1 testing positive for proteinase, lecithinase, and gelatinase activities. Frequent sanitization and regular deworming emerged as essential factors to minimize parasitic frequency. This integrated diagnosis procedure proved to be effective in the search for parasitic and fungal agents in rabbit medicine. Further research is needed to improve the knowledge on the transmission and pathogenicity of these agents in rabbits. Full article
(This article belongs to the Special Issue Advances in Veterinary Microbiology)
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14 pages, 2248 KB  
Article
Region-Specific Gut Microbiome Variation Between Changle Geese and Yellow-Feathered Broilers: Correlations with Growth and Intestinal Development
by Dingcheng Ye, Jianxing Qiu, Zitao Fan, Luwei Zhu, Chengyong Lv and Pingting Guo
Microorganisms 2025, 13(9), 2145; https://doi.org/10.3390/microorganisms13092145 (registering DOI) - 13 Sep 2025
Abstract
This study comparatively analyzed the spatial heterogeneity of the gut microbiome across gastrointestinal segments in Changle geese versus yellow-feathered broilers to discover their links with growth and intestinal development. Twelve 63-day-old male yellow-feathered broilers and twelve 70-day-old male Changle geese were selected. Body [...] Read more.
This study comparatively analyzed the spatial heterogeneity of the gut microbiome across gastrointestinal segments in Changle geese versus yellow-feathered broilers to discover their links with growth and intestinal development. Twelve 63-day-old male yellow-feathered broilers and twelve 70-day-old male Changle geese were selected. Body weight (BW), slaughter weight (SW), absolute lengths of the small intestine (LSI) and cecum (LC), and their relative lengths normalized to body size (RLSI/RLC) were measured. Additionally, 16S rDNA sequencing of crop, proventriculus, gizzard, jejunum, cecum, and rectum microbiota was conducted to assess microbial diversity, composition, and its correlation with phenotypes. Results demonstrated higher BW, SW, LSI, LC and lower RLSI and RLC in geese versus broilers (p < 0.001). Alpha diversity analysis revealed lower microbial richness and diversity in broilers across most gastrointestinal segments (p < 0.05), while beta diversity analysis confirmed distinct community structures between two species (p = 0.001). Firmicutes dominated broiler gut microbiota (94.49%), whereas geese exhibited greater phylum-level diversity (p < 0.05). Random forestry analysis identified Top 15 core Amplicon Sequencing Variants in both the cecum and rectum, with ASV12260 (unclassified Lachnospiraceae) and ASV12412 (uncultured Faecalibacterium sp.) as key biomarkers. Correlation analyses found 21 phenotype-related ASVs (p < 0.05). Specially, two Lactobacillus ingluviei strains showed negatively correlated with LSI and RLSI in the chicken foregut (p < 0.05). And two Gallibacterium anatis strains were associated with RLSI, with one strain also showing an inverse correlation with LSI in the goose foregut (p < 0.05). Interestingly, one Peptococcus strain was negatively correlated with BW and SW, while the other was inversely associated with LC and RLC in the goose hindgut (p < 0.05). These findings provide insights into species-specific distribution patterns of gut microbiota across poultry species and their correlation with growth performance and intestinal development, developing a theoretical foundation for advancing avian digestive physiology research and optimizing feeding strategies. Full article
(This article belongs to the Section Veterinary Microbiology)
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15 pages, 4126 KB  
Article
Identification of Adeno-Associate Virus (AAV) Serotype for Endometriosis Therapy and Effect of AAV-Mediated RNAi Delivery on Gene Expression and Cell Proliferation in In Vitro Endometrial Cell Culture
by Jin Kyung Baek, Jaekyung Lee, Yun Soo Chung and Seokkyo Seo
Microorganisms 2025, 13(9), 2144; https://doi.org/10.3390/microorganisms13092144 (registering DOI) - 13 Sep 2025
Abstract
Endometriosis is a chronic estrogen-dependent condition with limited treatment options, often requiring surgery and long-term hormonal therapy that may impair ovarian function. Despite advancements in gene therapy for other diseases, its application in endometriosis remains largely unexplored. This study aimed to evaluate the [...] Read more.
Endometriosis is a chronic estrogen-dependent condition with limited treatment options, often requiring surgery and long-term hormonal therapy that may impair ovarian function. Despite advancements in gene therapy for other diseases, its application in endometriosis remains largely unexplored. This study aimed to evaluate the potential of adeno-associated virus (AAV) vectors for targeted gene therapy in endometriosis. We screened multiple AAV serotypes for infectivity in primary human ectopic and eutopic endometrial cells as well as normal ovarian stromal cells. AAV serotype 3 (AAV3) demonstrated selective infectivity toward endometrial cells while sparing ovarian tissue. AAV3-mediated delivery of small interfering RNA targeting estrogen receptor 2 reduced Estrogen receptor beta (ERβ) expression to 27% in ectopic and 49% in eutopic cells. Under estradiol and inflammatory stimulation, ERβ knockdown led to modest reductions in cellular metabolic activity in eutopic cells, whereas effects in ectopic cells did not reach statistical significance. Dual targeting of ERβ and prostaglandin-endoperoxide synthase 2 (PTGS2) showed numerically lower metabolic activity than controls under some conditions but without consistent statistical significances. These findings suggest that AAV3 can serve as an ovary-sparing, endometriosis-specific vector that facilitates gene silencing while yielding limited phenotypic effects. This gene delivery system may provide a basis for developing future gene-based therapies for endometriosis. Full article
(This article belongs to the Section Medical Microbiology)
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17 pages, 1616 KB  
Article
Dams Determine the Composition and Activity of Microbial Communities in Semiclosed Marine Basins of the White and Barents Seas, Russia
by Alexander S. Savvichev, Nikolay A. Demidenko, Vitaly V. Kadnikov, Alexey V. Beletsky, Valeria V. Belenkova, Igor I. Rusanov, Pavel A. Sigalevich and Daria A. Ivanova
Microorganisms 2025, 13(9), 2143; https://doi.org/10.3390/microorganisms13092143 (registering DOI) - 12 Sep 2025
Abstract
Microbiological and biogeochemical investigation of the bottom sediments of semiclosed basins was carried out at the Kislaya Guba tidal power station (Barents Sea) and in Kanda Bay (White Sea). Suppressed tidal water mixing is known to affect the hydrological regime of isolated basins, [...] Read more.
Microbiological and biogeochemical investigation of the bottom sediments of semiclosed basins was carried out at the Kislaya Guba tidal power station (Barents Sea) and in Kanda Bay (White Sea). Suppressed tidal water mixing is known to affect the hydrological regime of isolated basins, resulting in the development of oxygen-free sediments. The upper sediments of the studied bays were shown to contain higher concentrations of sulfide and methane, with increased rates of sulfate reduction, methanogenesis, and methane oxidation. The relative abundance of truly marine microorganisms decreased, while microorganisms common in anoxic sediments of meromictic basins developed. The indicator microorganisms with increased relative abundance were archaea of the genera Methanoregula and Methanosaeta. Bacteria of the class Chlorobia, Chloroflexi of the family Anaerolineaceae, and Rhodoferax-related bacteria were indicators of the stagnant seawater. Members of the genus Woeseia were counter-indicators, occurring only in marine water. In our opinion, under reasonably regulated water exchange via the dams, the ecosystems of the Kanda and Kislaya Guba bays may retain the characteristics of marine bays. Otherwise, the studied bays may become stratified basins with anoxic near-bottom water, harboring microbial communities similar to those inhabiting meromictic basins. Full article
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15 pages, 2116 KB  
Article
Phylogenetic Analysis of Grapevine Fanleaf Virus, Grapevine Virus A, and Grapevine Leafroll-Associated Virus 3 in Kazakhstan
by Ivan G. Frolov, Karlygash P. Aubakirova, Zhibek N. Bakytzhanova, Akbota Rakhatkyzy, Laura S. Yerbolova and Nurbol N. Galiakparov
Microorganisms 2025, 13(9), 2142; https://doi.org/10.3390/microorganisms13092142 (registering DOI) - 12 Sep 2025
Abstract
Grapevine viruses reduce harvests and degrade fruit quality, but their genetic diversity in Kazakhstan has remained unexplored. We collected symptomatic leaves from local vineyards and recovered eleven fragments of the coat-protein gene: one from grapevine fanleaf virus, five from grapevine virus A, and [...] Read more.
Grapevine viruses reduce harvests and degrade fruit quality, but their genetic diversity in Kazakhstan has remained unexplored. We collected symptomatic leaves from local vineyards and recovered eleven fragments of the coat-protein gene: one from grapevine fanleaf virus, five from grapevine virus A, and five from grapevine leafroll-associated virus 3. After Sanger sequencing, we compared these fragments with more than one thousand international counterparts to place the Kazakh strains on the global family tree. The results reveal a clear spectrum of genetic diversity that mirrors each virus’s route of spread. Grapevine virus A, which is moved both mechanically and by insects, proved the most variable; grapevine fanleaf virus, carried by dagger nematodes and pruning sap, had intermediate variability; and grapevine leafroll-associated virus 3, moved only by mealybugs and scales, was highly conserved. All Kazakh sequences fell inside established foreign lineages, showing that the viruses were imported multiple times rather than evolving locally. Grapevine virus A will require broad-coverage or multiplex PCR primers to avoid false negatives, whereas the stable leafroll virus can be monitored with a single high-sensitivity assay. Combined with vector management—mealybug control for leafroll, and nematode testing for fanleaf—these data lay the groundwork for a national clean-plant program and more resilient vineyards across Central Asia. Full article
(This article belongs to the Section Virology)
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18 pages, 347 KB  
Article
A Retrospective Study on Coinfections, Antimicrobial Resistance, and Mortality Risk Among COVID-19 Patients (2020–2021) with Consideration of Long-COVID Outcomes
by Carlos Rescalvo-Casas, Rocío Fernández-Villegas, Marcos Hernando-Gozalo, Laura Seijas-Pereda, Lourdes Lledó García, Lars Arendt-Nielsen, Juan Cuadros-González and Ramón Pérez-Tanoira
Microorganisms 2025, 13(9), 2141; https://doi.org/10.3390/microorganisms13092141 (registering DOI) - 12 Sep 2025
Abstract
Coinfections in COVID-19 patients can worsen disease severity by enhancing SARS-CoV-2 replication and proinflammatory cytokine levels. This study analyzes the characteristics of coinfected COVID-19 patients across the pandemic and their association with in-hospital mortality. We retrospectively examined data from 351 COVID-19 patients hospitalized [...] Read more.
Coinfections in COVID-19 patients can worsen disease severity by enhancing SARS-CoV-2 replication and proinflammatory cytokine levels. This study analyzes the characteristics of coinfected COVID-19 patients across the pandemic and their association with in-hospital mortality. We retrospectively examined data from 351 COVID-19 patients hospitalized in a Spanish secondary hospital between March 2020 and February–March 2021. Nasopharyngeal swabs from 340 patients were analyzed using multiplex RT-PCR to identify 26 respiratory pathogens. A total of 136 patients were coinfected with 191 bacteria (100 Gram-negative and 91 Gram-positive), 20 viruses, 18 fungi, and 1 protist. In 2021, empirical cephalosporin use increased (p = 0.009). The incidence of enterococcal coinfections tripled from 2020 to 2021 (p < 0.001). In 2021, a greater proportion of patients experienced urine (p = 0.001) and bloodstream (p = 0.010) coinfections. In 2020, there was one bloodstream infection, while in 2021, there were seven, with half of them being fatal. Coinfected patients experienced longer hospital stays and higher odds of long COVID (p < 0.001; p = 0.014; p = 0.045). Non-respiratory coinfections in 2021 correlated with increased mortality (p = 0.002). Antimicrobial resistance remained stable (p = 0.149). The rise in cephalosporin use correlated with increased Enterococcus infections, notably bloodstream infections, which were linked to mortality (p = 0.016). In 2021, coinfections were linked to prolonged hospital stays and an increased risk of mortality in our patient cohort. Full article
(This article belongs to the Special Issue Pathogen Infection and Public Health)
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13 pages, 574 KB  
Article
Comparison of Two Lateral Flow Immunochromatographic Assays for Rapid Detection of KPC, NDM, IMP, VIM and OXA-48 Carbapenemases in Gram-Negatives
by Clara Morales Dominguez, Saoussen Oueslati, Nahed Al Laham, Réva Nermont, Hervé Volland and Thierry Naas
Microorganisms 2025, 13(9), 2140; https://doi.org/10.3390/microorganisms13092140 (registering DOI) - 12 Sep 2025
Abstract
The spread of carbapenemase-producing Gram-negative bacteria poses a significant clinical challenge due to their association with severe Difficult-to-Treat nosocomial infections, as available therapies are drastically reduced. Rapid and accurate detection of carbapenemase-producing Gram-negative bacteria is critical for effective patient management, guiding appropriate antibiotic [...] Read more.
The spread of carbapenemase-producing Gram-negative bacteria poses a significant clinical challenge due to their association with severe Difficult-to-Treat nosocomial infections, as available therapies are drastically reduced. Rapid and accurate detection of carbapenemase-producing Gram-negative bacteria is critical for effective patient management, guiding appropriate antibiotic therapy, and implementing infection control measures to limit their dissemination within healthcare settings. Lateral flow immunoassays that detect the five main carbapenemases have become cornerstones in the fight against carbapenemase-producing Gram-negative bacteria. Carbapenemases evolve in response to antibiotic exposure, and therefore regular evaluation of these lateral flow immunoassays is crucial. Here, we have evaluated a novel assay, the KINVO assay (Medomics Medical Technology) and compared it to the Gold Standard of LFIAs for carbapenemase detection, the NG-TEST CARBA 5 assay (NG-Biotech) on a large panel of carbapenemase variants. The comparison between the two assays highlighted that both share key advantages such as rapidity and simplicity. However, NG-Test CARBA 5 demonstrated superior performance overall, particularly in accurately detecting IMP-type carbapenemases and the OXA-48 variant OXA-505. In contrast, the KINVO assay was more effective at detecting a broader range of KPC variants, including some that have lost carbapenem-hydrolyzing activity but gained resistance to ceftazidime/avibactam. If we consider these variants no longer as carbapenemases, and thus that they should not be detected, the NG-Test CARBA 5 performed better for KPC carbapenemase detection. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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13 pages, 1276 KB  
Article
Mechanistic Insights into Eimeria tenella-Induced Host Cell Apoptosis Through Modulation of the Mitochondrial Permeability Transition Pore
by Rui Bai, Shuying Zhu, Hui Wang, Chenyang Lv, Wenlong Zhao, Li Zhang, Yao Liu, Hanze Gao, Xiaoling Lv, Jianhui Li and Xiaozhen Cui
Microorganisms 2025, 13(9), 2139; https://doi.org/10.3390/microorganisms13092139 (registering DOI) - 12 Sep 2025
Abstract
Coccidiosis due to Eimeria tenella remains a major constraint on the poultry industry. Previous studies have revealed that E. tenella infection triggers apoptosis in host cells. The mitochondrial permeability transition pore (MPTP) plays a pivotal role in the apoptosis and necrosis observed in [...] Read more.
Coccidiosis due to Eimeria tenella remains a major constraint on the poultry industry. Previous studies have revealed that E. tenella infection triggers apoptosis in host cells. The mitochondrial permeability transition pore (MPTP) plays a pivotal role in the apoptosis and necrosis observed in infected host cells. However, the effect of MPTP opening on mitochondrial apoptotic factors remains unclear. To elucidate the dynamic changes in apoptotic signals during MPTP-mediated apoptosis in host cells infected with E. tenella, we established a chicken embryo caecal epithelial cell infection model. Cyclosporin A (CsA) was used to inhibit the MPTP. The infection rate was assessed by Hematoxylin and eosin (H&E) staining, whereas MPTP opening and the abundances of the mitochondrial apoptotic factors Smac, Endo G, and AIF were determined by flow cytometry and ELISA, respectively. The results revealed that both the degree of MPTP opening was markedly reduced in the E. tenella+CsA group compared to the E. tenella group (p < 0.05). Between 24 and 120 h post-infection (hpi), the cytoplasmic levels of Smac, Endo G, and AIF were significantly elevated in the E. tenella group compared with the control group (p < 0.05), while their mitochondrial levels were markedly decreased (p < 0.05). In contrast, mitochondrial expression of these factors was restored in the E. tenella+CsA group (p < 0.05), accompanied by a reduction in their cytoplasmic abundance (p < 0.05). These findings indicate that E. tenella promotes MPTP-dependent release of mitochondrial pro-apoptotic factors into the cytosol during the mid-to-late stages of infection, whereas pharmacological inhibition of the MPTP limits this redistribution. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
24 pages, 3301 KB  
Article
Integrative Genomics and Metabolomics Analyses Provide New Insights into the Molecular Basis of Plant Growth Promotion by Pantoea agglomerans
by Anna Grazia Ficca, Francesca Luziatelli, Renée Abou Jaoudé and Maurizio Ruzzi
Microorganisms 2025, 13(9), 2138; https://doi.org/10.3390/microorganisms13092138 - 12 Sep 2025
Abstract
Plant Growth-Promoting Rhizobacteria (PGPR) are emerging as a sustainable alternative in agriculture due to their environmentally friendly properties and their ability to enhance crop productivity. Among these, Pantoea agglomerans has gained attention for its versatility as both a biofertilizer and a biocontrol agent. [...] Read more.
Plant Growth-Promoting Rhizobacteria (PGPR) are emerging as a sustainable alternative in agriculture due to their environmentally friendly properties and their ability to enhance crop productivity. Among these, Pantoea agglomerans has gained attention for its versatility as both a biofertilizer and a biocontrol agent. In this study, we use comparative genomics to gain insight into the genetic diversity and functional specialization of members of this species. The pan-genome analysis of 20 representative P. agglomerans strains revealed that 32% of the genes constitute the core genome (2856 out of 8899), while the remaining 68% are classified as accessory or singleton genes, indicating a high level of genomic diversity within the species. Functional annotation showed that core genes are predominantly involved in central metabolic processes, whereas genes associated with specialized metabolic functions are found within the accessory and singleton categories. The comparative analysis demonstrated a mosaic distribution of genes related to nitrogen and sulfur metabolism, heavy metal resistance, defense mechanisms, and oligopeptide uptake, suggesting niche-specific adaptations and metabolic capabilities within this species. Exometabolome profiling of strains associated with different hosts, specifically plant (C1) or human (DSM3493T), demonstrated that omics-centered approaches can be utilized to select P. agglomerans strains tailored to specific agronomic requirements. Full article
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18 pages, 2863 KB  
Article
The Ecological Trap: Biodegradable Mulch Film Residue Undermines Soil Fungal Network Stability
by Maolu Wei, Yiping Wang, Feiyu Xie, Qian Sun, Huanhuan Shao, Xiaojie Cheng, Xiaoyan Wang, Xiang Tao, Xinyi He, Bin Yong and Dongyan Liu
Microorganisms 2025, 13(9), 2137; https://doi.org/10.3390/microorganisms13092137 - 12 Sep 2025
Viewed by 26
Abstract
Biodegradable mulching films are promoted as alternatives to traditional polyethylene films, but their environmental impacts remain controversial. This study investigates how biodegradable films affect microplastic pollution of soil, fungal community structure, and ecological network stability. We conducted a maize field experiment comparing conventional [...] Read more.
Biodegradable mulching films are promoted as alternatives to traditional polyethylene films, but their environmental impacts remain controversial. This study investigates how biodegradable films affect microplastic pollution of soil, fungal community structure, and ecological network stability. We conducted a maize field experiment comparing conventional polyethylene (CF, PE) and biodegradable (BF, PLA + PBAT) film residues. We used scanning electron microscopy and high-throughput sequencing of fungal ITS genes. We assessed soil properties, microplastic release, fungal communities, and network stability through co-occurrence analysis. BF degraded rapidly, releasing microplastic concentrations much higher than CF. BF increased soil carbon and nitrogen and substantially enhanced maize biomass. However, it significantly reduced soil pH and decreased key functional fungi (saprotrophs and symbionts) abundance. The fungal ecological network complexity and stability declined significantly. Correlation analysis revealed positive associations between saprotrophic and symbiotic fungi abundance and network stability. In contrast, CF reduced some nutrient levels but improved fungal network complexity and stability. This study reveals that biodegradable films create an “ecological trap.” Short-term nutrient benefits mask systematic damage to soil microbial network stability. Our findings challenge the notion that “biodegradable equals environmentally friendly.” Environmental assessments of agricultural materials must extend beyond degradability to include microplastic release, functional microbial responses, and ecological network stability. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 2nd Edition)
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20 pages, 12230 KB  
Article
Bacillus amyloliquefaciens SC06 Ameliorated Intestinal Mucosal Injury by Regulated Intestinal Stem Cells Proliferation and Differentiation via Activating Wnt/β-Catenin Signal Pathway in Clostridium perfringens-Challenged Mouse
by Hongbin Deng, Si Cheng, Jiemei Fan, Haibin Hao, Dandong Fang, Weiqin Li and Qi Wang
Microorganisms 2025, 13(9), 2136; https://doi.org/10.3390/microorganisms13092136 - 12 Sep 2025
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Abstract
The objective of our study was to verify the intervention effect of Bacillus amyloliquefaciens SC06 on NE by constructing a C. perfringens-induced intestinal damage mouse model. A total of 40 mice were randomly assigned to four treatments: CON (basal diet), CP (basal [...] Read more.
The objective of our study was to verify the intervention effect of Bacillus amyloliquefaciens SC06 on NE by constructing a C. perfringens-induced intestinal damage mouse model. A total of 40 mice were randomly assigned to four treatments: CON (basal diet), CP (basal diet + C. perfringens), SC06 + CP (basal diet + SC06 + C. perfringens) and SC06 (basal diet + SC06). Our findings indicated that SC06 supplementation was effective in maintaining the integrity of the intestinal barrier, enhancing the antioxidant capacity of the intestine, reducing the generation of an inflammatory response, and suppressing enterocyte apoptosis in the presence of C. perfringens. Furthermore, SC06 supplementation enhanced the prefoliation of intestinal stem cells (ISC) and prompted their differentiation into goblet cells and Paneth cells. Moreover, our findings indicate that SC06 promotes the proliferation of C. perfringens-induced jejunum organoids and the expression of genes and proteins associated with ISC differentiation and regeneration. The mechanism by which SC06 modulates ISCs has been validated, and the results align with those obtained in vivo. In conclusion, the findings demonstrated that SC06 stimulates the proliferation and differentiation of ISCs through the activation of the Wnt/β-catenin signaling pathway, thereby accelerating epithelial regeneration and repair. Full article
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16 pages, 2136 KB  
Review
Crossing the Barrier: Eikenella corrodens Bacteremia Following CNS Infection in a Patient Treated with Nivolumab—A Case Report and Literature Review
by Terenzio Cosio, Cataldo Maria Mannavola, Barbara Fiori, Matteo Zelinotti, Francesco Taccari, Brunella Posteraro, Tiziana D'Inzeo and Maurizio Sanguinetti
Microorganisms 2025, 13(9), 2135; https://doi.org/10.3390/microorganisms13092135 - 12 Sep 2025
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Abstract
Eikenella corrodens is a facultative anaerobic Gram-negative bacillus, part of the normal oropharyngeal flora, with opportunistic pathogenic potential particularly in immunocompromised hosts. The progression from localized intracranial infections such as cerebritis and subdural empyema to secondary bloodstream infection represents a rare but clinically [...] Read more.
Eikenella corrodens is a facultative anaerobic Gram-negative bacillus, part of the normal oropharyngeal flora, with opportunistic pathogenic potential particularly in immunocompromised hosts. The progression from localized intracranial infections such as cerebritis and subdural empyema to secondary bloodstream infection represents a rare but clinically significant pathway, especially in immuno-compromised patients. Here, we report a case of secondary E. corrodens bacteremia following left temporal cerebritis and ipsilateral subdural empyema in a 50-year-old man with advanced nasopharyngeal carcinoma treated with nivolumab. The patient presented neurological deficits and systemic inflammatory response, suggesting for a bacterial infection. Neuroimaging confirmed the intracranial infectious foci and blood cultures identified E. corrodens via MALDI-TOF MS and 16S rRNA gene sequencing. We discuss how cancer-associated immune dysregulation and immune checkpoint inhibition could modulate host susceptibility and clinical presentation of infection, potentially facilitating microbial dissemination across compromised blood–brain barriers. Additionally, we examine the cases of E. corrodens bacteremia secondary to CNS and head and neck infections. This case underscores the importance of heightened clinical vigilance for secondary bacteremia in oncologic patients with CNS infections and highlights the need for integrated microbiological and radiological assessment to optimize outcomes. Full article
(This article belongs to the Special Issue Oral Microbiota: Diseases, Health, and Beyond)
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14 pages, 244 KB  
Article
Compassionate Use of Encapsulated MKB-01 Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection: A Single-Center Experience
by Ángela Cano, Elisa Ruiz Arabi, Lourdes Ruiz, Borja José Nadales, Andrés Baumela, Manuel Recio, Isabel Machuca, Juan José Castón, Elena Pérez-Nadales and Julian Torre Cisneros
Microorganisms 2025, 13(9), 2134; https://doi.org/10.3390/microorganisms13092134 - 12 Sep 2025
Viewed by 44
Abstract
Fecal microbiota transplantation (FMT) is a safe and effective treatment for recurrent Clostridiodes difficile infection (rCDI). However, experience with the oral biologic product MKB-01 remains limited. We describe a series of 13 patients with rCDI treated with FMT using MKB-01 capsules administered orally. [...] Read more.
Fecal microbiota transplantation (FMT) is a safe and effective treatment for recurrent Clostridiodes difficile infection (rCDI). However, experience with the oral biologic product MKB-01 remains limited. We describe a series of 13 patients with rCDI treated with FMT using MKB-01 capsules administered orally. Each patient received a single dose of 4 capsules (≥2.1–2.5 × 1011 microorganisms) with water after a 2 h fasting period. Antibiotic therapy was discontinued pre FMT. Clinical evaluation was performed at weeks 8 and 12. The mean number of prior recurrences was 1.5 (range: 1–3 episodes). In 12 patients (92.3%), FMT was administered after resolution of the current episode; in one patient (7%), it was administered on day 3 of fidaxomicin therapy, prior to symptom resolution. At week 8, clinical cure (Absence of baseline symptoms for at least 72 h) was achieved in 11 patients (84.6%). An additional patient (7%) responded to a second FMT. One recurrence occurred at 8 weeks and was resolved with a second FMT. Therefore, the overall clinical response rate after one or more FMTs was 12 out of 13 patients (92.3%). The procedure was well tolerated; only one patient experienced self-limited diarrhea. These findings support oral FMT with MKB-01 capsules as a safe and effective option for treating rCDI. Full article
(This article belongs to the Special Issue Latest Research on Clostridioides difficile)
16 pages, 4106 KB  
Article
Halogenation and Dehalogenation Potential of Microorganisms in Yangtze River Waters
by Zhixuan Wang, Lin Hu, Li Wang and Rulong Liu
Microorganisms 2025, 13(9), 2133; https://doi.org/10.3390/microorganisms13092133 - 12 Sep 2025
Viewed by 36
Abstract
The discharge of pollutants into rivers has been increasing with the rapid industrial development and extensive agricultural use of pesticides and herbicides. Halogenated organic compounds (HOCs) represent a significant class of environmental pollutants. It has been found that microorganisms have the ability not [...] Read more.
The discharge of pollutants into rivers has been increasing with the rapid industrial development and extensive agricultural use of pesticides and herbicides. Halogenated organic compounds (HOCs) represent a significant class of environmental pollutants. It has been found that microorganisms have the ability not only to degrade HOCs but also to synthesize them. Little is known about the halogenation and dehalogenation potential of microorganisms in river waters. In this study, we investigated the halogenation and dehalogenation potentials of microorganisms in the Yangtze River, which originates from the Tibetan Plateau, flows through southwestern, central and eastern China, and finally joins the East China Sea. A systematic metagenomic and bioinformatics analysis identified and quantified genes encoding four dehalogenases and two halogenases, providing fundamental data for the halogen cycle in the Yangtze River water body. The study showed that the microbial community in the Yangtze water body was mainly associated with dehalogenation potential, and the relative abundance of dehalogenase genes was higher than that of halogenase genes. Among the microorganisms with halogenation and dehalogenation potentials, Pseudomonadota and Actinomycetota dominated. Some microorganisms possessed both halogenation and dehalogenation functions, suggesting a potential adaptive strategy to environmental fluctuations. The presence of diverse and complete dehalogenation metabolic pathways highlights the microbial potential for bioremediation. These microorganisms not only contribute to the degradation of halogenated organic matter but also play crucial roles in carbon, nitrogen, and sulfur cycling. This study provides essential data for understanding microbial halogenation and dehalogenation potential in the Yangtze River, offering insights into the microbial-driven biogeochemical cycling mechanisms in its waters. Full article
(This article belongs to the Collection Biodegradation and Environmental Microbiomes)
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12 pages, 257 KB  
Article
Epidemiological and Microbiological Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates in a Regional Greek Hospital: A Retrospective Study
by Pandora Tsolakidou and Maria Chatzidimitriou
Microorganisms 2025, 13(9), 2132; https://doi.org/10.3390/microorganisms13092132 - 12 Sep 2025
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Abstract
Carbapenemase-producing Klebsiella pneumoniae (CRKP) is a critical public health threat, particularly in Greece, where high prevalence limits therapeutic options. This retrospective study analyzed 26 CRKP isolates recovered at the General Hospital of Volos between July 2024 and January 2025, aiming to correlate carbapenemase [...] Read more.
Carbapenemase-producing Klebsiella pneumoniae (CRKP) is a critical public health threat, particularly in Greece, where high prevalence limits therapeutic options. This retrospective study analyzed 26 CRKP isolates recovered at the General Hospital of Volos between July 2024 and January 2025, aiming to correlate carbapenemase phenotypes with clinical and epidemiological parameters. Demographic, clinical, and microbiological data were extracted from patient records, and isolates underwent phenotypic carbapenemase detection, antimicrobial susceptibility testing, and molecular characterization using real-time PCR; four isolates were further analyzed using whole-genome sequencing. CRKP was detected across multiple hospital departments, notably in the Emergency Department (n = 5) and Intensive Care Unit (n = 6). KPC producers predominated (n = 9), followed by NDM (n = 6), VIM (n = 1), and OXA-48 (n = 6). All VIM- or NDM + VIM-positive cases were associated with mortality. High-risk clones, including ST15, ST11, and ST307, were identified, with one ST15 isolate harboring blaNDM-1, blaVIM-1, and chromosomal colistin resistance; this is the first such report in Greece. Colistin and gentamicin were the most active agents in vitro; three isolates were pan-drug-resistant. The findings highlight significant CRKP circulation outside ICUs, the role of horizontal gene transfer in resistance dissemination, and the need to expand screening and rapid diagnostics to non-ICU settings. Enhanced molecular surveillance targeted at infection control and strengthened antimicrobial stewardship programs are essential for limiting the spread of CRKP. Full article
17 pages, 2360 KB  
Article
Harvest Stage Dictates the Nutritive Value of Sorghum Stalk Silage by Shaping Its Fermentation Profile and Microbial Composition
by Xiaoqiang Zhao, Ruiyi Liu, Jing Wang, Yawei Zhang, Shuo Zhang, Wenbin Bai, Qingshan Liu and Yuanqing Zhang
Microorganisms 2025, 13(9), 2131; https://doi.org/10.3390/microorganisms13092131 - 11 Sep 2025
Viewed by 152
Abstract
The present experiment aimed to investigate the effects of harvest stages on the fermentation quality and nutritional value of sorghum stalk silage. Sorghum stalks were harvested at the three stages (milk, dough, and ripe), chopped, and ensiled for 60 d. Each treatment had [...] Read more.
The present experiment aimed to investigate the effects of harvest stages on the fermentation quality and nutritional value of sorghum stalk silage. Sorghum stalks were harvested at the three stages (milk, dough, and ripe), chopped, and ensiled for 60 d. Each treatment had five replicates, and the silages were evaluated for fermentation quality, nutritional composition, in vitro rumen fermentation characteristics, and bacterial community profiles. The results showed that the crude protein, neutral detergent fiber, and acid detergent fiber contents decreased significantly with harvest maturity (p < 0.05). Consequently, silage from the ripe stage possessed the highest dry matter, relative feed value, and total digestible nutrients (p < 0.05). In vitro rumen fermentation indicated that the ripe stage silage exhibited the greatest gas production, and the lowest concentrations of ruminal ammonia–nitrogen (p < 0.05). Microbial analysis revealed a shift from dominant epiphytic Proteobacteria to fermentative Firmicutes post-ensiling, with the ripe stage community co-dominated by Lactobacillus and Leuconostoc, in contrast to the milk stage’s enrichment with Klebsiella. In conclusion, harvesting sorghum at the ripe stage is the optimal strategy as it establishes a beneficial microbial community, resulting in silage with superior nutritional value and rumen fermentation efficiency. Full article
(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)
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14 pages, 1772 KB  
Article
Biosurfactant-Mediated Inhibition of Salmonella Typhimurium Biofilms on Plastics: Influence of Lipopolysaccharide Structure
by Shadi Khonsari, Andrea Cossu, Milan Vu, Dallas Roulston, Massimiliano Marvasi and Diane Purchase
Microorganisms 2025, 13(9), 2130; https://doi.org/10.3390/microorganisms13092130 - 11 Sep 2025
Viewed by 143
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium is a major foodborne pathogen whose ability to form biofilms contributes to persistent contamination in food-processing and clinical environments. This study investigated the anti-biofilm activity of the biosurfactant surfactin, produced by Bacillus subtilis, against S. [...] Read more.
Salmonella enterica subsp. enterica serovar Typhimurium is a major foodborne pathogen whose ability to form biofilms contributes to persistent contamination in food-processing and clinical environments. This study investigated the anti-biofilm activity of the biosurfactant surfactin, produced by Bacillus subtilis, against S. Typhimurium wild type (LT2) and its lipopolysaccharide (LPS)-modified mutants on commonly used plastic surfaces such as polypropylene (PP) and polystyrene (PS). Biofilm formation was quantified using the crystal violet assay, revealing significantly higher biomass on PS compared to PP (p < 0.0001). Surfactin at 5 µg/mL was identified as the minimum biofilm inhibitory concentration (MBIC), significantly reducing biofilm formation in the wild-type and LPS mutants rfaL, rfaJ, rfaF (all p < 0.0001), and rfaI (p < 0.01). Further analysis using fluorescence microscopy and SYPRO® Ruby staining confirmed a significant reduction in extracellular polymeric substances (EPSs) on PP surfaces following surfactin treatment, particularly in strains LT2 (p < 0.0001), rfa (p < 0.01), rfaL (p < 0.0001), rfaG (p < 0.05), and rfaE (p < 0.0001). These findings highlight the influence of LPS structure on biofilm development and demonstrate surfactin’s potential as an eco-friendly antimicrobial agent for controlling S. Typhimurium biofilms on food-contact surfaces. Analysis of mutants revealed that disruption of the rfa gene, which is involved in the biosynthesis of the outermost region of the lipopolysaccharide (LPS), significantly reduced bacterial attachment to polypropylene. This suggests that interactions between the external LPS layer and the plastic surface are important for colonisation. In contrast, mutants in core LPS biosynthesis genes such as rfaE and rfaD did not show any notable differences in attachment compared to the wild-type strain. This highlights the specific importance of outer LPS components, particularly under surfactant conditions, in mediating interactions with plastic surfaces. This work supports the application of biosurfactants in food safety strategies to reduce the risk of biofilm-associated contamination. Full article
(This article belongs to the Section Biofilm)
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16 pages, 698 KB  
Review
Autoimmune Skin Diseases in the Era of COVID-19: Pathophysiological Insights and Clinical Implications
by Aikaterini I. Liakou, Eleni Routsi, Kalliopi Plisioti, Eleni Tziona, Dimitra Koumaki, Magdalini Kalamata, Evangelia-Konstantina Bompou, Rozeta Sokou, Petros Ioannou, Stefanos Bonovas, George Samonis, Andreas G. Tsantes and Alexander Stratigos
Microorganisms 2025, 13(9), 2129; https://doi.org/10.3390/microorganisms13092129 - 11 Sep 2025
Viewed by 180
Abstract
The COVID-19 pandemic has highlighted intricate associations between SARS-CoV-2 infection and autoimmune skin diseases (ASDs). This review examines the bidirectional relationship between COVID-19 and ASDs including hidradenitis suppurativa, psoriasis, atopic dermatitis, alopecia areata, autoimmune bullous diseases, cutaneous and systemic lupus erythematosus, systemic sclerosis, [...] Read more.
The COVID-19 pandemic has highlighted intricate associations between SARS-CoV-2 infection and autoimmune skin diseases (ASDs). This review examines the bidirectional relationship between COVID-19 and ASDs including hidradenitis suppurativa, psoriasis, atopic dermatitis, alopecia areata, autoimmune bullous diseases, cutaneous and systemic lupus erythematosus, systemic sclerosis, dermatomyositis, and lichen planus. Current evidence indicates that SARS-CoV-2 may precipitate or worsen ASDs via mechanisms such as molecular mimicry, dysregulated cytokine signaling, and enhanced Th1/Th17 immune responses, leading to loss of self-tolerance and autoantibody production. Epidemiological studies have identified increased incidence and flares of psoriasis, hidradenitis suppurativa, and other ASDs following both COVID-19 infection and vaccination, with mRNA vaccines associated with a higher risk of flare in hidradenitis suppurativa compared with non-mRNA vaccines. Notably, severe COVID-19 is associated with a greater risk of new-onset autoimmune disease, and patients with pre-existing inflammatory skin conditions may have increased susceptibility to SARS-CoV-2 infection but experience less severe COVID-19 courses. These findings underscore the need for ongoing surveillance and mechanistic studies to clarify the immunopathogenic links between SARS-CoV-2 and ASDs and inform management strategies for affected patients in the context of both infection and vaccination. Full article
(This article belongs to the Special Issue SARS-CoV-2: Infection, Transmission, and Prevention)
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30 pages, 920 KB  
Review
A Comprehensive Review of Digestive Endoscopy-Associated Infections: Bacterial Pathogens, Host Susceptibility, and the Impact of Viral Hepatitis
by Deniz Günșahin, Vasile Șandru, Gabriel Constantinescu, Mădălina Ilie, Teodor Cabel, Ramona Ștefania Popescu, Bogdan Silviu Ungureanu, Victor Daniel Miron, Gheorghe G. Balan, Diana Cotigă, Bogdan Miutescu, Gülşen Özkaya Şahin and Oana Săndulescu
Microorganisms 2025, 13(9), 2128; https://doi.org/10.3390/microorganisms13092128 - 11 Sep 2025
Viewed by 192
Abstract
Gastrointestinal (GI) interventional endoscopy has evolved into a cornerstone of modern gastroenterology, offering minimally invasive solutions for complex conditions. However, these procedures are not without risk, particularly with respect to post-procedural infections. While rare, such infections can have significant clinical consequences and are [...] Read more.
Gastrointestinal (GI) interventional endoscopy has evolved into a cornerstone of modern gastroenterology, offering minimally invasive solutions for complex conditions. However, these procedures are not without risk, particularly with respect to post-procedural infections. While rare, such infections can have significant clinical consequences and are increasingly recognized as a public health concern. This narrative review provides a comprehensive overview of infections associated with GI endoscopy, focusing on transmission mechanisms, microbial agents involved, host susceptibility, preventive strategies, and diagnostic and therapeutic approaches. Infections following GI endoscopy remain infrequent but clinically significant, particularly in high-risk procedures such as endoscopic retrograde cholangiopancreatography and endoscopic ultrasound. Duodenoscopes represent a major vector for exogenous infection, often involving multidrug-resistant bacteria such as Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterococcus spp. Host-related factors increase the risk of infection. Risk factors associated with post-endoscopic infections include advanced age, male sex, non-white ethnicity, immunosuppression, presence of cholangiocarcinoma, autoimmune diseases, liver cirrhosis of viral and/or alcoholic etiology, chronic kidney disease, high-risk cardiac conditions, or chemotherapy. New reprocessing methods, such as ethylene oxide gas sterilization, automated endoscope reprocessors, and selective use of single-use endoscopes and duodenoscopes, may contribute to lowering infection rates. Greater awareness of infection risks, improved infection control practices, and adherence to updated guidelines are crucial for enhancing patient safety in digestive endoscopy. Multidisciplinary strategies, including surveillance, device innovation, and personalized risk assessment, are needed to address this evolving challenge. Full article
(This article belongs to the Section Public Health Microbiology)
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31 pages, 2807 KB  
Article
The Hidden Microbial World in the Gut of the Terrestrial Snail Cornu aspersum maxima and the Unexpected Negative Effects of Synbiotics
by Efstratios Efstratiou, Maria V. Alvanou, Dimitrios Loukovitis, Ioannis A. Giantsis and Alexandra Staikou
Microorganisms 2025, 13(9), 2127; https://doi.org/10.3390/microorganisms13092127 - 11 Sep 2025
Viewed by 181
Abstract
The intestinal microbiome plays a pivotal role in the physiology and health of terrestrial gastropods yet remains largely unexplored. This study aimed to characterize the gut microbial communities of the farmed snail Cornu aspersum maxima and to assess the effects of dietary supplementation [...] Read more.
The intestinal microbiome plays a pivotal role in the physiology and health of terrestrial gastropods yet remains largely unexplored. This study aimed to characterize the gut microbial communities of the farmed snail Cornu aspersum maxima and to assess the effects of dietary supplementation with the probiotic Lactobacillus plantarum, the prebiotic inulin, and their combination (synbiotic) on microbial diversity, snail growth, and survival. In total, 300 sexually immature snails (~9.8 g average body mass, ~5 months old) were assigned to four dietary groups (Control, Probiotic, Prebiotic, Synbiotic), each comprising three replicates of 25 snails. Individuals of similar size were placed in each container within the treatment groups. The Probiotic group received 1.25 mg of L. plantarum (1010 CFU/g) per 5 g of feed, the Prebiotic group received 1 g of inulin per 5 g of feed, and the Synbiotic group received both supplements at the same dosages. Over the 60-day trial, the gut microbiota was analyzed via 16S rRNA amplicon sequencing using Oxford Nanopore technology. The results revealed significant treatment-dependent shifts (p < 0.05) in microbial composition at both the phylum and genus levels. The dominant bacterial phyla identified were Proteobacteria and Actinobacteria, while a notable increase in unclassified microbial taxa was observed, especially in the inulin-supplemented groups. Despite its known probiotic properties, L. plantarum was not detected post-administration, suggesting a transient effect. The synbiotic group exhibited significantly higher microbial diversity (Shannon index, p < 0.05) but also the highest mortality rate. All groups showed limited weight gain, with reductions observed after day 30. Potentially pathogenic genera (e.g., Klebsiella, Mycoplasma, Staphylococcus) were detected but showed reduced abundance in the probiotic- and prebiotic-treated groups, suggesting a protective effect. Overall, probiotic supplementation with L. plantarum enhanced the abundance of beneficial Actinobacteria and reduced potentially pathogenic taxa, while the prebiotic inulin promoted the growth of unclassified but potentially beneficial genera. However, synbiotic administration, despite increasing microbial diversity, was associated with adverse outcomes including 100% mortality at day 60. These findings highlight both the potential and the risks of dietary manipulation of the snail microbiome, underscoring the need for cautious application of synbiotics in snail farming. They also underscore the dynamic nature of the snail gut microbiome and its responsiveness to dietary interventions, providing valuable insights for sustainable snail farming and future probiotic applications in invertebrate species. Full article
(This article belongs to the Special Issue Gut Microbiota: Metagenomics to Study Ecology, 2nd Edition)
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12 pages, 281 KB  
Article
Assessment of the Impact of Antimicrobial Photodynamic Therapy Using a 635 nm Diode Laser and Toluidine Blue on the Susceptibility of Selected Strains of Candida and Staphylococcus aureus: An In Vitro Study
by Marcin Tkaczyk, Anna Mertas, Anna Kuśka-Kiełbratowska, Jakub Fiegler-Rudol, Elżbieta Bobela, Maria Cisowska, Dariusz Skaba and Rafał Wiench
Microorganisms 2025, 13(9), 2126; https://doi.org/10.3390/microorganisms13092126 - 11 Sep 2025
Viewed by 113
Abstract
Yeasts of the genus Candida (C.) and the bacterium Staphylococcus aureus (S. aureus) are among the most common pathogens responsible for infections that are difficult to treat, including those resistant to standard therapy. In recent decades, this has become [...] Read more.
Yeasts of the genus Candida (C.) and the bacterium Staphylococcus aureus (S. aureus) are among the most common pathogens responsible for infections that are difficult to treat, including those resistant to standard therapy. In recent decades, this has become an increasing clinical problem. In response to the limitations of traditional procedures, antimicrobial photodynamic therapy (aPDT), which combines light, a photosensitizer, and oxygen, is gaining growing interest. The aim of this study was to evaluate the in vitro effectiveness of aPDT using a 635 nm diode laser in combination with toluidine blue O (TBO) against Candida spp. and S. aureus. Reference strains of C. albicans, C. glabrata, C. krusei, and S. aureus were subjected to aPDT. In phase I of this study, the optimal TBO incubation time was assessed with constant laser parameters. In phase II, the impact of the physical parameters of the laser, irradiation time, and output power, was analyzed, with the TBO incubation time set based on the phase I results, to evaluate the degree of microbial reduction (CFU/mL). Statistical analyses were then conducted to assess significance. TBO-mediated aPDT significantly reduced microbial viability, depending on incubation time and laser settings. The minimal effective incubation times were 10 min for Candida spp. and 5 min for S. aureus. The highest pathogen inactivation efficacy was observed at an output power of 400 mW and an irradiation time of 120 s. The use of the photosensitizer or laser alone did not result in significant antimicrobial effects. TBO-mediated aPDT may serve as an effective complement to conventional antimicrobial therapy and, in selected cases (e.g., drug resistance), has the potential to partially or fully replace it. The observed minimal effective incubation times provide a practical baseline, but further statistical comparisons are required to determine whether these durations are truly optimal. Full article
23 pages, 2293 KB  
Article
Bioconversion of a Dairy By-Product (Scotta) into Mannitol-Stabilized Violacein via Janthinobacterium lividum Fermentation
by Mario Trupo, Rosaria Alessandra Magarelli, Salvatore Palazzo, Vincenzo Larocca, Maria Martino, Anna Spagnoletta and Alfredo Ambrico
Microorganisms 2025, 13(9), 2125; https://doi.org/10.3390/microorganisms13092125 - 11 Sep 2025
Viewed by 217
Abstract
Violacein is a natural pigment with a wide range of biological activities, including antimicrobial, antitumor, and immunostimulatory properties. However, its industrial-scale production is hindered by low yields from microbial fermentation. This study investigated the use of scotta, a low-value by-product of the [...] Read more.
Violacein is a natural pigment with a wide range of biological activities, including antimicrobial, antitumor, and immunostimulatory properties. However, its industrial-scale production is hindered by low yields from microbial fermentation. This study investigated the use of scotta, a low-value by-product of the dairy industry, as an alternative and cost-effective substrate for violacein biosynthesis using Janthinobacterium lividum DSM1522. Different types of scotta, including one derived from lactose-free cheese production, were characterized and tested in flask cultures and a 2 L bioreactor. The results demonstrated that both medium dilution and increased oxygen-transfer coefficient (kLa) significantly enhanced violacein production. In the bioreactor, a final yield of 58.72 mg of violacein for each litre of diluted scotta was achieved. The pigment was then stabilized through a spray-drying process using mannitol as a carrier, resulting in a water-soluble powder that retained antibacterial activity against Bacillus subtilis. The drying process also improved pigment solubility in water, suggesting its potential application in formulations to control Gram-positive bacteria. Overall, this study highlights the potential of scotta as a sustainable fermentation substrate and presents a promising encapsulation approach for violacein stabilization. However, further investigations are needed to optimize the spray-drying process, specifically, to characterize the microgranules and to determine their storage stability. Full article
(This article belongs to the Special Issue Industrial Microbiology)
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15 pages, 3123 KB  
Article
Canine Parvovirus and Vaccine-Origin Feline Panleukopenia Virus in Wastewater, Arizona, USA: July 2022–June 2023
by Jacqueline Vargas, Brenda Bermudez-Rivera, Izabella Block, Gray Shaffer, Lesley Estrada, Tegan Dadd, Tanner Dickerson, Courtney Curtis, Craig Woods, Erin M. Driver, Rolf U. Halden, Arvind Varsani, Matthew Scotch and Temitope O. C. Faleye
Microorganisms 2025, 13(9), 2124; https://doi.org/10.3390/microorganisms13092124 - 11 Sep 2025
Viewed by 124
Abstract
Canine parvovirus (CPV) is a virus of veterinary health significance and a member of the Parvoviridae family. Despite its clinical significance and global distribution, surveillance is often limited to cases serious enough to result in veterinary visit and/or hospitalization, thereby limiting our understanding [...] Read more.
Canine parvovirus (CPV) is a virus of veterinary health significance and a member of the Parvoviridae family. Despite its clinical significance and global distribution, surveillance is often limited to cases serious enough to result in veterinary visit and/or hospitalization, thereby limiting our understanding of its evolution and diversity. In this study, we coupled wastewater surveillance (WWS), long-range polymerase chain reaction (PCR) and long-read sequencing and demonstrate the utility of this approach for community-level monitoring of parvovirus diversity. We screened archived viral concentrates from wastewater (WW) collected monthly from July 2022 to June 2023 as part of a previous virus surveillance study from a population of ~500,000 people in Maricopa County, Arizona, USA. Using long-range PCR, the coding-complete sequences (~4.5 kb) were amplified as single contigs and sequenced on a long-read sequencer (MinION). Reads were trimmed, assembled, and contigs subjected to a bioinformatics workflow that includes phylogenetics, immuno-informatics and protein structure modelling. The ~4.5 kb amplicons were amplified from all the samples and sequenced. Twelve contigs (length: 4555 nt to 4675 nt: GC%: 35% to 36%) were assembled from 86,858 trimmed and size-selected reads (length 4400 nt–4900 nt) and all typed as parvoviruses. Overall, there were 11 CPV variants (2a, 2b and 2c) and 1 feline panleukopenia virus (FPV) variant. The FPV was 100% similar in the VP2 genomic region to the 1964 Johnson snow leopard strain present in the Felocell vaccine, suggesting recent shedding post-vaccination. For the CPVs, our analysis showed multiple amino acid substitutions in the VP2 and NS1 proteins, suggestive of host immune pressure and viral adaptation, respectively. The CPV variants clustered predominantly with North and South American variants, suggesting transboundary viral movement and multiple CPV-2c transmission chains seem evident. To the best of our knowledge, we here document the first detection of vaccine-origin FPV in WW. We show the presence of CPV-2a, 2b and 2c in the population sampled and provide evidence that suggests transmission of CPVs across the Americas. Our results also show that WWS coupled with long-range PCR and long-read sequencing is a feasible population-level complement to clinical case surveillance that also facilitates detection of vaccine-origin virus variants. The model we demonstrate here for tracking parvoviruses can also be easily extended to other DNA viruses of human and veterinary health significance. Full article
(This article belongs to the Special Issue Surveillance of Pathogens in the Environment)
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18 pages, 5498 KB  
Article
Dose-Dependent Effect of Tilmicosin Residues on ermA Rebound Mediated by IntI1 in Pig Manure Compost
by Pengfei Zhang, Qingnan Mo, Chang Liu, Qing Liu, Jiaojiao Xu, Yan Wang, Xin Wen and Yinbao Wu
Microorganisms 2025, 13(9), 2123; https://doi.org/10.3390/microorganisms13092123 - 11 Sep 2025
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Abstract
The impact of varying antibiotic residue levels on antibiotic resistance gene (ARG) removal during composting is still unclear. This study investigated the impact of different residue levels of tilmicosin (TIM), a common veterinary macrolide antibiotic, on ARG removal during pig manure composting. Three [...] Read more.
The impact of varying antibiotic residue levels on antibiotic resistance gene (ARG) removal during composting is still unclear. This study investigated the impact of different residue levels of tilmicosin (TIM), a common veterinary macrolide antibiotic, on ARG removal during pig manure composting. Three groups were used: the CK group (no TIM), the L group (246.49 ± 22.83 mg/kg TIM), and the H group (529.99 ± 16.15 mg/kg TIM). Composting removed most targeted macrolide resistance genes (MRGs) like ereA, ermC, and ermF (>90% removal), and reduced ermB, ermX, ermQ, acrA, acrB, and mefA (30–70% removal). However, ermA increased in abundance. TIM altered compost community structure, driving succession through a deterministic process. At low doses, TIM reduced MRG–bacteria co-occurrence, with horizontal gene transfer via intI1 being the main cause of ermA rebound. In conclusion, composting reduces many MRG levels in pig manure, but the persistence and rebound of genes like ermA reveal the complex interactions between composting conditions and microbial gene transfer. Full article
(This article belongs to the Special Issue Antimicrobial Resistance (AMR): From the Environment to Health)
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9 pages, 8844 KB  
Brief Report
Ducklings Were Susceptible to Swine Acute Diarrhea Syndrome Coronavirus Under Experimental Conditions
by Teng Zhang, Longfa Li, Jiayi Wang, Jiale Yao, Guoqing Xu, Chaoliang Leng, Yong Wang and Lunguang Yao
Microorganisms 2025, 13(9), 2122; https://doi.org/10.3390/microorganisms13092122 - 11 Sep 2025
Viewed by 100
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV), similar to other coronaviruses, exhibits extensive host tropism and has caused huge losses to the pig industry since its first outbreak in 2017. However, the susceptibility of SADS-CoV in waterfowl remains unclear. In the present study, 10-day-old [...] Read more.
Swine acute diarrhea syndrome coronavirus (SADS-CoV), similar to other coronaviruses, exhibits extensive host tropism and has caused huge losses to the pig industry since its first outbreak in 2017. However, the susceptibility of SADS-CoV in waterfowl remains unclear. In the present study, 10-day-old ducklings were orally administered 5.95 log10 TCID50 (the tissue culture infective dose 50%) of SADS-CoV, with a medium serving as a control treatment, to assess ducklings’ susceptibility. Results indicated that the ducklings exhibited mild diarrhea symptoms, experienced slow weight gain, and one duckling died seven days after inoculation. Histopathological examination revealed that the viral infection caused pathological damage to the spleen, intestine, and lungs. Tissue immunofluorescence demonstrated viral replication in the spleen, lungs, and intestine. This study provides the first evidence that SADS-CoV can infect ducklings under laboratory conditions. Given that waterfowl may serve as significant reservoirs for various viruses, this finding raises considerable concerns. Full article
(This article belongs to the Special Issue Avian Pathogens: Importance in Animal Health and Zoonotic Risks)
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22 pages, 6309 KB  
Article
Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions
by Magnolia del Carmen Ramírez-Hernández, Javier Gaytán-Cervantes, Carolina González-Torres, Miguel Ángel Loyola-Cruz, Rebeca Eunice García-Mendiola, Clemente Cruz-Cruz, Iliana Alejandra Cortés-Ortíz, Eduardo García-Moncada, Teresa López-Flores, Emilio Mariano Durán-Manuel, Nancy Gómez-Mancilla, María Fernanda Oviedo-López, Carlos Alberto Jiménez-Zamarripa, Araceli Rojas-Bernabé, Omar Agni García-Hernández, Jonathan Puente-Rivera, Adolfo López-Ornelas, Nayeli Goreti Nieto-Velázquez, Dulce Milagros Razo Blanco-Hernández, Julio César Castañeda-Ortega, Benito Hernández-Castellanos, Gabriela Anaya-Saavedra, Claudia Camelia Calzada-Mendoza and Juan Manuel Bello-Lópezadd Show full author list remove Hide full author list
Microorganisms 2025, 13(9), 2121; https://doi.org/10.3390/microorganisms13092121 - 11 Sep 2025
Viewed by 162
Abstract
Progressive immune damage associated with Human Immunodeficiency Virus (HIV) alters mucosal homeostasis, favouring oral microbial imbalance and the development of opportunistic infections. The aim of this study was to characterize the composition and structure of the oral microbiota in different clinical conditions of [...] Read more.
Progressive immune damage associated with Human Immunodeficiency Virus (HIV) alters mucosal homeostasis, favouring oral microbial imbalance and the development of opportunistic infections. The aim of this study was to characterize the composition and structure of the oral microbiota in different clinical conditions of HIV infection. A cross-sectional study was conducted in 99 Mexican men divided into five groups: HIV-negative controls, newly diagnosed without antiretroviral treatment, virally suppressed, with oral candidiasis, and with HPV infection. Metagenomic DNA was obtained from salivary samples, and the V1–V3 region of the 16S rRNA gene was massively sequenced. Taxonomic profiles, alpha/beta diversity, differential abundance, microbial co-occurrence networks and degree of dysbiosis were analysed. The results showed distinctive profiles between the groups. Alpha and beta diversity was significantly higher in the groups with oral Candida and HPV lesions, reflecting a disturbance of microbial balance. Differential abundance analysis revealed an increase in Streptococcus, Veillonella, Lactobacillus and Actinomyces genera in HIV patients, while healthy subjects showed higher abundance of Neisseria, Treponema, and Rothia, associated with a eubiotico state. The group of patients with HPV lesions had the highest number of taxa with differential abundance, suggesting an ecological environment altered by the lesion. Analysis of co-occurrence networks revealed a progressive pattern of microbial complexity: controls presented simple networks with weak positive correlations, while HIV groups showed increased connection density and appearance of structured nuclei. The group of patients with HPV lesions presented the highest connectivity, with multiple strongly correlated cores and core nodes such as Prevotella melaninogenica and Shuttleworthia. The dysbiosis score increased progressively from healthy subjects to those with HPV lesions, indicating a gradient of oral microbial disruption. These findings suggest that HIV immunosuppression and the presence of oral lesions are associated with enhanced dysbiosis, although their individual contributions could not be independently assessed due to the absence of non-HIV lesion controls. The integration of microbial networks and dysbiosis scores could be useful for assessing mucosal and immune health in people with HIV and used as biomarkers of clinical progression. Full article
(This article belongs to the Section Virology)
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19 pages, 3429 KB  
Article
Time-Course Gene Expression of ‘Candidatus Liberibacter solanacearum’, Prophage, and Wolbachia Genes in Bactericera cockerelli from Ingestion to in Planta Transmission
by Esmaeil Saberi, Jawwad A. Qureshi and Judith K. Brown
Microorganisms 2025, 13(9), 2120; https://doi.org/10.3390/microorganisms13092120 - 11 Sep 2025
Viewed by 180
Abstract
Psyllids are vectors of fastidious plant pathogenic ‘Candidatus Liberibacter’ species that infect both the psyllid vector and plant host. Understanding the molecular and cellular basis of ‘Ca. Liberibacter’ interactions with the psyllid host will aid in identification of effectors involved [...] Read more.
Psyllids are vectors of fastidious plant pathogenic ‘Candidatus Liberibacter’ species that infect both the psyllid vector and plant host. Understanding the molecular and cellular basis of ‘Ca. Liberibacter’ interactions with the psyllid host will aid in identification of effectors involved in invasion and multiplication and facilitate transmission to the host plant. The differential expression of previously identified genes/loci with predicted involvement in tomato host–plant– ‘Ca. L. solanacearum’–prophage–Wolbachia endosymbiont dynamics was quantified by RT-qPCR amplification. Fifteen ‘Ca. Liberibacter solanacearum genes and/or prophage loci and four predicted Wolbachia spp. loci were analyzed in potato psyllids in a 14-day time-course study, post-48-h acquisition-access period by potato psyllids on ‘Ca. L. solanacearum’-infected tomato plants. The ‘Ca. L. solanacearum’-infected tomato host plants were used as an infected host ‘calibrator’ species lacking involvement of psyllid effectors. ‘Ca. L. solanacearum’ genes with predicted functions in adhesion, motility, transport, and virulence that are associated with the prophage lysogenic lifestyle were differentially expressed. In contrast, the prophage-loci expression was synchronous with early or late phase of psyllid-‘Ca. L. solanacearum’ infection, respectively. The observations are consistent with the previously in silico-predicted ‘Ca. L. solanacearum’ gene and prophage/Wolbachia loci functions and time-course global expression patterns. Knockdown of ‘Ca. L. solanacearum’ genes involved in invasion, biofilm formation, and colonization would be expected to impair the vertical and horizontal transmission of ‘Ca. L. solanacearum’ to psyllid offspring and host plants, respectively. Full article
(This article belongs to the Section Plant Microbe Interactions)
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21 pages, 4667 KB  
Article
CGRP Suppresses Protective SiglecFhi Neutrophil Development in Neonatal Group B Streptococcus Pneumonia
by Inês Lorga, Ana Sofia Teixeira, Bárbara Carvalho, Joana Soares, Nuno Ribeiro, Marcos S. Cardoso, Joana Cunha, Joana Santos, Regina A. Silva, Manuel Vilanova and Elva Bonifácio Andrade
Microorganisms 2025, 13(9), 2119; https://doi.org/10.3390/microorganisms13092119 - 11 Sep 2025
Viewed by 180
Abstract
Neonatal pneumonia, a leading cause of morbidity and mortality, is frequently caused by Group B Streptococcus (GBS). The mechanisms underlying protective immunity to this pathogen in the neonatal lung remain incompletely understood. Using a clinically relevant neonatal mouse model of GBS pneumonia, we [...] Read more.
Neonatal pneumonia, a leading cause of morbidity and mortality, is frequently caused by Group B Streptococcus (GBS). The mechanisms underlying protective immunity to this pathogen in the neonatal lung remain incompletely understood. Using a clinically relevant neonatal mouse model of GBS pneumonia, we investigated the immune mechanisms influencing disease severity. We demonstrate that neutrophils are effectively recruited to the lungs of infected neonates, but their phenotype differs with disease severity. In pups with moderate disease, we observe significant infiltration of SiglecFhi neutrophils, a phenotype associated with enhanced phagocytic capacity and bacterial clearance. In contrast, pups with severe disease failed to develop SiglecFhi neutrophils, resulting in reduced bacterial clearance and worsened pathology. We further show that severity is associated with increased expression of calcitonin gene-related peptide (CGRP) in the lungs. CGRP suppressed neutrophil activation into the SiglecFhi phenotype, thereby limiting their antibacterial function. Our findings show that GBS exploits the neuroimmune axis to evade host immunity through CGRP-mediated suppression of neutrophil activation. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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25 pages, 2766 KB  
Review
Effects of Micro(nano)plastics on Anaerobic Digestion and Their Influencing Mechanisms
by Xinghua Qi, Hezhen Wang, Yixuan Li, Jing Liu, Jiameng Sun, Wanli Zhang, Wanli Xing and Rundong Li
Microorganisms 2025, 13(9), 2118; https://doi.org/10.3390/microorganisms13092118 - 10 Sep 2025
Viewed by 218
Abstract
Micro(nano)plastics are important emerging contaminants and a current research hotspot in the environmental field. Micro(nano)plastics widely exist in various organic wastes such as waste sludge, food waste (FW) and livestock manure and often enter into digesters along with anaerobic digestion (AD) treatment of [...] Read more.
Micro(nano)plastics are important emerging contaminants and a current research hotspot in the environmental field. Micro(nano)plastics widely exist in various organic wastes such as waste sludge, food waste (FW) and livestock manure and often enter into digesters along with anaerobic digestion (AD) treatment of these wastes, thereby exerting extensive and profound influences on anaerobic process performance. This study reviews sources of micro(nano)plastics and their pathways entering the anaerobic system and summarizes the quantities, sizes, shapes and micromorphology of various micro(nano)plastics in waste sludge, FW, livestock manure, yard waste and municipal solid waste. The current advances on the effects of multiple micro(nano)plastics mainly polyvinyl chloride (PVC), polystyrene (PS) and polyethylene (PE) with different sizes and quantities (or concentrations) on AD of organic wastes in terms of methane production, organic acid degradation and process stability are comprehensively overviewed and mechanisms of micro(nano)plastics affecting AD involved in microbial cells, key enzymes, microbial communities and antibiotic resistance genes are analyzed. Meanwhile, coupling effects of micro(nano)plastics with some typical pollutants such as antibiotics and heavy metals on AD are also reviewed. Due to the extreme complexity of the anaerobic system, current research still lacks full understanding concerning composite influences of different types, sizes and concentrations of micro(nano)plastics on AD under various operating modes. Future research should focus on elucidating mechanisms of micro(nano)plastics affecting organic metabolic pathways and the expression of specific functional genes of microorganisms, exploring the fate and transformation of micro(nano)plastics along waste streams including but not limited to AD, investigating the interaction between micro(nano)plastics and other emerging contaminants (such as perfluorooctanoic acid and perfluorooctane sulphonate) and their coupling effects on anaerobic systems, and developing accurate detection and quantification methods for micro(nano)plastics and technologies for eliminating the negative impacts of micro(nano)plastics on AD. Full article
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