Microorganisms

13 pages, 2979 KiB

Open AccessArticle

Taxon-Dependent Community Assembly of Bacteria and Protists in River Ecosystems: A Case Study from the Yujiang River

by Yusen Li, Wenjian Chen, Yaoquan Han, Jianjun Lei, Bo Huang, Youjie Qin, Feng Lin, Caijin Li, Dapeng Wang and Lei Zhou

Microorganisms 2025, 13(7), 1650; https://doi.org/10.3390/microorganisms13071650 (registering DOI) - 12 Jul 2025

Abstract

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan [...] Read more.

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan communities along the Yujiang River using environmental DNA metabarcoding. Bacterial communities exhibited significantly greater alpha diversity and broader habitat niches compared to protists. Additionally, a negative correlation was found between alpha diversity and niche breadth for both groups. Protistan communities exhibited significantly higher beta diversity (Bray–Curtis distance) than bacterial communities, with species turnover being the principal factor driving the variations in both communities. Null model results indicated that heterogeneous selection primarily structured bacterial communities, while stochastic processes (drift) mainly governed protist communities. Redundancy analysis and Mantel tests showed significant associations between environmental factors (e.g., temperature and pH) and bacterial community composition. Moreover, the longitude of sampling sites was linked to spatial variations in both bacterial and protistan communities. Further analyses, including distance-decay patterns, variation partitioning, and multiple regression on distance matrices, demonstrated that bacterial communities were driven by both environmental and spatial factors, while protist communities exhibited a stronger response to spatial factors. These results enhance our understanding of microbial community assembly in river ecosystems and provide valuable insights for the conservation and sustainable management of freshwater systems. Full article

(This article belongs to the Section Environmental Microbiology)

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12 pages, 2424 KiB

Open AccessArticle

Surface Display of Avian H5 and H9 Hemagglutinin Antigens on Non-Genetically Modified Lactobacillus Cells for Bivalent Oral AIV Vaccine Development

by Fuyi Liu, Jingbo Chang, Jingqi Huang, Yuping Liao, Xiaonan Deng, Tingting Guo, Jian Kong and Wentao Kong

Microorganisms 2025, 13(7), 1649; https://doi.org/10.3390/microorganisms13071649 - 11 Jul 2025

Abstract

A novel bivalent oral vaccine candidate against H5N1 and H9N2 avian influenza virus (AIV) was developed using Lactobacillus surface display technology without genetic modification. The hemagglutinin subunit 1 (HA1) antigens from both subtypes were fused to the surface layer-binding domain of Lactobacillus crispatus [...] Read more.

A novel bivalent oral vaccine candidate against H5N1 and H9N2 avian influenza virus (AIV) was developed using Lactobacillus surface display technology without genetic modification. The hemagglutinin subunit 1 (HA1) antigens from both subtypes were fused to the surface layer-binding domain of Lactobacillus crispatus K313, expressed in Escherichia coli, and purified. Wild-type Lactobacillus johnsonii H31, isolated from chicken intestine, served as a delivery vehicle by adsorbing and stably displaying the HA1 proteins on its surface. This approach eliminates the need for bacterial engineering while utilizing lactobacilli’s natural capacity to protect surface-displayed antigens, as evidenced by HA1’s protease resistance. Mouse immunization studies demonstrated induction of strong systemic IgG and mucosal IgA responses against both H5N1 and H9N2 HA1. The system offers several advantages, including safety through non-GMO probiotics, potential for multivalent vaccine expansion, and intrinsic antigen protection by lactobacilli. These findings suggest this platform could enable development of cost-effective, multivalent AIV vaccines. Full article

(This article belongs to the Section Food Microbiology)

19 pages, 2862 KiB

Open AccessArticle

Characterization of Soil Bacterial Communities in Different Vegetation Types on the Lava Plateau of Jingpo Lake

by Yanli Zhang, Jiaxing Huang, Jiaxin Xue, Kaining Zhang, Xintong Chen, Jianhui Jia and Qingyang Huang

Microorganisms 2025, 13(7), 1648; https://doi.org/10.3390/microorganisms13071648 - 11 Jul 2025

Abstract

To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical [...] Read more.

To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical properties were identified among these types (p < 0.05). The soil bacterial community structures also varied significantly (p < 0.05), with Actinobacteriota, Proteobacteria, and Acidobacteria as the dominant phyla, exhibiting notable genus-level differences (p < 0.05). The soil organic matter (SOM), available nitrogen (AN), total nitrogen (TN), and soil water content (SWC) were significantly correlated with the bacterial community structure (p < 0.05 or p < 0.01), acting as key determinants of the microbial community structure and function. PICRUSt2 functional predictions revealed significant variations in the metabolic functions of the soil bacterial communities across vegetation types, indicating distinct functional specializations. In conclusion, the Jingpo Lake lava plateau harbors abundant bacterial resources. When devising vegetation adaptation strategies, it is essential to take into account variations in the rhizosphere soil bacteria across different vegetation types. Furthermore, prioritizing the implementation of forest vegetation is crucial in the adaptive management of the lava plateau. This approach holds significant implications for studying the bacterial diversity in the lava plateau and exploring the cultivation and application of functional bacteria in extreme environments. Full article

(This article belongs to the Special Issue Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes)

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10 pages, 1272 KiB

Open AccessCommunication

Antibiotic Resistance in Bifidobacterium animalis subsp. lactis and Bifidobacterium longum: Definition of Sensitivity/Resistance Profiles at the Species Level

by Mario Terlizzi, Barbara Speranza, Milena Sinigaglia, Maria Rosaria Corbo and Antonio Bevilacqua

Microorganisms 2025, 13(7), 1647; https://doi.org/10.3390/microorganisms13071647 - 11 Jul 2025

Abstract

Antimicrobial resistance is a threat to probiotic microorganisms due to their potential role in harboring and transmitting resistance genes. This study focuses on two Bifidobacterium species (B. animalis subsp. lactis and B. longum) by analyzing 657 Minimal Inhibitory Concentration (MIC) values [...] Read more.

Antimicrobial resistance is a threat to probiotic microorganisms due to their potential role in harboring and transmitting resistance genes. This study focuses on two Bifidobacterium species (B. animalis subsp. lactis and B. longum) by analyzing 657 Minimal Inhibitory Concentration (MIC) values extracted from research articles indexed in Scopus, PubMed, and Web of Science, published since 2014, and considering 17 different antibiotics. MIC values were used for descriptive statistical analysis (boxplots and violin plots) to evaluate both inter- and intraspecies distributions. The results showed an overall increase in MIC values compared to historical data, with B. longum exhibiting high resistance to tetracyclines and streptomycin—approximately 25% to 50% of the strains had MIC values > EFSA cut-offs. The violin plots revealed the presence of resistant subpopulations, particularly within B. longum. These findings support the relevance of longitudinal MIC analysis as a tool for detecting early shifts in antimicrobial susceptibility and highlight the importance of data-driven approaches for microbiological risk assessment in probiotic applications. Full article

(This article belongs to the Section Food Microbiology)

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19 pages, 1297 KiB

Open AccessReview

Biology and Application of Chaetomium globosum as a Biocontrol Agent: Current Status and Future Prospects

by Shailja Sharma, Saurabh Pandey, Sourabh Kulshreshtha and Mukesh Dubey

Microorganisms 2025, 13(7), 1646; https://doi.org/10.3390/microorganisms13071646 - 11 Jul 2025

Abstract

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum [...] Read more.

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum has attracted considerable scientific interest due to its potential as a biocontrol agent [BCA] against a wide array of diseases in numerous plant species. While the precise mechanisms of C. globosum as a BCA remain poorly understood, interference competition through antibiosis is one of the key mechanisms. Moreover, C. globosum can enhance plant health by promoting nutrient availability, manipulating the rhizosphere microbiome, and inducing plant defense responses. The formulation of C. globosum for agricultural applications has been reported, which can significantly improve stability and efficacy under field conditions. However, despite significant advancements in omics and molecular biology technologies, the biology of C. globosum is understudied. Enhanced research into the genetics and functional genomics of C. globosum could pave the way for its applications in sustainable agriculture. This review summarizes the role of C. globosum as a BCA, focusing on its underlying mechanisms such as genomics and transcriptomics, and the effects of C. globosum application on soil health and the rhizosphere microbiome. Full article

(This article belongs to the Section Plant Microbe Interactions)

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14 pages, 2225 KiB

Open AccessArticle

Gut Microbiota Diversity in 16 Stingless Bee Species (Hymenoptera: Apidae: Meliponini)

by María de Lourdes Ramírez-Ahuja, Kenzy I. Peña-Carrillo, Mayra A. Gómez-Govea, Mariana Lizbeth Jiménez-Martínez, Gerardo de Jesús Trujillo-Rodríguez, Marisol Espinoza-Ruiz, Antonio Guzmán Velasco, Adriana E. Flores, José Ignacio González-Rojas, Diana Reséndez-Pérez and Iram Pablo Rodríguez-Sánchez

Microorganisms 2025, 13(7), 1645; https://doi.org/10.3390/microorganisms13071645 - 11 Jul 2025

Abstract

Bacterial symbionts play an important role in insect survival by contributing to key metabolic and defensive functions. While stingless bees are known to harbor diverse microbial communities, their core bacterial symbionts remain poorly characterized. In this study, we analyzed the gut microbiota of [...] Read more.

Bacterial symbionts play an important role in insect survival by contributing to key metabolic and defensive functions. While stingless bees are known to harbor diverse microbial communities, their core bacterial symbionts remain poorly characterized. In this study, we analyzed the gut microbiota of sixteen stingless bee species collected from different regions of Mexico using 16S rRNA gene sequencing on the Illumina^® MiSeq™ platform. Our results revealed that Proteobacteria, Firmicutes, and Actinobacteria are the most abundant bacterial phyla across species. Among the dominant genera, lactic acid bacteria, such as Lactobacillus spp., Bifidobacterium, and Fructobacillus spp., were the most prevalent. These bacteria are responsible for developing biochemical functions in metabolic processes like lactic fermentation and the biotransformation of complex organic compounds into molecules that are more easily assimilated by bees. This study offers a novel perspective on the diversity and predicted composition of gut microbiota in Mexican stingless bees. By highlighting differences in microbial communities among species with different feeding habits, our results emphasize the importance of preserving microbial biodiversity in these pollinators. Full article

(This article belongs to the Section Gut Microbiota)

18 pages, 3518 KiB

Open AccessArticle

Fusobacterium nucleatum Is Associated with Tumor Characteristics, Immune Microenvironment, and Survival in Appendiceal Cancer

by Christopher Sherry, Neda Dadgar, Hyun Park, Chelsea Knotts, Erin Grayhack, Rose Blodgett, Kunhong Xiao, Ashten N. Omstead, Albert D. Donnenberg, David L. Bartlett, Vera Donnenberg, Ajay Goel, Ali H. Zaidi and Patrick L. Wagner

Microorganisms 2025, 13(7), 1644; https://doi.org/10.3390/microorganisms13071644 - 11 Jul 2025

Abstract

Emerging evidence highlights the role of the tumor microbiome, including Fusobacterium nucleatum (Fn), in a wide range of gastrointestinal cancers. Fn purportedly contributes to tumorigenesis by activating oncogenic pathways and modulating immune responses. Although the prevalence and impact of Fn has been extensively [...] Read more.

Emerging evidence highlights the role of the tumor microbiome, including Fusobacterium nucleatum (Fn), in a wide range of gastrointestinal cancers. Fn purportedly contributes to tumorigenesis by activating oncogenic pathways and modulating immune responses. Although the prevalence and impact of Fn has been extensively studied in colorectal cancer, no previous systematic or in situ studies have been performed in appendiceal cancer (AC). The aim of this study was to evaluate the prevalence and association of Fn density in AC with clinical factors and oncologic outcomes. Archival tissue from 54 patients with AC was assessed for Fn density using RNA in situ hybridization. Clinicopathological variables were obtained for each case through electronic medical record review, and the immune microenvironment was characterized in each case using immunohistochemistry to quantify CD3+ and CD8+ T lymphocytes and M1-/M2-like tumor-associated macrophages. In AC, Fn density was associated with patient age, tumor grade, and histologic subtype. Fn was negatively associated with CD3+ and CD8+ T lymphocytes and positively associated with M2-like TAMs in low-grade AC. Interestingly, tumor Fn content was associated with better overall and progression-free survival, even when controlling for tumor grade. In this exploratory study, we found that Fn is prevalent in AC. Fn is associated with a number of clinical, pathologic, immunologic, and prognostic variables in AC that are distinct from the corresponding observed associations in colorectal cancer. Further research is warranted to validate these findings and explore the mechanistic contributions of Fn to AC pathogenesis or immune response. Full article

(This article belongs to the Special Issue The Microbiome in Ecosystems)

20 pages, 1766 KiB

Open AccessArticle

In Vitro Evaluation of the Probiotic Properties and Whole Genome Sequencing of Lacticaseibacillus rhamnosus J3205 Isolated from Home-Made Fermented Sauce

by Yiming Chen, Lingchao Ma, Weiye Chen, Yiwen Chen, Zile Cheng, Yongzhang Zhu, Min Li, Yan Zhang, Xiaokui Guo and Chang Liu

Microorganisms 2025, 13(7), 1643; https://doi.org/10.3390/microorganisms13071643 - 11 Jul 2025

Abstract

Lacticaseibacillus rhamnosus J3205 was isolated from traditional fermented sauces and demonstrated potential probiotic properties. The strain exhibited high tolerance to simulated saliva (93.24% survival) and gastrointestinal conditions (69.95% gastric and 50.44% intestinal survival), along with strong adhesion capacity (58.25%) to intestinal epithelial cells. [...] Read more.

Lacticaseibacillus rhamnosus J3205 was isolated from traditional fermented sauces and demonstrated potential probiotic properties. The strain exhibited high tolerance to simulated saliva (93.24% survival) and gastrointestinal conditions (69.95% gastric and 50.44% intestinal survival), along with strong adhesion capacity (58.25%) to intestinal epithelial cells. Safety assessments confirmed the absence of virulence and antibiotic resistance genes. Genomic analysis revealed stress-response genes and 34 insertion sequence (IS) elements, while proteomic profiling identified Pgk as a key enzyme in lactic acid production and SecY in oxidative stress resistance. Functionally, J3205 significantly reduces pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and enhances antioxidant markers (SOD, GSH) in vitro. These results position L. rhamnosus J3205 as a promising candidate for gut-health foods, anti-inflammatory nutraceuticals, and oxidative-stress therapeutics, warranting further in vivo validation. Full article

(This article belongs to the Section Food Microbiology)

16 pages, 528 KiB

Open AccessArticle

Elixhauser Comorbidity Measure and Charlson Comorbidity Index in Predicting the Death of Spanish Inpatients with Diabetes and Invasive Pneumococcal Disease

by Enrique Gea-Izquierdo, Rossana Ruiz-Urbaez, Valentín Hernández-Barrera and Ángel Gil-de-Miguel

Microorganisms 2025, 13(7), 1642; https://doi.org/10.3390/microorganisms13071642 - 11 Jul 2025

Abstract

Invasive pneumococcal disease (IPD) is a serious infection caused by the bacterium Streptococcus pneumoniae (pneumococcus) that can produce a wide spectrum of clinical manifestations. The aim of this study was to analyze the comorbidity factors that influenced the mortality in patients with diabetes [...] Read more.

Invasive pneumococcal disease (IPD) is a serious infection caused by the bacterium Streptococcus pneumoniae (pneumococcus) that can produce a wide spectrum of clinical manifestations. The aim of this study was to analyze the comorbidity factors that influenced the mortality in patients with diabetes (D) according to IPD. A retrospective study to analyze patients with D and IPD was carried out. Based on the discharge reports from the Spanish Minimum Basic Data Set (MBDS) from 1997 to 2022, the Elixhauser Comorbidity Index (ECI) and the Charlson Comorbidity Index (CCI) were calculated to predict in-hospital mortality (IHM) in Spain. A total of 12,994,304 patients with D were included, and 84,601 cases of IPD were identified. The average age for men was 70.23 years and for women 73.94 years. In all years, ECI and CCI were larger for type 2 D than for type 1 D, with men having a higher mean than women. An association was found between risk factors ECI, age, type 1 D, COVID-19, IPD (OR = 1.31; 95% CI: 1.29–1.35; p < 0.001); CCI, age, type 1 D, COVID-19, IPD (OR = 1.45; 95% CI: 1.42–1.49; p < 0.001), and increased mortality. The IHM increased steadily with the number of comorbidities and index scores from 1997 to 2022. D remains a relevant cause of hospitalization in Spain. Comorbidities reflected a great impact on patients with D and IPD, which would mean a higher risk of mortality. Predicting mortality events and length of stay by comparing indices showed that CCI outperforms ECI in predicting inpatient death after IPD. Full article

(This article belongs to the Section Public Health Microbiology)

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13 pages, 1938 KiB

Open AccessArticle

Encapsulation of Fresh Spirulina Biomass in Alginate Spheres for Yogurt Fortification

by Domenico Siclari, Maria Rosaria Panuccio and Rossana Sidari

Microorganisms 2025, 13(7), 1641; https://doi.org/10.3390/microorganisms13071641 - 11 Jul 2025

Abstract

A new spherification of Spirulina (Arthrospira platensis) was developed for its use as a food supplement. The novelty of this study is the incorporation of fresh Spirulina biomass into alginate spheres formulated with 3% sodium alginate and 1.5% calcium lactate and [...] Read more.

A new spherification of Spirulina (Arthrospira platensis) was developed for its use as a food supplement. The novelty of this study is the incorporation of fresh Spirulina biomass into alginate spheres formulated with 3% sodium alginate and 1.5% calcium lactate and its addition into yogurt. The spheres and the fortified yogurt were stored at 4 °C for 15 days. The viability of Spirulina, either in contact with the yogurt or not, was evaluated both by OD_550nm measurements and microscopic observations. Furthermore, the effect of Spirulina spheres on Streptococcus thermophilus and Lactobacillus bulgaricus was evaluated by enumerating them in standard media. Spirulina retained its viability for up to 15 days when stored separately from the yogurt matrix. Spirulina had a stimulating effect on the lactic acid bacteria: after 15 days, L. bulgaricus and S. thermophilus showed a load increase of 2.66% and 1.64%, respectively, compared to the load detected in the unfortified yogurt. Our study has demonstrated the technical feasibility of producing fresh Spirulina spheres, which can be used alone or added to food preparation. Nevertheless, additional investigations—including quantitative assessment of bioactive compounds and comprehensive sensory analysis—are essential to validate the methodology and support its scalability. Full article

(This article belongs to the Special Issue Microorganisms in Functional Foods: 2nd Edition)

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18 pages, 437 KiB

Open AccessArticle

Validation of a Real-Time PCR Assay for Fully Automated Detection of Bacillus cereus in Donor Human Milk

by Gemma Aran, Vanessa Pleguezuelos, Margarita Blanco, Cristina Garcia, Mariama Jallow, Mar López, Sara Monge, Natalia Casamitjana, Eva Alonso-Nogués and Gloria Soria

Microorganisms 2025, 13(7), 1640; https://doi.org/10.3390/microorganisms13071640 - 11 Jul 2025

Abstract

Donor human milk (DHM) can harbor microbial contaminants that cause serious infections in premature infants. Bacillus cereus is a pathogen frequently found in DHM, capable of forming spores that can resist Holder pasteurization (62.5 °C, 30 min). Since no microbial growth is acceptable [...] Read more.

Donor human milk (DHM) can harbor microbial contaminants that cause serious infections in premature infants. Bacillus cereus is a pathogen frequently found in DHM, capable of forming spores that can resist Holder pasteurization (62.5 °C, 30 min). Since no microbial growth is acceptable in post-pasteurized DHM, microbiological testing of pre-pasteurized DHM provides information about its contamination level to determine if it should be accepted for pasteurization. Culture is the gold standard in microbiological control but it requires 24–48 h to provide results. In this study we developed and validated a non-commercial real-time PCR assay for the detection of Bacillus cereus (BC test) in DHM specimens on a fully automated high-throughput platform, the cobas^® 6800 system. The BC test showed excellent sensitivity and specificity, repeatability and linearity over an 8-log range and a low limit of detection in milk specimens, as well as good agreement with selective culture methods. BC test was then used to systematically control all milk donations (3439) over a 24-month period. Bacillus cereus was detected in 14.2% of DHM, with monthly rates ranging from 6 to 29% and a significantly higher incidence in warmer months. Incorporating this assay into our laboratory workflow improved efficiency and reduced turnaround time. Full article

(This article belongs to the Section Food Microbiology)

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16 pages, 1265 KiB

Open AccessReview

Novel Treatments for Diabetic Foot Osteomyelitis: A Narrative Review

by Crystal Jing, Julia E. Ralph, Jamie Lim, Jackson M. Cathey, Conor N. O'Neill and Albert T. Anastasio

Microorganisms 2025, 13(7), 1639; https://doi.org/10.3390/microorganisms13071639 - 11 Jul 2025

Abstract

Diabetic foot osteomyelitis (DFO) is a severe complication of diabetes mellitus and a leading cause of non-traumatic lower extremity amputation. Treatment remains clinically challenging with high recurrence rates despite standard antibiotic therapy and surgical debridement. This narrative review synthesizes current evidence on novel [...] Read more.

Diabetic foot osteomyelitis (DFO) is a severe complication of diabetes mellitus and a leading cause of non-traumatic lower extremity amputation. Treatment remains clinically challenging with high recurrence rates despite standard antibiotic therapy and surgical debridement. This narrative review synthesizes current evidence on novel operative and nonoperative therapies for DFO, focusing on emerging biomaterials, local antibiotic delivery systems, innovative surgical techniques, and adjunctive topical agents. Studies examining bioabsorbable and nonabsorbable antibiotic carriers, such as calcium sulfate beads, collagen sponges, and bioactive glass, demonstrate promising infection resolution rates and a potential to reduce the surgical burden, though most are limited by small cohorts and observational designs. Similarly, alternative surgical approaches (i.e., cancelloplasty, conservative bone excision, and tibial cortex distraction) have shown early success in limb preservation. Nonoperative strategies, including adjunct antimicrobials, antimicrobial peptides, and topical oxygen, offer additional options, particularly for patients unfit for surgery. While initial outcomes are encouraging, the supporting evidence is heterogeneous and primarily limited to case series and small, noncomparative trials. Overall, these novel therapies show potential as adjuncts to established DFO management, but further prospective research is indicated to define their long-term efficacy, safety, and role in clinical practice. Full article

(This article belongs to the Section Medical Microbiology)

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20 pages, 2279 KiB

Open AccessArticle

Enhancing Soil Health and Corn Productivity with a Co-Fermented Microbial Inoculant (CFMI-8): A Field-Based Evaluation

by Raul De Jesus Cano, Judith M. Daniels, Martha Carlin and Don Huber

Microorganisms 2025, 13(7), 1638; https://doi.org/10.3390/microorganisms13071638 - 11 Jul 2025

Abstract

Soil degradation and declining fertility threaten sustainable agriculture and crop productivity. This study evaluates the effects of CFMI-8, a co-fermented microbial inoculant comprising eight bacterial strains selected through genomic and metabolic modeling, on soil health, nutrient availability, and corn performance. Conducted in a [...] Read more.

Soil degradation and declining fertility threaten sustainable agriculture and crop productivity. This study evaluates the effects of CFMI-8, a co-fermented microbial inoculant comprising eight bacterial strains selected through genomic and metabolic modeling, on soil health, nutrient availability, and corn performance. Conducted in a randomized complete block design at Findlay Farm, Wisconsin, the field trial assessed soil biological activity, nutrient cycling, and crop yield responses to CFMI-8 treatment. Treated soils exhibited significant increases in microbial organic carbon (+224.1%) and CO₂ respiration (+167.1%), indicating enhanced microbial activity and organic matter decomposition. Improvements in nitrate nitrogen (+20.2%), cation exchange capacity (+23.1%), and potassium (+27.3%) were also observed. Corn yield increased by 28.6%, with corresponding gains in silage yield (+9.6%) and nutritional quality. Leaf micronutrient concentrations, particularly iron, manganese, boron, and zinc, were significantly higher in treated plants. Correlation and Random Forest analyses identified microbial activity and nitrogen availability as key predictors of yield and nutrient uptake. These results demonstrate CFMI-8’s potential to enhance soil fertility, promote nutrient cycling, and improve crop productivity under field conditions. The findings support microbial inoculants as viable tools for regenerative agriculture and emphasize the need for long-term studies to assess sustainability impacts. Full article

(This article belongs to the Section Plant Microbe Interactions)

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14 pages, 6052 KiB

Open AccessArticle

Comparative Analysis of Soil Microbial Community Structures in Rhizosphere of Two Texture-Differentiated Lotus Root Varieties

by Xinni Li, Qiyue Liang, Meiping Gao, Yangxiu Ou, Yifeng Hu, Wen Jiang, Huiping Jiang and Shangdong Yang

Microorganisms 2025, 13(7), 1637; https://doi.org/10.3390/microorganisms13071637 - 10 Jul 2025

Abstract

To investigate the relationship between the rhizosphere microbial community structure and lotus root texture, the biological properties, and the rhizosphere microbial composition of mealy (ML) and crunchy lotus (CL) varieties were all analyzed using traditional and high-throughput sequencing technologies. The results showed that [...] Read more.

To investigate the relationship between the rhizosphere microbial community structure and lotus root texture, the biological properties, and the rhizosphere microbial composition of mealy (ML) and crunchy lotus (CL) varieties were all analyzed using traditional and high-throughput sequencing technologies. The results showed that the ML varieties exhibited significantly lower moisture but higher starch contents than those of CL. Meanwhile, the rhizosphere fungal richness of ML was also significantly higher than that of CL. Moreover, the relative abundances of bacterial phyla and genera, such as Nitrospirota, Bacteroidota, Proteobacteria, and Bacillus, alongside fungal phyla and genera, i.e., Ascomycota and Emericellopsis, were enriched in rhizosphere of ML compared to CL. Functional prediction also revealed that elevated nitrogen cycling, polysaccharide degradation and cellulose breakdown functions could be detected in ML, potentially driving starch accumulation and cell wall modification. These results suggest that rhizosphere microbial composition, particularly nitrogen-cycling bacteria and lignocellulose-degrading fungi, may contribute to texture formation between texture-differentiated lotus root varieties. Full article

(This article belongs to the Section Plant Microbe Interactions)

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15 pages, 6783 KiB

Open AccessArticle

Disruptive DNA Intercalation Is the Mode of Interaction Behind Niacinamide Antimicrobial Activity

by Michal Rasis, Noa Ziklo and Paul Salama

Microorganisms 2025, 13(7), 1636; https://doi.org/10.3390/microorganisms13071636 - 10 Jul 2025

Abstract

Niacinamide was recently shown to directly interact with bacterial DNA and interfere with cell replication; niacinamide mode of interaction and efficacy as a natural anti-microbial molecule were also described. The aim of this study is to elucidate the exact binding mechanism of niacinamide [...] Read more.

Niacinamide was recently shown to directly interact with bacterial DNA and interfere with cell replication; niacinamide mode of interaction and efficacy as a natural anti-microbial molecule were also described. The aim of this study is to elucidate the exact binding mechanism of niacinamide to microbial DNA. Intercalation is a binding mode where a small planar molecule, such as niacinamide, is inserted between base pairs, causing structural changes in the DNA. Melting curve analysis with various intercalating dyes demonstrated that niacinamide interaction with bacterial DNA reduces its melting temperature in a linear dose-dependent manner. Niacinamide’s effect on the melting temperature was found to be % GC-dependent, while purine stretches were also found to influence the binding kinetics. Finally, fluorescent intercalator displacement (FID) assays demonstrated that niacinamide strongly reduces SYBR Safe signal in a dose-dependent manner. Interestingly, competition assays with a minor groove binder also reduced Hoechst signal but in a non-linear manner, which can be attributed to strand lengthening and unwinding following niacinamide intercalation. Taken altogether; our results suggest a “disruptive intercalation” as the mode of interaction of niacinamide with bacterial DNA. Formation of locally destabilized DNA portions by niacinamide might interfere with protein–DNA interaction and potentially affect several crucial bacterial cellular processes, e.g., DNA repair and replication, subsequently leading to cell death. Full article

(This article belongs to the Special Issue Research on Antimicrobial Activity of Natural Products, Second Edition)

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24 pages, 2913 KiB

Open AccessArticle

Generative and Contrastive Self-Supervised Learning for Virulence Factor Identification Based on Protein–Protein Interaction Networks

by Yalin Yao, Hao Chen, Jianxin Wang and Yeru Wang

Microorganisms 2025, 13(7), 1635; https://doi.org/10.3390/microorganisms13071635 - 10 Jul 2025

Abstract

Virulence factors (VFs), produced by pathogens, facilitate pathogenic microorganisms to invade, colonize, and damage the host cells. Accurate VF identification advances pathogenic mechanism understanding and provides novel anti-virulence targets. Existing models primarily utilize protein sequence features while overlooking the systematic protein–protein interaction (PPI) [...] Read more.

Virulence factors (VFs), produced by pathogens, facilitate pathogenic microorganisms to invade, colonize, and damage the host cells. Accurate VF identification advances pathogenic mechanism understanding and provides novel anti-virulence targets. Existing models primarily utilize protein sequence features while overlooking the systematic protein–protein interaction (PPI) information, despite pathogenesis typically resulting from coordinated protein–protein actions. Moreover, a severe imbalance exists between virulence and non-virulence proteins, which causes existing models trained on balanced datasets by sampling to fail in incorporating proteins’ inherent distributional characteristics, thus restricting generalization to real-world imbalanced data. To address these challenges, we propose a novel Generative and Contrastive self-supervised learning framework for Virulence Factor identification (GC-VF) that transforms VF identification into an imbalanced node classification task on graphs generated from PPI networks. The framework encompasses two core modules: the generative attribute reconstruction module learns attribute space representations via feature reconstruction, capturing intrinsic data patterns and reducing noise; the local contrastive learning module employs node-level contrastive learning to precisely capture local features and contextual information, avoiding global aggregation losses while ensuring node representations truly reflect inherent characteristics. Comprehensive benchmark experiments demonstrate that GC-VF outperforms baseline methods on naturally imbalanced datasets, exhibiting higher accuracy and stability, as well as providing a potential solution for accurate VF identification. Full article

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

25 pages, 2374 KiB

Open AccessArticle

Pulmonary Embolism in COVID-19: Trends from a Single-Center Study Across Ten Pandemic Waves in Romania

by Alexandra Herlo, Adelina Raluca Marinescu, Talida Georgiana Cut, Ruxandra Laza, Adina Maria Marza, Claudia Raluca Balasa Virzob, Cristian Iulian Oancea, Lucian-Flavius Herlo, Ioana-Melinda Luput-Andrica and Voichita Elena Lazureanu

Microorganisms 2025, 13(7), 1634; https://doi.org/10.3390/microorganisms13071634 - 10 Jul 2025

Abstract

The COVID-19 pandemic has significantly impacted global health, with pulmonary embolism (PE) emerging as a critical complication due to the hypercoagulable state induced by SARS-CoV-2 infection. Despite advancements in prevention and treatment, PE remains a major cause of morbidity and mortality in COVID-19 [...] Read more.

The COVID-19 pandemic has significantly impacted global health, with pulmonary embolism (PE) emerging as a critical complication due to the hypercoagulable state induced by SARS-CoV-2 infection. Despite advancements in prevention and treatment, PE remains a major cause of morbidity and mortality in COVID-19 patients. This study analyzes the trends, outcomes, and contributing factors of PE across ten pandemic waves in Romania, highlighting the evolving clinical burden and management approaches. This retrospective observational study was conducted on confirmed COVID-19 patients that also developed PE, who were admitted to “Victor Babeș” Hospital and Municipal Emergency Hospital in Timișoara, Romania. Data on demographics, clinical features, inflammatory markers, comorbidities, and treatment were collected from medical records. Statistical analyses, including ANOVA and Kaplan–Meier survival analysis, were conducted to evaluate trends and survival outcomes over time. The study included 166 patients, with a mean age of 67.26 ± 13.57 years. Mortality peaked at 50% in Wave 1, declined to 12% in Wave 7, and increased again to 28% in Wave 10. Intubation rates varied, with a high of 29% in Wave 6 and a low of 12% in Wave 8. Lung involvement was the most severe in Wave 4 (mean 0.54 ± 0.18) but improved in later waves, reaching a mean of 0.24 ± 0.12 in Wave 8. This study highlights the dynamic trends in PE during the COVID-19 pandemic in Romania. Improved clinical management, vaccination, and adaptive healthcare strategies contributed to better outcomes in later waves. Full article

(This article belongs to the Special Issue Infectious Disease Surveillance in Romania)

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18 pages, 3653 KiB

Open AccessArticle

Significant Increase of Cinnamic Acid in Metabolites of Chicks Infected with Infectious Bronchitis Virus and Its Remarkable Antiviral Effects In Vitro and In Vivo

by Lan-Ping Wei, Tao-Ni Zhang, Yu Zhang, Li-Na Ren, Yan-Peng Lu, Tian-Chao Wei, Teng Huang, Jian-Ni Huang and Mei-Lan Mo

Microorganisms 2025, 13(7), 1633; https://doi.org/10.3390/microorganisms13071633 - 10 Jul 2025

Abstract

Avian infectious bronchitis virus (IBV) infection has caused significant economic losses to the poultry industry. Unfortunately, there is currently no effective cure for this disease. Understanding the pathogenic mechanism is crucial for the treatment of the disease. Studying the pathogenic mechanism of IBV [...] Read more.

Avian infectious bronchitis virus (IBV) infection has caused significant economic losses to the poultry industry. Unfortunately, there is currently no effective cure for this disease. Understanding the pathogenic mechanism is crucial for the treatment of the disease. Studying the pathogenic mechanism of IBV based on metabolomics analysis is helpful for identifying antiviral drugs. However, studies on metabolomics analysis of IBV infection have been relatively limited, particularly without metabolomics analysis in sera after IBV infection. In this study, 17-day-old SPF chicks were infected with the IBV GX-YL5 strain, and serum samples were collected 7 days post-infection (DPI) for metabolomics analysis using ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). A total of 143 differential metabolites were identified across 20 metabolic pathways, with the phenylalanine pathway showing the most significant changes. The level of cinnamic acid (CA), an upstream metabolite in the phenylalanine pathway, was notably increased following IBV infection. To investigate the antiviral effects of CA, chicken embryo kidney (CEK) cells and SPF chicks infected with IBV were treated with different concentrations of CA to assess its effect on viral replication. The results demonstrated that CA at 25 μg/mL effectively inhibited IBV replication in vitro; meanwhile, CA at 50 μg/mL and 25 μg/mL effectively inhibited IBV replication in vivo. Molecular docking and molecular dynamics simulation studies showed that CA interacts with the N domains of the IBV nucleocapsid (N) protein. In conclusion, the serum metabolite CA is significantly elevated following IBV infection and demonstrates remarkable antiviral effects both in vitro and in vivo, providing a promising avenue for the development of antiviral therapies to combat IBV infection. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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20 pages, 10628 KiB

Open AccessArticle

Temporal and Spatial Dynamics of Tumor–Host Microbiota in Breast Cancer Progression

by Qi Xu, Aikun Fu, Nan Wang and Zhizhen Zhang

Microorganisms 2025, 13(7), 1632; https://doi.org/10.3390/microorganisms13071632 - 10 Jul 2025

Abstract

Deciphering the spatiotemporal distribution of bacteria during breast cancer progression may provide critical insights for developing bacterial-based therapeutic strategies. Using a murine breast cancer model, we longitudinally profiled the microbiota in breast tumor tissue, mammary gland, spleen, and cecal contents at 3-, 5-, [...] Read more.

Deciphering the spatiotemporal distribution of bacteria during breast cancer progression may provide critical insights for developing bacterial-based therapeutic strategies. Using a murine breast cancer model, we longitudinally profiled the microbiota in breast tumor tissue, mammary gland, spleen, and cecal contents at 3-, 5-, and 7- weeks post-tumor implantation through 16S rRNA gene sequencing. Breast tumor progression was associated with lung metastasis and splenomegaly, accompanied by distinct tissue-specific microbial dynamics. While alpha diversity remained stable in tumors, mammary tissue, and cecal contents, it significantly increased in the spleen (p < 0.05). Longitudinal analysis revealed a progressive rise in Firmicutes and a decline in Proteobacteria abundance within tumors, mammary tissue, and cecum, whereas the spleen microbiota displayed unique phylum-level compositional shifts. Tissue- and time-dependent microbial signatures were identified at phylum, genus, and species levels during breast tumor progression. Strikingly, the spleen microbiota integrated nearly all genera enriched in other sites, suggesting its potential role as a microbial reservoir. Gut-associated genera (Lactobacillus, Desulfovibrio, Helicobacter) colonized both cecal contents and the spleen, with Lactobacillus consistently detected across all tissues, suggesting microbial translocation. The spleen exhibited uniquely elevated diversity and compositional shifts, potentially driving splenomegaly. These results delineated the trajectory of microbiota translocation and colonization, and demonstrated tissue-specific microbial redistribution during breast tumorigenesis, offering valuable implications for advancing microbiome-targeted cancer therapies. Full article

(This article belongs to the Special Issue Host–Microbiome Cross-Talk in Cancer Development and Progression)

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18 pages, 3287 KiB

Open AccessArticle

Evaluation of the Application Effects of Siniperca chuatsi in Biofloc Systems: A Comparative Study on the Use of Bamboo Flour and Rice Straw as Carbon Sources

by Huiling Zhang, Zhaojie Deng, Shijun Chen, Xi Xiong, Wenhui Zeng, Fang Chen, Huanjiao Tan, Xuran Chen, Canmin Yang, Yuhui He, Dizhi Xie and Lian Gan

Microorganisms 2025, 13(7), 1631; https://doi.org/10.3390/microorganisms13071631 - 10 Jul 2025

Abstract

A 56-day trial was conducted to assess the effects of rice straw (RS) and bamboo flour (BF) on growth performance, water quality, gill histology, and the bacterial community of water and the intestine of mandarin fish (Siniperca chuatsi) in biofloc technology [...] Read more.

A 56-day trial was conducted to assess the effects of rice straw (RS) and bamboo flour (BF) on growth performance, water quality, gill histology, and the bacterial community of water and the intestine of mandarin fish (Siniperca chuatsi) in biofloc technology systems. The results showed that mandarin fish in the RS and BF groups had comparable survival rates of 100.00 ± 0.00 and 93.33 ± 3.85%; feed conversion ratios of 1.13 ± 0.02 and 1.40 ± 0.15; and weight gain rates of 112.21 ± 1.56 and 100.92 ± 6.45%, respectively. From days 11 to 56 of the farming period, the BF group was more effective than the RS group in removing total ammonia nitrogen (TAN) and NO₂⁻-N, maintaining TAN levels below 0.24 ± 0.05 mg/L. During the early stage of the experiment, the TAN level in the RS group was higher; however, with the supplementation of a carbon source, it gradually decreased and eventually stabilized at 0.13 ± 0.03 mg/L later in the farming period. The secondary gill lamella in the RS group was curved and showed hyperplasia, and the basal gill lamellae showed an increase in the volume of interlamellar cell mass in the BF group. Genes related to denitrification (narG, napA, nirS, nirK, and nosZ) and anammox showed higher expression levels in the BF group than in the RS group, although the differences were not statistically significant (p > 0.05). The results of 16S rRNA sequencing research showed that both treatment groups’ intestinal and water bacterial communities had comparable levels of richness and diversity. Pseudomonas mosselii was the dominant bacterial species in the water. In the BF group, the dominant intestinal species were Bacillus halodurans and Caldalkalibacillus thermarum, while in the RS group, the dominant species was Plesiomonas shigelloides. In conclusion, rice straw and bamboo flour are applicable in BFT systems for mandarin fish culture, with good growth performance and water quality. The BF group showed higher nitrogen removal efficiency and denitrification gene expression than the RS group. Full article

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

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16 pages, 2623 KiB

Open AccessArticle

Grapevine Responses to the Entomopathogenic Fungi Beauveria bassiana and Isaria fumosorosea and the Effects of Salicylic Acid on Their Virulence Against the European Grapevine Moth, Lobesia botrana

by Evangelos Beris, Xenophon Venios, Dimitrios Papachristos, Mathilde Ponchon, Dimitrios Kontodimas, Elias Korkas, Georgios Banilas and Annette Reineke

Microorganisms 2025, 13(7), 1630; https://doi.org/10.3390/microorganisms13071630 - 10 Jul 2025

Abstract

Entomopathogenic fungi (EPF) are substantial biocontrol agents reducing the populations of economically important pests in numerous crops. Recent findings indicate that their role in agroecosystems is more complex and extends to affecting plant physiology and growth. This study examined the effects of Beauveria [...] Read more.

Entomopathogenic fungi (EPF) are substantial biocontrol agents reducing the populations of economically important pests in numerous crops. Recent findings indicate that their role in agroecosystems is more complex and extends to affecting plant physiology and growth. This study examined the effects of Beauveria bassiana and Isaria fumosorosea, as well as Salicylic acid (SA), on physiological parameters of grapevine (Vitis vinifera cv. Sauvignon Blanc). Additionally, the impact of SA on spore germination and pathogenicity of EPF against larvae of the European grapevine moth (Lobesia botrana) was tested. Foliar application of EPF was found to increase the electron transport rate (ETR) from PSII to PSI, indicating higher photosynthetic activity compared to control plants. EPF also elevated the transpiration rate (E) and stomatal conductance (gs). In contrast, SA treatments decreased E and gs, while the high dose (10 mM) exhibited reduced Fv/Fm value, accompanied by phytotoxic spots on leaves. Spore germination of both fungi was significantly reduced only by the SA concentration of 2 mM, while 0.5 and 1 mM did not affect germination. Combination EPF and SA treatments presented the highest larval mortality of L. botrana (87.5% at 28 °C and 77.5% at 24 °C for B. bassiana and I. fumosorosea, respectively). However, SA reduced larval mycosis in most cases. Overall, the results suggest that EPF and SA can be co-applied and included in vineyard integrated strategies to support grapevine health. Full article

(This article belongs to the Special Issue Microbiology of the Grape-Wine System)

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19 pages, 3179 KiB

Open AccessArticle

Development of a Multiplex Real-Time PCR Assay for the Detection of Eight Pathogens Associated with Bovine Respiratory Disease Complex from Clinical Samples

by Fuxing Hao, Chunhao Tao, Ruilong Xiao, Ying Huang, Weifeng Yuan, Zhen Wang and Hong Jia

Microorganisms 2025, 13(7), 1629; https://doi.org/10.3390/microorganisms13071629 - 10 Jul 2025

Abstract

Bovine respiratory disease complex (BRDC) is one of the primary causes of morbidity, mortality, and economic loss in cattle worldwide. Accurate and rapid identification of causative pathogenic agents is essential for effective disease management and control. In this study, a novel multiplex fluorescence-based [...] Read more.

Bovine respiratory disease complex (BRDC) is one of the primary causes of morbidity, mortality, and economic loss in cattle worldwide. Accurate and rapid identification of causative pathogenic agents is essential for effective disease management and control. In this study, a novel multiplex fluorescence-based quantitative polymerase chain reaction (qPCR) assay was developed for the simultaneous detection of eight major pathogens associated with BRDC. The targeted pathogens included the following: bovine viral diarrhea virus (BVDV), bovine parainfluenza virus type 3 (BPIV3), bovine respiratory syncytial virus (BRSV), bovine coronavirus (BcoV), Mycoplasma bovis (M.bovis), Pasteurella multocida (PM), Mannheimia haemolytica (MH), and infectious bovine rhinotracheitis virus (IBRV). The assay was rigorously optimized to ensure high specificity with no cross-reactivity among targets. The limit of detection (LOD) was determined to be as low as 5 copies per reaction for all target pathogens. The coefficient of variation (CVs) for both intra-assay and inter-assay measurements were consistently below 2%, demonstrating excellent reproducibility. To validate the clinical utility of the assay, a total of 1012 field samples were tested, including 504 nasal swabs from Farm A and 508 from Farm B in Jiangsu Province. BVDV, BcoV, PM, and MH were detected from Farm A, with a BVDV-positive rate of 21.63% (109/504), BcoV-positive rate of 26.79% (135/504), PM-positive rate of 28.77% (145/504), and MH-positive rate of 15.08% (76/504). Also, BcoV, PM, MH, and IBRV were detected from Farm B, with a BcoV-positive rate of 2.36% (12/508), PM-positive rate of 1.38% (7/508), MH-positive rate of 14.76% (75/508), and IBRV-positive rate of 5.51% (28/508). Notably, a significant proportion of samples showed evidence of mixed infections, underscoring the complexity of BRDC etiology and the importance of a multiplex diagnostic approach. In conclusion, the developed multiplex qPCR assay provides a reliable, rapid, and cost-effective tool for simultaneous detection of multiple BRDC-associated pathogens, which will hold great promise for enhancing disease surveillance, early diagnosis, and targeted intervention strategies, ultimately contributing to improved BRDC management and cattle health outcomes. Full article

(This article belongs to the Special Issue Animal Viral Infectious Diseases)

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12 pages, 4263 KiB

Open AccessArticle

Characterization of a Novel Lentzea Species Isolated from the Kumtagh Desert and Genomic Insights into the Secondary Metabolite Potential of the Genus

by Ying Wen, Jiahui Li, Fujun Qiao, Wanyin Luo, Tuo Chen, Guangxiu Liu and Wei Zhang

Microorganisms 2025, 13(7), 1628; https://doi.org/10.3390/microorganisms13071628 - 10 Jul 2025

Abstract

A novel actinobacterial strain, designated E54^T, was isolated from a hyper-arid desert soil sample collected from the Kumtagh Desert in Dunhuang, Gansu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain E54^T within the genus Lentzea, [...] Read more.

A novel actinobacterial strain, designated E54^T, was isolated from a hyper-arid desert soil sample collected from the Kumtagh Desert in Dunhuang, Gansu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain E54^T within the genus Lentzea, showing highest similarity to Lentzea waywayandensis DSM 44232^T (98.9%) and Lentzea flava NBRC 15743^T (98.5%). However, whole-genome comparisons revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between E54^T and these related strains were below the thresholds for species delineation. Strain E54^T exhibited typical morphological characteristics of the genus Lentzea, forming a branched substrate. It grew optimally at 28–30 °C, pH 7.0–9.0, and tolerated up to 10% NaCl. The cell wall contained meso-diaminopimelic acid, the predominant menaquinone was MK-9(H₄), and major fatty acids included iso-C_16:0. The polar lipid profile comprised diphosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl inositol, hydroxyphosphatidyl ethanolamine, and an unidentified lipid. The characteristic amino acid type of the cell wall was meso-DAP. Whole-cell hydrolysis experiments revealed the characteristic cell wall sugar fractions: ribose and galactose. The genome of strain E54^T is approximately 8.0 Mb with a DNA G+C content of 69.38 mol%. Genome mining revealed 39 biosynthetic gene clusters (BGCs), including non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), terpenes, and siderophores. Comparative antiSMASH-based genome analysis across 38 Lentzea strains further demonstrated the genus’ remarkable biosynthetic diversity. NRPS and type I PKS (T1PKS) were the most prevalent BGC types, indicating a capacity to synthesize structurally complex and pharmacologically relevant metabolites. Together, these findings underscore the untapped biosynthetic potential of the genus Lentzea and support the proposal of strain E54^T as a novel species. The strain E54^T (=JCM 34936^T = GDMCC 4.216^T) should represent a novel species, for which the name Lentzea xerophila sp. nov. is proposed. Full article

(This article belongs to the Section Environmental Microbiology)

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11 pages, 239 KiB

Open AccessArticle

Carbapenem-Resistant Enterobacteriaceae (CRE) in Children with Cancer: The Impact of Rapid Diagnostics and Targeted Colonization Strategies on Improving Outcomes

by Youssef Madney, Sally Mahfouz, Ahmed Bayoumi, Omayma Hassanain, Omneya Hassanain, Ahmed A. Sayed, Deena Jalal, Maryam Lotfi, May Tolba, Ghada A. Ziad, Mervat Elanany, Mohamed Hashem, Gehad Taha, Lobna Shalaby and Alaa Elhaddad

Microorganisms 2025, 13(7), 1627; https://doi.org/10.3390/microorganisms13071627 - 10 Jul 2025

Abstract

Carbapenem-resistant Enterobacteriaceae (CRE) pose an emerging threat, with a high mortality rate among children with cancer. This study aimed to evaluate the impact of routine rectal swab surveillance and rapid PCR-based detection of carbapenemase genes to facilitate the early initiation of appropriate treatment [...] Read more.

Carbapenem-resistant Enterobacteriaceae (CRE) pose an emerging threat, with a high mortality rate among children with cancer. This study aimed to evaluate the impact of routine rectal swab surveillance and rapid PCR-based detection of carbapenemase genes to facilitate the early initiation of appropriate treatment and assess its effects on outcomes. The study compared two groups of pediatric cancer patients with CRE bloodstream infections: a retrospective cohort of 254 patients from 2013 to 2017, and a prospective cohort of 186 patients from 2020 to 2022, following the implementation of these tools. A rapid diagnostic test in the prospective cohort resulted in the early initiation of proper antibiotics in 85% (165/186) of patients, compared to only 58% (147/254) in the retrospective group. This led to a decrease in the need for ICU admission related to sepsis from CRE and a significant reduction in the 30-day mortality rate (16% vs. 30%, p ≤ 0.01). Genotypic profiling revealed that class B carbapenemases were the most prevalent (69%), with the NDM type being identified in 67% of patients. OXA-48 and KPC enzymes were detected in 59% and 4% of patients, respectively. Multivariate analysis revealed that patients having Klebsiella pneumoniae, NDM genotype carbapenemases, presence of pneumonia, and septic shock requiring ICU admission were predictors of poor outcomes. Rapid diagnostics and targeted colonization lead to the appropriate use of targeted antibiotics, resulting in improved patient outcomes. Understanding carbapenemase-producing microorganisms and administering newer antibiotics may further reduce mortality and enhance treatment strategies for high-risk patients. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: Challenges and Innovative Solutions)

18 pages, 607 KiB

Open AccessArticle

Both, Limited and Often Fatal Systemic Infections Caused by Leuconostoc spp. in Older, Previously Ill Men Are Usually Acquired in the Outpatient Setting

by Johanna Butt, Cristian Arva and Stefan Borgmann

Microorganisms 2025, 13(7), 1626; https://doi.org/10.3390/microorganisms13071626 - 10 Jul 2025

Abstract

Leuconostoc spp. are vancomycin-resistant Gram-positive cocci that are used in food production and as pre- and probiotics. However, Leuconostoc spp. can also cause infections. In the present study, the records of patients with Leuconostoc spp. detection between January 2012 and March 2025 were [...] Read more.

Leuconostoc spp. are vancomycin-resistant Gram-positive cocci that are used in food production and as pre- and probiotics. However, Leuconostoc spp. can also cause infections. In the present study, the records of patients with Leuconostoc spp. detection between January 2012 and March 2025 were analyzed, inclusive of the underlying risk factors. Leuconostoc spp. was isolated from 32 patients (21 male, 11 females), including nine patients with blood culture evidence. In the majority of patients, Leuconostoc spp. were obtained on the day of admission to the hospital or in the first few days thereafter, arguing against nosocomial acquisition. The median age of men and women (65.3 and 67.8 years) was similar, but seven of the 14 male patients over the age of 65 had the bacteria in blood culture. The female patients with blood culture evidence had suffered from peripartum thrombophlebitis and from anorexia nervosa (BMI 8.8 kg/m²). In contrast, men with Leuconostoc spp. in the blood culture had severe, limiting underlying diseases. While the two women survived, five of the seven blood-culture-positive men died. Overall, our results show that Leuconostoc spp. is mainly acquired in outpatient settings, but men are at a higher risk of acquisition. Colonized men over the age of 60 with severe underlying diseases have a high risk of systemic infection with a fatal outcome. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria in Food Fermentation and Biotechnology)

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18 pages, 409 KiB

Open AccessReview

Impact of Drought on Soil Microbial Communities

by Sujani De Silva, Lithma Kariyawasam Hetti Gamage and Vesh R. Thapa

Microorganisms 2025, 13(7), 1625; https://doi.org/10.3390/microorganisms13071625 - 10 Jul 2025

Abstract

Drought, an increasingly prevalent climate stressor due to global warming, profoundly impacts agricultural systems, particularly the soil microbiome. Soil microorganisms are crucial for nutrient cycling, plant health, and ecosystem stability; however, drought-induced changes disrupt microbial community structure, function, and interactions with plants. This [...] Read more.

Drought, an increasingly prevalent climate stressor due to global warming, profoundly impacts agricultural systems, particularly the soil microbiome. Soil microorganisms are crucial for nutrient cycling, plant health, and ecosystem stability; however, drought-induced changes disrupt microbial community structure, function, and interactions with plants. This review synthesizes current knowledge on the effects of drought on soil microbiomes, with a focus on microbial diversity, resilience, and functional shifts in agricultural contexts. It highlights key microbial mechanisms underpinning plant drought tolerance, including symbioses with plant growth-promoting bacteria and fungi. Furthermore, it addresses knowledge gaps in the long-term effects of repeated drought events, microbial adaptations, and plant–soil feedback mechanisms. By advancing our understanding of drought–microbiome dynamics, this review aims to inform sustainable agricultural practices and resilience strategies to mitigate the adverse impacts of drought on crop productivity and ecosystem health. Full article

(This article belongs to the Section Environmental Microbiology)

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18 pages, 3395 KiB

Open AccessArticle

Characterization, Microbial Community Structure, and Pathogen Occurrence in Two Typical Eel Farms

by Jing-Ying Lai, Hui-Rong Lin, Xiao-Hui Sun, Gong-Ren Hu, Rui-Lian Yu and Jia-Qi Li

Microorganisms 2025, 13(7), 1624; https://doi.org/10.3390/microorganisms13071624 - 10 Jul 2025

Abstract

Pollutants and pathogens in aquaculture systems may cause economic losses and threaten public health. Yet, the risks associated with microbiological contaminants and their relationship with environmental factors remain largely unknown. In this study, two typical eel farms in southeast China were chosen for [...] Read more.

Pollutants and pathogens in aquaculture systems may cause economic losses and threaten public health. Yet, the risks associated with microbiological contaminants and their relationship with environmental factors remain largely unknown. In this study, two typical eel farms in southeast China were chosen for investigation of water quality and microbial community in the treatment processes. It was found that flocculant addition can only effectively reduce total phosphorus (TP) in both farms. However, excessive total nitrogen (TN) was found (6.16 mg/L and 6.74 mg/L, respectively). NH₄⁺ (3.98 mg/L) was the main nitrogen pollutant in QR farm, while NO₃⁻ (3.81 mg/L) and NO₂⁻ (1.22 mg/L) were the main nitrogen pollutants in ZJ farm. The treatment processes could not effectively remove nitrogen pollution, and the abundance of nitrogen functional bacteria was low. NO₂⁻ was positively correlated with Verrucomicrobiota (p < 0.05). NH₄⁺ and TN were significantly negatively correlated with Nitrospirota and unclassified_f_Anaerolineaceae, respectively (p < 0.05). Some typical pathogens associated with aquaculture (e.g., Lactococcus) and human beings (e.g., Escherichia-Shigella,) were found in the systems. This study proposes suggestions for aquaculture tailwater by analyzing the shortcomings of the existing treatment processes. Meanwhile, it offers certain support for the prevention of pathogen risks in aquaculture systems. Full article

(This article belongs to the Special Issue Microbes in Aquaculture)

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13 pages, 2175 KiB

Open AccessArticle

Remote BV Management via Metagenomic Vaginal Microbiome Testing and Telemedicine

by Krystal Thomas-White, Genevieve Olmschenk, David Lyttle, Rob Markowitz, Pita Navarro and Kate McLean

Microorganisms 2025, 13(7), 1623; https://doi.org/10.3390/microorganisms13071623 - 9 Jul 2025

Abstract

Bacterial vaginosis (BV) affects 30% of women annually, but many face barriers to in-person care. Here we present real-world outcomes of remote BV diagnosis and management through self-collected vaginal microbiome (VMB) testing and telemedicine visits, focusing on symptom resolution, recurrence, and overall microbial [...] Read more.

Bacterial vaginosis (BV) affects 30% of women annually, but many face barriers to in-person care. Here we present real-world outcomes of remote BV diagnosis and management through self-collected vaginal microbiome (VMB) testing and telemedicine visits, focusing on symptom resolution, recurrence, and overall microbial shifts. Among the 1159 study participants, 75.5% experienced symptom resolution at four weeks when managed with our algorithm-guided treatment protocol. At a median follow-up of 4.4 months after the initial visit, 30.0% of patients experienced recurrent BV, which is lower than the typical recurrence rates seen in historical in-person cohorts. Across the entire cohort, metagenomic data demonstrated a significant increase in Lactobacillus abundance (mean of 32.9% to 48.4%, p < 0.0001) and a corresponding decrease in BV-associated taxa such as Gardnerella, Prevotella, and Fannyhessea. A PERMANOVA of pairwise Bray–Curtis distances showed significant separation between pre-and post-treatment samples (pseudo-F = 37.6, p < 0.0001), driven by an increase in Lactobacillus-dominated samples. Treatment adherence was high (a total of 78% reported perfect or near-perfect adherence), and adverse events were generally mild (in total, 22% reported vaginal irritation, and 13% reported abnormal discharge). These results demonstrate that Evvy’s at-home metagenomic platform, paired with telemedicine and a smart treatment algorithm, delivers robust clinical and microbial outcomes. This work offers a novel approach to managing bacterial vaginosis, a challenging condition characterized by persistently high recurrence rates. Full article

(This article belongs to the Special Issue The Vaginal Microbiome in Health and Disease)

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28 pages, 1879 KiB

Open AccessArticle

Rapamycin Plays a Pivotal Role in the Potent Antifungal Activity Exhibited Against Verticillium dahliae by Streptomyces iranensis OE54 and Streptomyces lacaronensis sp. nov. Isolated from Olive Roots

by Carla Calvo-Peña, Marina Ruiz-Muñoz, Imen Nouioui, Sarah Kirstein, Meina Neumann-Schaal, José María Sánchez-López, Seyedehtannaz Ghoreshizadeh, Rebeca Cobos and Juan José R. Coque

Microorganisms 2025, 13(7), 1622; https://doi.org/10.3390/microorganisms13071622 - 9 Jul 2025

Abstract

Verticillium wilt, caused by Verticillium dahliae, poses a significant threat to olive trees (Olea europaea L.). The isolation of endophytic Streptomyces strains from olive roots has led to the discovery of several strains showing strong antifungal activity against V. dahliae, [...] Read more.

Verticillium wilt, caused by Verticillium dahliae, poses a significant threat to olive trees (Olea europaea L.). The isolation of endophytic Streptomyces strains from olive roots has led to the discovery of several strains showing strong antifungal activity against V. dahliae, as demonstrated through in vitro and small-scale soil experiments. Molecular analyses confirmed that strain OE54 belongs to Streptomyces iranensis. The main antifungal compound identified in this strain was rapamycin. Rapamycin displayed potent antifungal effects, notably inhibiting conidiospore germination (IC₅₀ = 87.36 μg/mL) and the hyphal growth of V. dahliae, with a minimum inhibitory concentration (MIC₅₀) of 3.91 ng/mL. Additionally, a second rapamycin-producing strain, OE57^T, was isolated. Phenotypic and genotypic analyses indicated that OE57^T represents a new species, which is proposed to be named Streptomyces lacaronensis sp. nov., with OE57^T designated as the type strain (=DSM 118741^T; CECT 31164^T). The discovery of two endophytic rapamycin-producing Streptomyces strains residing within olive roots is especially notable, given the rarity of rapamycin production among microorganisms. These findings highlight the potential of rapamycin-producing Streptomyces strains in developing biofertilizers to manage V. dahliae and reduce the impact of Verticillium wilt on olive trees and other crops. Full article

(This article belongs to the Special Issue Microorganisms as Biocontrol Agents in Plant Pathology, 2nd Edition)

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17 pages, 3221 KiB

Open AccessArticle

Removal of Chemical Oxygen Demand (COD) from Swine Farm Wastewater by Corynebacterium xerosis H1

by Jingyi Zhang, Meng Liu, Heshi Tian, Lingcong Kong, Wenyan Yang, Lianyu Yang and Yunhang Gao

Microorganisms 2025, 13(7), 1621; https://doi.org/10.3390/microorganisms13071621 - 9 Jul 2025

Abstract

Swine wastewater (SW) has a high chemical oxygen demand (COD) content and is difficult to degrade; an effective strategy to address this issue is through biodegradation, which poses negligible secondary pollution risks and ensures cost-efficiency. The objectives of this study were to isolate [...] Read more.

Swine wastewater (SW) has a high chemical oxygen demand (COD) content and is difficult to degrade; an effective strategy to address this issue is through biodegradation, which poses negligible secondary pollution risks and ensures cost-efficiency. The objectives of this study were to isolate an effective COD-degrading strain of SW, characterize (at the molecular level) its transformation of SW, and apply it to practical production. A strain of Corynebacterium xerosis H1 was isolated and had a 27.93% ± 0.68% (mean ± SD) degradation rate of COD in SW. This strain precipitated growth in liquids, which has the advantage of not needing to be immobilized, unlike other wastewater-degrading bacteria. Based on analysis by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), this bacterium removed nitrogen-containing compounds in SW, with proteins and lipids decreasing from 41 to 10% and lignins increasing from 51 to 82%. Furthermore, the enhancement of the sequencing batch reactor (SBR) with strain H1 improved COD removal in effluent, with reductions in the fluorescence intensity of aromatic protein I, aromatic protein II, humic-like acids, and fulvic acid regions. In addition, based on 16S rRNA gene sequencing analysis, SBR_H1 successfully colonized some H1 bacteria and had a higher abundance of functional microbiota than SBR_C. This study confirms that Corynebacterium xerosis H1, as a carrier-free efficient strain, can be directly applied to swine wastewater treatment, reducing carrier costs and the risk of secondary pollution. The discovery of this strain enriches the microbial resource pool for SW COD degradation and provides a new scheme with both economic and environmental friendliness for large-scale treatment. Full article

(This article belongs to the Section Microbial Biotechnology)

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Microorganisms, Volume 13, Issue 7 (July 2025) – 217 articles

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