Microorganisms

25 pages, 4898 KiB

Open AccessArticle

The Role of Coffee Microbiomes in Pathogen Resistance Across Varieties and Ecological Niches

by Yihong Wu, Xiu Zhao, Zuquan Wang, Xuejun Li, Xuesong Zhang, Chun Xie, Huabo Du, Kuaile Jiang, Peng Qu and Chuanli Zhang

Microorganisms 2025, 13(8), 1909; https://doi.org/10.3390/microorganisms13081909 - 15 Aug 2025

Abstract

The plant microbiome plays a role in pathogen defense, but its role in different resistant varieties and ecological niches remains unclear. This study used 16S rRNA and ITS sequencing to investigate microbial communities and interactions in disease-resistant (PT) and susceptible (Bourbon) coffee varieties [...] Read more.

The plant microbiome plays a role in pathogen defense, but its role in different resistant varieties and ecological niches remains unclear. This study used 16S rRNA and ITS sequencing to investigate microbial communities and interactions in disease-resistant (PT) and susceptible (Bourbon) coffee varieties of five ecological niches: leaves, fruits, roots, rhizosphere soil, and non-rhizosphere soil. We found that the microbial communities differed significantly between the two varieties. The resistant variety was enriched in beneficial bacteria from the Actinobacteriota phylum and a stable, modular microbial network dominated by saprotrophic fungi. In contrast, the susceptible variety had a higher abundance of opportunistic pathogens and stress-indicator fungi, including Neurospora spp., which were more prominent in the rhizosphere and non-rhizosphere soils. These networks were fragile and dominated by pathotrophic fungi, reflecting ecological imbalance. Our findings show that plant disease resistance is influenced not only by host genetics but also by co-evolutionary interactions with the microbiome. These insights provide a foundation for developing targeted biocontrol strategies to manage plant-associated microbial communities. Full article

(This article belongs to the Section Plant Microbe Interactions)

16 pages, 1377 KiB

Open AccessArticle

Climate Change Adaptation in Winemaking: Combined Use of Non-Saccharomyces Yeasts to Improve the Quality of Pedro Ximénez Wines

by Fernando Sánchez-Suárez, Rafael Martínez-García and Rafael A. Peinado

Microorganisms 2025, 13(8), 1908; https://doi.org/10.3390/microorganisms13081908 - 15 Aug 2025

Abstract

This study evaluates the impact of two non-Saccharomyces yeasts, Lachancea thermotolerans and Metschnikowia pulcherrima, on the oenological and sensory characteristics of Pedro Ximénez (PX) white wines produced in warm regions of southern Spain. PX wines are particularly affected by climate change, [...] Read more.

This study evaluates the impact of two non-Saccharomyces yeasts, Lachancea thermotolerans and Metschnikowia pulcherrima, on the oenological and sensory characteristics of Pedro Ximénez (PX) white wines produced in warm regions of southern Spain. PX wines are particularly affected by climate change, often exhibiting low acidity and limited aromatic complexity. Fermentations were performed using pure and sequential cultures of these yeasts and compared to a control inoculated with Saccharomyces cerevisiae. Wines fermented with L. thermotolerans showed increased titratable acidity (up to 6.83 g/L), reduced pH (down to 3.02), and higher lactic acid concentrations, contributing to improved freshness and microbial stability. The use of M. pulcherrima led to a significant rise in ester production, enhancing fruity and floral aromatic notes. Sequential fermentation using both yeasts produced wines with the highest overall aromatic complexity and superior performance in sensory evaluations. These findings support the use of L. thermotolerans and M. pulcherrima as a promising biotechnological strategy to improve white wine quality under climate change conditions. Full article

(This article belongs to the Special Issue Wine Fermentation Microorganisms)

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14 pages, 908 KiB

Open AccessArticle

Fusobacterium nucleatum Infection Drives Glutathione Depletion in Gastric Cancer: Integrated Multi-Omics and Experimental Validation

by Siru Nie, Yuehua Gong, Ang Wang, Rui Guo, Xiaohui Chen and Yuan Yuan

Microorganisms 2025, 13(8), 1907; https://doi.org/10.3390/microorganisms13081907 - 15 Aug 2025

Abstract

The colonization of Fusobacterium nucleatum (F. nucleatum) in the microenvironment of gastric cancer (GC) is closely associated with tumor progression, but its impact on host metabolic remodeling remains unclear. This study aims to elucidate the mechanistic link between F. nucleatum infection [...] Read more.

The colonization of Fusobacterium nucleatum (F. nucleatum) in the microenvironment of gastric cancer (GC) is closely associated with tumor progression, but its impact on host metabolic remodeling remains unclear. This study aims to elucidate the mechanistic link between F. nucleatum infection and metabolic changes in GC tissue. By integrating 16S rRNA microbiome sequencing and LC-MS/MS metabolomics, the differences in microbial composition and metabolic profiles between Fusobacterium sp.-positive and -negative GC tissues were systematically compared, and the correlation of differential microbes and differential metabolites was analyzed. The impact of F. nucleatum on the glutathione (GSH) metabolic pathway was validated through in vitro tissue testing and the use of the infection model of GC cell lines (such as AGS and HGC27). Integrative omics analysis showed a strong negative correlation between Fusobacterium sp. infection and antioxidant metabolite GSH levels in GCs (p < 0.001). Metabolic reprogramming features: Eleven differentially expressed metabolites were identified using LC-MS/MS metabolomics screening (p < 0.05). GSH was significantly depleted in the Fusobacterium sp.-positive group. Experimental validation: At the histological level, the abundance of F. nucleatum in GC tissues was higher than that in the paired adjacent non-cancerous (NC) tissues; at the cellular level, after F. nucleatum infection of GC cells, the intracellular GSH level decreased (p < 0.01), accompanied by a decrease in glutathione synthetase (GSS) mRNA expression and reactive oxygen species (ROS). This study is the first to demonstrate that F. nucleatum suppresses the GSH synthesis pathway, leading to the breakdown of antioxidant capacity and the formation of an oxidative stress microenvironment in GC cells. These findings provide new insights into the metabolic mechanism of F. nucleatum in promoting GC progression and suggest that targeting the F. nucleatum-GSH axis could offer a novel strategy for GC therapeutic intervention. Full article

(This article belongs to the Section Medical Microbiology)

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23 pages, 5076 KiB

Open AccessArticle

Effects of Near-Natural Forest Management on Soil Microbial Communities in the Temperate–Subtropical Transition Zone of China

by Tian Zhang, Xibin Dong, Jin Yang, Zhenhua Li and Jiangxiong Zhu

Microorganisms 2025, 13(8), 1906; https://doi.org/10.3390/microorganisms13081906 - 15 Aug 2025

Abstract

In order to precisely improve the quality of major tree species in northern China, near-natural differentiated management has been gradually introduced into forestry practice, aiming to optimize forest structure, enhance forest quality, and promote nutrient cycling and water conservation. As an essential element [...] Read more.

In order to precisely improve the quality of major tree species in northern China, near-natural differentiated management has been gradually introduced into forestry practice, aiming to optimize forest structure, enhance forest quality, and promote nutrient cycling and water conservation. As an essential element of forest ecosystems, soil microbes contribute to biodiversity preservation and nutrient turnover in soils. This study selected three typical forest types (Quercus acutissima forest, Pinus tabulaeformis forest, and Pinus tabulaeformis × Quercus mixed forest) that have been managed with target trees on Zhongtiao Mountain. Using 16S/ITS rRNA high-throughput sequencing, this study systematically assessed the influences of forest type and soil depth (0–60 cm) on the soil properties and microbial communities. The results showed that the fungal alpha diversity indices were the highest in Pinus tabulaeformis forest, which decreased with soil depth. Actinobacteriota exhibited the greatest relative abundance in mixed forest, whereas Ascomycota predominated in the Pinus tabulaeformis forest. The microbial co-occurrence network exhibited greater complexity compared to the pure forest. Microbial carbon and nitrogen cycling functions showed strong correlation with soil pH and nutrient levels. Symbiotrophs dominated the fungal community, and ectomycorrhizae were significantly abundant in mixed forests. pH is the dominant factor driving changes in microbial communities. In summary, the mixed forest improved soil nutrients, enhanced the complexity of microbial networks, and supported higher ectomycorrhizal abundance. These findings provide practical guidance for improving soil health and stability of forest ecosystems through near-natural management. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 2nd Edition)

25 pages, 2721 KiB

Open AccessReview

Next-Generation Nucleic Acid-Based Diagnostics for Viral Pathogens: Lessons Learned from the SARS-CoV-2 Pandemic

by Amy Papaneri, Guohong Cui and Shih-Heng Chen

Microorganisms 2025, 13(8), 1905; https://doi.org/10.3390/microorganisms13081905 - 15 Aug 2025

Abstract

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), catalyzed unprecedented innovation in molecular diagnostics to address critical gaps in rapid pathogen detection. Over the past five years, CRISPR-based systems, isothermal amplification techniques, and portable biosensors have emerged as transformative [...] Read more.

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), catalyzed unprecedented innovation in molecular diagnostics to address critical gaps in rapid pathogen detection. Over the past five years, CRISPR-based systems, isothermal amplification techniques, and portable biosensors have emerged as transformative tools for nucleic acid detection, offering improvements in speed, sensitivity, and point-of-care applicability compared to conventional PCR. While numerous reviews have cataloged the technical specifications of these platforms, a critical gap remains in understanding the strategic and economic hurdles to their real-world implementation. This review provides a forward-looking analysis of the feasibility, scalability, and economic benefits of integrating these next-generation technologies into future pandemic-response pipelines. We synthesize advances in coronavirus-specific diagnostic platforms and attempt to highlight the need for their implementation as a cost-saving measure during surges in clinical demand. We evaluate the feasibility of translating these technologies—particularly CRISPR-Cas integration with recombinase polymerase amplification (RPA)—into robust first-line diagnostic pipelines for novel viral threats. By analyzing the evolution of diagnostic strategies during the COVID-19 era, we aim to provide strategic insights and new directions for developing and deploying effective detection platforms to better confront future viral pandemics. Full article

(This article belongs to the Special Issue New Advancements in Clinical Microbiology: Surveillance, Diagnosis, and Treatment)

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19 pages, 4317 KiB

Open AccessArticle

Native Rhizobial Inoculation Improves Tomato Yield and Nutrient Uptake While Mitigating Heavy Metal Accumulation in a Conventional Farming System

by Luis Alberto Manzano-Gómez, Clara Ivette Rincón-Molina, Esperanza Martínez-Romero, Simón Samuel Stopol-Martínez, Amado Santos-Santiago, Juan José Villalobos-Maldonado, Víctor Manuel Ruíz-Valdiviezo and Reiner Rincón-Rosales

Microorganisms 2025, 13(8), 1904; https://doi.org/10.3390/microorganisms13081904 - 15 Aug 2025

Abstract

Enhancing crop productivity through biological strategies is critical for agriculture, particularly under conventional farming systems heavily reliant on chemical inputs. Plant probiotic bacteria offer promising alternatives by promoting plant growth and yield. This is the first field study to assess the effects of [...] Read more.

Enhancing crop productivity through biological strategies is critical for agriculture, particularly under conventional farming systems heavily reliant on chemical inputs. Plant probiotic bacteria offer promising alternatives by promoting plant growth and yield. This is the first field study to assess the effects of biofertilization with native rhizobial strains Rhizobium sp. ACO-34A, Sinorhizobium mexicanum ITTG-R7^T, and S. chiapasense ITTG-S70^T on Solanum lycopersicum (tomato) cultivated under conventional farming conditions. Key parameters assessed include plant performance (plant height, plant stem width, plant dry weight, and chlorophyll content), fruit yield (fruits per plant, fruit height, fruit width, fruit weight, and estimated fruit volume), and macronutrient and micronutrient contents in plant tissue. Additionally, rhizospere bacterial communities were characterized through 16S rRNA amplicon sequencing to evaluate alpha and beta diversity. Inoculation with ITTG-R7^T significantly improved plant height, stem width, and plant dry weight, while ITTG-S70^T enhanced stem width and chlorophyll content. ACO-34A inoculation notably increased fruit number, size, and yield parameters. Moreover, inoculated plants exhibited reduced Fe and Cu accumulation compared to non-inoculated controls. Metagenomic analyses indicated that rhizobial inoculation did not significantly disrupt the native rhizosphere bacterial community. These findings highlight the potential of rhizobial strains as effective plant probiotics that enhance tomato productivity while preserving microbial community structure, supporting the integration of microbial biofertilizers into conventional farming systems. Full article

(This article belongs to the Special Issue Feature Papers in Plant–Microbe Interactions in North America)

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17 pages, 1459 KiB

Open AccessArticle

Effectiveness of Feed-Based Monovalent Aeromonas Vaccine in Farmed Carp

by Nimra Mubeen, Farzana Abbas, Muhammad Hafeez-ur-Rehman, Margaret Crumlish, Haris Mahboob, Muhammad Akmal, Ayesha Sadiqa, Talha Mahboob Alam and Samama Jalil

Microorganisms 2025, 13(8), 1903; https://doi.org/10.3390/microorganisms13081903 - 15 Aug 2025

Abstract

Aeromonas hydrophila (A. hydrophila) is responsible for causing abdominal dropsy, swimming abnormalities, skin ulcerations, and pale gills in fish. Vaccination is an essential strategy for disease prevention in aquaculture. This study evaluated the efficacy of an oral vaccine against A. hydrophila [...] Read more.

Aeromonas hydrophila (A. hydrophila) is responsible for causing abdominal dropsy, swimming abnormalities, skin ulcerations, and pale gills in fish. Vaccination is an essential strategy for disease prevention in aquaculture. This study evaluated the efficacy of an oral vaccine against A. hydrophila in Ctenopharyngodon idella (C. idella). The vaccine was formulated as feed-based monovalent pellets, incorporating or spraying formalin-killed A. hydrophila on/into commercial feed with 30% crude protein. Mineral and fish oils were used as adjuvants at 10% of the feed. Prior to the trial, the experimental feed groups were subjected to quality and safety tests. Grass carp fingerlings (20 ± 5 g) were divided into seven groups (n = 20 per group): sprayed vaccinated feed with fish oil (SVFF), incorporated vaccinated feed with fish oil (IVFF), sprayed vaccinated feed with mineral oil (SVFM), incorporated vaccinated feed with mineral oil (IVFM), sprayed vaccinated feed (SVF), incorporated vaccinated feed (IVF), and a control group. Feed was provided at 3% of body weight for 60 days. Immunomodulation was investigated through lysozyme activity, antibody titers, and immunoglobulin M (IgM). The IVFF group showed significantly enhanced immunity and growth performance, with an 87% protection rate, 13% mortality, and the highest relative percentage survival (83%) following intraperitoneal A. hydrophila (6.8 × 10⁹ CFU/mL) challenge. Histological analysis indicated minimal pathological changes in the IVFF group compared to controls. Fish oil as an adjuvant enhanced immunity without adverse health effects. Overall, this study demonstrated that feed-based monovalent vaccines effectively improve immune responses and provide protection against A. hydrophila in C. idella. Full article

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

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24 pages, 2865 KiB

Open AccessArticle

Isolation and Screening of the Novel Multi-Trait Strains for Future Implications in Phytotechnology

by Zhuldyz Batykova, Valentina Pidlisnyuk, Aida Kistaubayeva, Sergey Ust’ak, Irina Savitskaya, Laila Saidullayeva and Aigerim Mamirova

Microorganisms 2025, 13(8), 1902; https://doi.org/10.3390/microorganisms13081902 - 15 Aug 2025

Abstract

Plant growth-promoting rhizobacteria (PGPRs) colonise the rhizosphere and root surfaces, enhancing crop development through a variety of mechanisms. This study evaluated microbial strains isolated from Triticum aestivum L. for key plant growth-promoting traits, including indole-3-acetic acid (IAA) production, phosphate and zinc (Zn) solubilisation, [...] Read more.

Plant growth-promoting rhizobacteria (PGPRs) colonise the rhizosphere and root surfaces, enhancing crop development through a variety of mechanisms. This study evaluated microbial strains isolated from Triticum aestivum L. for key plant growth-promoting traits, including indole-3-acetic acid (IAA) production, phosphate and zinc (Zn) solubilisation, nitrogen (N₂) fixation, and antifungal activity. Among 36 isolates, 3 (AS8, AS23, AS31) exhibited strong growth-promoting potential. IAA production, citrate assimilation, carbohydrate fermentation, and catalase activity were observed to a comparable extent among the selected strains. AS8 showed the highest protease, lipase, and amylolytic activity, while AS23 demonstrated superior phosphate and Zn solubilisation. Notably, AS31 emerged as the most promising multi-trait isolate, exhibiting the highest levels of IAA production, N₂ fixation, antifungal activity against five phytopathogens (Fusarium graminearum, F. solani, F. oxysporum, Pythium aphanidermatum, and Alternaria alternata), potentially linked to its hydrogen sulphide (H₂S) production, and cellulolytic activity. Molecular identification based on 16S rRNA gene sequencing revealed the isolates as Stenotrophomonas indicatrix AS8, Pantoea agglomerans AS23, and Bacillus thuringiensis AS31. Seed germination assays confirmed the plant growth-promoting efficacy of these PGPR strains, with vigour index increases of up to 43.4-fold. Given their positive impact on seed germination and significant Zn-solubilising abilities, the selected strains represent promising candidates for use as bio-inoculants, offering a sustainable and eco-friendly strategy to enhance agricultural productivity in nutrient-deficient soils. Future research should validate the efficacy of these PGPR strains under pot conditions to confirm their potential for practical agricultural applications. Full article

(This article belongs to the Special Issue Plant Microbiome: Pioneering Microbiome-Driven Strategies for Climate-Resilient Agriculture)

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15 pages, 4180 KiB

Open AccessArticle

BOL Lectin: A Protein Derived from Cauliflower Exhibits Antibiofilm Activity in In Vitro Assays Against Staphylococcus aureus

by Leandro Augusto Mariano Silva, Natália Pereira, Mareliza Possa de Menezes, Romário Alves Rodrigues, Milena Souza Reis, Giordano Eugenio Oliveira, Hugo Leandro dos Santos, Lucas José Luduverio Pizauro, Ana Karen de Mendonça Ludgero, Christiane Eliza Motta Duarte, Leandro Licursi de Oliveira, Caio Roberto Soares Bragança and Marita Vedovelli Cardozo

Microorganisms 2025, 13(8), 1901; https://doi.org/10.3390/microorganisms13081901 - 15 Aug 2025

Abstract

The BOL lectin, a 34 kDa protein with a hemagglutination titer of 64 hemagglutination units (HU), was extracted from cauliflower (Brassica oleracea spp. botrytis L.), purified by affinity and ion exchange chromatography, and confirmed, in this study, by Sodium Dodecyl Sulfate-Polyacrylamide Gel [...] Read more.

The BOL lectin, a 34 kDa protein with a hemagglutination titer of 64 hemagglutination units (HU), was extracted from cauliflower (Brassica oleracea spp. botrytis L.), purified by affinity and ion exchange chromatography, and confirmed, in this study, by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE). The antibiofilm activity of BOL was evaluated at two concentrations (0.1 mg/mL and 1.0 mg/mL) against bacterial strains of importance to human health (Bacillus cereus ATCC 10876, Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29213, and Streptococcus agalactiae ATCC 12403). In addition to a biofilm formation assay, a pre-formed biofilm assay was conducted, with biofilm structure analyzed by Scanning Electron Microscopy (SEM). The antimicrobial potential of BOL was also investigated using the Minimum Inhibitory Concentration (MIC) assay in 96-well microplates. Among the tested bacterial strains, BOL exhibited activity against S. aureus at 1.0 mg/mL, interfering with both biofilm formation and disrupting pre-formed biofilms, which may be explained by a possible interaction between BOL and the components present in the biofilm matrix. However, no antibiofilm activity was observed against E. coli, B. cereus, or S. agalactiae, possibly due to differences in the composition of their biofilm matrices. Furthermore, BOL showed no detectable bactericidal or bacteriostatic activity in the antimicrobial assays. In conclusion, BOL lectin, at the tested concentrations, does not exhibit direct antimicrobial activity but effectively disrupts the extracellular matrix in S. aureus ATCC 29213. Full article

(This article belongs to the Special Issue Lectins and Human Pathogenic Microorganisms: Mechanisms and Applications)

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16 pages, 1211 KiB

Open AccessFeature PaperArticle

“Encyclopaedia Cloacae”—Mapping Wastewaters from Pathogen A to Z

by Aurora Hirvonen, Sara Comero, Simona Tavazzi, Giulio Mariani, Caterina Cacciatori, Roberta Maffettone, Francesco Pierannunzi, Giulia Panzarella, Luis Bausa-Lopez, Sorin Sion, Tanja Casado Poblador, Natalia Głowacka, Davey L. Jones, Mauro Petrillo, Antonio Marchini, Maddalena Querci, Bernd Manfred Gawlik and on behalf of the Encyclopaedia Cloacae Collaborators

Microorganisms 2025, 13(8), 1900; https://doi.org/10.3390/microorganisms13081900 - 15 Aug 2025

Abstract

The Encyclopaedia Cloacae is a novel and centralised digital platform designed to support and advance wastewater-based epidemiology (WBE) by cataloguing pathogens detectable in wastewater and their relevance to public health surveillance. The platform is hosted on the EU Wastewater Observatory for Public Health [...] Read more.

The Encyclopaedia Cloacae is a novel and centralised digital platform designed to support and advance wastewater-based epidemiology (WBE) by cataloguing pathogens detectable in wastewater and their relevance to public health surveillance. The platform is hosted on the EU Wastewater Observatory for Public Health (EU4S) website, where it is populated with peer-reviewed research through a structured workflow under harmonised criteria which address the presence of pathogens in human excreta, detectability in wastewater, and integration into public health systems. This tri-criteria approach ensures that the database is both scientifically robust and operationally actionable. Complemented by the Visualising the Invisible dashboard, the platform offers geospatial insights into global WBE research activity. By consolidating peer-reviewed evidence on pathogen detectability in wastewater and human excreta, the Encyclopaedia Cloacae enables early detection of infectious diseases, whether already known or newly emerging. The continuously updated repository and geospatial dashboards help to identify surveillance gaps and research hotspots, to support timely public health responses, enhance pandemic preparedness, and strengthen global health security. In addition, it supports One Health strategies, connecting the health of humans, animals, and the shared environment. This article outlines the platform’s architecture, data curation methodology, and future directions, including automation and expansion to encompass broader health determinants such as antimicrobial resistance and chemical hazards. Full article

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

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13 pages, 1459 KiB

Open AccessArticle

Hepatitis E Virus Detection in Swine Livers and Feces in Heilongjiang, Northeastern China

by Haijuan He, Hai Li, Lei Yan, Gang Wang, Yonggang Liu, Tongqing An, Yabin Tu, Shujie Wang and Xuehui Cai

Microorganisms 2025, 13(8), 1899; https://doi.org/10.3390/microorganisms13081899 - 14 Aug 2025

Abstract

Hepatitis E virus (HEV) is an emerging zoonotic pathogen capable of both human-to-human and animal-to-human transmission. However, limited data are available regarding HEV infections in pigs in Heilongjiang Province, China. To investigate the prevalence of HEV in pigs in this region, liver samples [...] Read more.

Hepatitis E virus (HEV) is an emerging zoonotic pathogen capable of both human-to-human and animal-to-human transmission. However, limited data are available regarding HEV infections in pigs in Heilongjiang Province, China. To investigate the prevalence of HEV in pigs in this region, liver samples from diseased or deceased pigs and fecal samples from healthy pigs were collected and analyzed. A total of 82 liver samples and 86 fecal samples were obtained from 13 farms and tested for HEV genotypes 3 and 4 using nested RT-PCR assays targeting the ORF2 gene. Samples with high viral loads were further subjected to direct sequencing and phylogenetic analysis. Overall, 32 samples tested positive for HEV RNA and were classified as genotype 3 or 4, with genotype 4 being the most prevalent. The identified subtypes included 3a, 4a, and 4d, among which subtype 4d was the most common. Phylogenetic analysis revealed that swine HEV genotype 3 (subtype 3a) and genotype 4 (subtypes 4a and 4d) clustered closely with reference sequences 3a/AB089824/JA10, 4a/JX9974449/NJ6, and 4d/JX997439/NJ5. These strains exhibited close genetic similarity to human HEV isolates previously reported in Tokyo, Japan, and eastern China. These findings indicate that HEV genotypes 3 and 4 are distributed in pig farms across Heilongjiang Province and suggest that zoonotic transmission between pigs and humans is frequent in China. Full article

(This article belongs to the Section Veterinary Microbiology)

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10 pages, 223 KiB

Open AccessArticle

Assessment of Sonication for Diagnosing Implant-Associated Infections in Spinal Surgery Routine Practice

by Estibaliz Torrecilla-Sádaba, Santiago Gabardo, Ignacio Mahillo-Fernández, Pierre Ferrer Pomares, Félix Tome-Bermejo, Luis Álvarez-Galovich, Joaquín García-Cañete, Jaime Esteban and Charles Mengis

Microorganisms 2025, 13(8), 1898; https://doi.org/10.3390/microorganisms13081898 - 14 Aug 2025

Abstract

Infections following spinal surgery can result in potentially devastating complications. An accurate microbiological diagnosis is crucial for proper treatment. Sonication is a diagnostic method that can be beneficial in patients with acute or low-grade infections. This study aimed to assess the sensitivity and [...] Read more.

Infections following spinal surgery can result in potentially devastating complications. An accurate microbiological diagnosis is crucial for proper treatment. Sonication is a diagnostic method that can be beneficial in patients with acute or low-grade infections. This study aimed to assess the sensitivity and effectiveness of sonication as a method for diagnosing spinal implant infections in cases of both suspected and unsuspected infections during spinal surgical revision. We conducted a retrospective observational study that included all patients who underwent revision spinal surgery between March 2011 and October 2022. We collected the implants and surrounding tissues from these patients for microbiological analysis. The implant sonication was performed according to a previously published protocol. Patients were categorised into those undergoing surgical revision for suspected spinal implant infection (SSII) and those for non-suspected spinal implant infection (NSSII). We collected comprehensive patient data, including demographics, risk factors, Charlson Comorbidity Index (CCI), surgical details, microbiological findings, antibiotic regimens, and clinical outcomes. Sensitivity and specificity analyses were conducted on both sonicated and non-sonicated samples. A total of 158 patients met the inclusion criteria; 51 of them were diagnosed with infection during surgery revision. Patients with SSII had higher CCIs than those with NSSII. The sensitivity was significantly higher in sonicated samples (68.6%; 95% CI: 55.9–81.4%) than in non-sonicated samples (42%; 95% CI: 28.3–55.7%). The specificities were similar, with sonicated samples at 93.5% (95% CI: 88.8–98.1%) and non-sonicated samples at 99.05% (95% CI: 97.2–100.9%). Combining both methods resulted in sensitivity and specificity rates of 76% (95% CI: 64.2–87.8%) and 93.3% (95% CI: 88.2–98.1%), respectively. Methicillin-susceptible Staphylococcus aureus (MSSA) was common in SSII, whereas Cutibacterium acnes and coagulase-negative Staphylococcus (CNS) were predominant in NSSII. This study supports the routine use of implant sonication as a valuable supplementary method for peri-implant tissue cultures, especially for identifying low-grade spinal implant infections. Full article

(This article belongs to the Collection Device-Related Infections and Bacterial Biofilms)

16 pages, 4270 KiB

Open AccessArticle

Subsoiling-Induced Shifts in Nitrogen Dynamics and Microbial Community Structure in Semi-Arid Rainfed Maize Agroecosystems

by Jian Gu, Hao Sun, Xu Zhou, Yongqi Liu, Mingwei Zhou, Ningning Ma, Guanghua Yin and Shijun Sun

Microorganisms 2025, 13(8), 1897; https://doi.org/10.3390/microorganisms13081897 - 14 Aug 2025

Abstract

Global agricultural intensification has exacerbated soil compaction and nitrogen (N) inefficiency, thereby threatening sustainable crop production. Sub-soiling, a tillage technique that fractures subsurface layers while preserving surface structure, offers potential solutions by modifying soil physical properties and enhancing microbial-mediated N cycling. This study [...] Read more.

Global agricultural intensification has exacerbated soil compaction and nitrogen (N) inefficiency, thereby threatening sustainable crop production. Sub-soiling, a tillage technique that fractures subsurface layers while preserving surface structure, offers potential solutions by modifying soil physical properties and enhancing microbial-mediated N cycling. This study investigated the effects of subsoiling depth (0, 20, and 40 cm) on soil microbial communities and N transformations in a semi-arid maize system in China. The results demonstrated that subsoiling to a depth of 40 cm (D2) significantly enhanced the retention of nitrate-N and ammonium-N, which correlated with improved soil porosity and microbial activity. High-throughput 16S rDNA sequencing revealed subsoiling depth-driven reorganization of microbial communities, with D2 increasing the abundance of Proteobacteria (+11%) and ammonia-oxidizing archaea (Nitrososphaeraceae, +19.9%) while suppressing denitrifiers (nosZ gene: −41.4%). Co-occurrence networks indicated greater complexity in microbial interactions under subsoiling, driven by altered aeration and carbon redistribution. Functional gene analysis highlighted a shift from denitrification to nitrification-mineralization coupling, with D2 boosting maize yield by 9.8%. These findings elucidate how subsoiling depth modulates microbiome assembly to enhance N retention, providing a mechanistic basis for optimizing tillage practices in semi-arid agroecosystems. Full article

(This article belongs to the Special Issue Microbial Communities and Nitrogen Cycling)

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15 pages, 3077 KiB

Open AccessArticle

Cascade CRISPR/cas Enables More Sensitive Detection of Toxoplasma gondii and Listeria monocytogenes than Single CRISPR/cas

by Dawei Chen, Min Sun, Bingbing Li, Jian Ma, Qinjun Zhang, Wanli Yin, Jie Li, Mingyue Wei, Liang Liu, Pengfei Yang and Yujuan Shen

Microorganisms 2025, 13(8), 1896; https://doi.org/10.3390/microorganisms13081896 - 14 Aug 2025

Abstract

Foodborne pathogens represent a class of pathogenic microorganisms capable of causing food poisoning or serving as foodborne vectors, constituting a major source of food safety concerns. With increasing demands for rapid diagnostics, conventional culture-based methods and PCR assays face limitations due to prolonged [...] Read more.

Foodborne pathogens represent a class of pathogenic microorganisms capable of causing food poisoning or serving as foodborne vectors, constituting a major source of food safety concerns. With increasing demands for rapid diagnostics, conventional culture-based methods and PCR assays face limitations due to prolonged turnaround times and specialized facility requirements. While CRISPR-based detection has emerged as a promising rapid diagnostic platform, its inherent inability to detect low-abundance targets necessitates coupling with isothermal amplification, thereby increasing operational complexity. In this study, we preliminarily developed a novel amplification-free Cascade-CRISPR detection system utilizing a hairpin DNA amplifier. This method achieves detection sensitivity as low as 10 fM (82 parasites/μL) for DNA targets within 30 min without requiring pre-amplification, with background signal suppression achieved through optimized NaCl concentration. Validation using artificially contaminated food samples demonstrated the platform’s robust performance for both Toxoplasma gondii (T. gondii) and Listeria monocytogenes (L. monocytogenes) detection, confirming broad applicability. In summary, this study preliminarily establishes an amplification-free Cascade-CRISPR detection platform that achieves high sensitivity and rapid turnaround, demonstrating strong potential for on-site screening of foodborne pathogens. Full article

(This article belongs to the Section Food Microbiology)

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13 pages, 4828 KiB

Open AccessArticle

Dynamics of Water Quality and Microbial Communities in the Middle Route of the South-to-North Water Diversion Project: Characterization and Driving Mechanisms

by Xinyong Liu, Zhibing Chang, Li Liu, Juechun Li, Jing Gao, Yingcai Wang, Yuming Su, Yuxin Hu and Yu Peng

Microorganisms 2025, 13(8), 1895; https://doi.org/10.3390/microorganisms13081895 - 14 Aug 2025

Abstract

Microbial communities, as critical functional components of riverine ecosystems, play a pivotal role in biogeochemical cycles and water quality regulation. The South-to-North Water Diversion Middle Route Project (SNWD-MRP) is a major cross-basin water transfer initiative, and bacteria are essential for the stability of [...] Read more.

Microbial communities, as critical functional components of riverine ecosystems, play a pivotal role in biogeochemical cycles and water quality regulation. The South-to-North Water Diversion Middle Route Project (SNWD-MRP) is a major cross-basin water transfer initiative, and bacteria are essential for the stability of water quality in the project. This study employed environmental DNA (eDNA) metabarcoding targeting the 16S rRNA gene to investigate spatiotemporal variations in water quality and bacterial communities along the SNWD-MRP during summer and winter. Integrated analyses, including redundancy analysis (RDA), Mantel tests, and ecological network modeling, were applied to unravel the driving mechanisms of microbial succession. The water quality along the SNWD-MRP is generally classified as Grade I, with significant seasonal variations in water quality parameters and microbial community composition. In the summer, higher temperatures lead to an increased abundance of cyanobacteria. In contrast, during the winter, lower water temperatures and higher dissolved oxygen levels result in the dominance of Pseudomonas and Bacillota species. RDA identified the permanganate index as the primary driver of microbial composition across seasons, with total phosphorus and total nitrogen having a greater influence in winter. Mantel tests highlighted significant correlations between Cyanobacteria and total phosphorus during winter. Ecological network analysis revealed that the complexity and connectivity of the winter network increased, likely due to suitable nutrient levels rendering the microbial network more complex and stable. These findings underscore the synergistic effects of temperature and nutrient availability on microbial succession, providing actionable insights for optimizing water quality management and ecological stability in large-scale water diversion systems. Full article

(This article belongs to the Section Environmental Microbiology)

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26 pages, 2080 KiB

Open AccessReview

Therapeutic Potential of Probiotics in Metabolic Dysfunction-Associated Steatohepatitis: A Comprehensive Review

by Xueying Wang, Zhiying Wei, Qing Xiang, Lijie Tang and Weichun Xie

Microorganisms 2025, 13(8), 1894; https://doi.org/10.3390/microorganisms13081894 - 14 Aug 2025

Abstract

Metabolic dysfunction-associated steatohepatitis (MASH) constitutes a significant and progressive liver disease, characterized by a complex pathogenesis that involves dysbiosis of the gut microbiota. While the multifaceted nature of MASH is widely recognized, its underlying mechanisms remain the subject of active investigation. Contemporary research [...] Read more.

Metabolic dysfunction-associated steatohepatitis (MASH) constitutes a significant and progressive liver disease, characterized by a complex pathogenesis that involves dysbiosis of the gut microbiota. While the multifaceted nature of MASH is widely recognized, its underlying mechanisms remain the subject of active investigation. Contemporary research highlights the critical role of the gut–liver axis, suggesting that disturbances in the gut microbiome may contribute to the progression of the disease. Probiotics have notably emerged as a promising therapeutic approach for MASH, with the potential to modulate the gut microbiome and mitigate symptoms. This review aims to examine the alterations in the gut microbiome associated with MASH pathogenesis, the interaction of probiotics with the gut–liver axis, and their significance in the development and management of MASH. By synthesizing current evidence on the mechanisms of action of probiotics, clinical trials, and comparative efficacy of different strains, as well as existing controversies, challenges, and future research directions, this review seeks to establish a scientific foundation for probiotic-based interventions as an innovative therapeutic strategy for MASH. Full article

(This article belongs to the Special Issue Probiotics, Gut Microbiota, and Health)

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15 pages, 1328 KiB

Open AccessArticle

Climate Change-Related Temperature Impact on Human Health Risks of Vibrio Species in Bathing and Surface Water

by Franciska M. Schets, Irene E. Pol-Hofstad, Harold H. J. L. van den Berg and Jack F. Schijven

Microorganisms 2025, 13(8), 1893; https://doi.org/10.3390/microorganisms13081893 - 14 Aug 2025

Abstract

Vibrio species are part of the indigenous microbial flora in marine, brackish and fresh water in moderate and tropical climates that thrive and multiply in water at elevated water temperatures. The number of human non-cholera Vibrio infections due to exposure to contaminated surface [...] Read more.

Vibrio species are part of the indigenous microbial flora in marine, brackish and fresh water in moderate and tropical climates that thrive and multiply in water at elevated water temperatures. The number of human non-cholera Vibrio infections due to exposure to contaminated surface water increases worldwide. To study possible climate change-related changes in Vibrio concentrations, prevalent species, and risks of illness, water samples from coastal and inland water bodies in the Netherlands were tested in 2019–2021. Data were combined with data from previous studies in 2009–2012 in order to develop a regression model to predict current and future risks of Vibrio illness. Year-to-year and site-specific variations in Vibrio concentrations and water temperature were observed, but there was no trend of increasing Vibrio concentrations or water temperature over time. In 2019–2021, Vibrio species distribution had not changed since 2009–2012; V. alginolyticus and V. parahaemolyticus were still the dominant species. Statistical analysis demonstrated a significant effect of water temperature on Vibrio concentrations. The model predicted a concentration increase of a factor of 1.5 for each degree Celsius temperature increase. Predicted risks of illness were higher at higher water temperatures, and higher for children than for adults. Based on the most recent climate change scenarios for the Netherlands, the risks of Vibrio illness will increase with factors ranging from 1.6 to 7.6 in 2050 and 2100. These outcomes warrant adequate information about Vibrio risks to water managers, public health workers and the general public. Full article

(This article belongs to the Special Issue Water Microorganisms Associated with Human Health, 2nd Edition)

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14 pages, 6190 KiB

Open AccessArticle

Effects of Transgenic Insect-Resistant Maize HGK60 on Rhizosphere Soil Bacterial Communities

by Yanjun Chen, Junyi Yang, Libo Pan, Meng Liu, Qiuming Wang, Nengwen Xiao and Xiao Guan

Microorganisms 2025, 13(8), 1892; https://doi.org/10.3390/microorganisms13081892 - 14 Aug 2025

Abstract

While genetically modified crops bring significant economic benefits, the environmental safety issues they may pose have also received increasing attention. To study the impact of planting genetically modified insect-resistant crops on soil ecosystems, this research employed methods such as 16S rDNA amplicon full-length [...] Read more.

While genetically modified crops bring significant economic benefits, the environmental safety issues they may pose have also received increasing attention. To study the impact of planting genetically modified insect-resistant crops on soil ecosystems, this research employed methods such as 16S rDNA amplicon full-length sequencing, using transgenic Cry1Ah insect-resistant corn HGK60 and its conventional counterpart Zheng 58 as subjects for a three-year continuous survey to analyze the effects of planting transgenic Cry1Ah insect-resistant corn HGK60 on the rhizosphere bacterial community. The following results were obtained. (1) A total of 216 corn rhizosphere soil samples were annotated to 51 phyla, 119 orders, 221 families, and 549 genera. (2) Overall, there was no significant difference in the composition of the rhizosphere bacterial community between HGK60 and Zheng 58 at the phylum, class, order, or family levels (p > 0.05), and the planting of HGK60 did not significantly affect the relative abundance of rhizosphere probiotics (p > 0.05). Some differences appeared only briefly and were not reproducible. (3) Alpha and beta diversity analyses showed that overall, the planting of HGK60 had no significant impact on the structure of the rhizosphere bacterial community (p > 0.05). (4) Significant changes in the rhizosphere bacterial community were observed across different growth stages of corn. It can be concluded that the planting of HGK60 has no significant impact on the rhizosphere bacteria. This study provides valuable data support for the environmental safety assessment of genetically modified crops. Full article

(This article belongs to the Section Plant Microbe Interactions)

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19 pages, 599 KiB

Open AccessReview

Bioeconomy-Based Approaches for the Microbial Valorization of Citrus Processing Waste

by Ioannis Stavrakakis, Paraschos Melidis, Nektarios Kavroulakis, Michael Goliomytis, Panagiotis Simitzis and Spyridon Ntougias

Microorganisms 2025, 13(8), 1891; https://doi.org/10.3390/microorganisms13081891 - 13 Aug 2025

Abstract

The citrus processing industry is an economically important agro-industrial sector worldwide; however, it produces significant amounts of waste annually. The biorefinery concept and the recovery of bio-based materials from agro-industrial residues, including citrus processing waste, are emphasized in the European Green Deal, reflecting [...] Read more.

The citrus processing industry is an economically important agro-industrial sector worldwide; however, it produces significant amounts of waste annually. The biorefinery concept and the recovery of bio-based materials from agro-industrial residues, including citrus processing waste, are emphasized in the European Green Deal, reflecting the EU’s commitment to fostering circularity. Biotreatment of citrus processing waste, including bioconversion into biomethane, biohydrogen, bioethanol and biodiesel, has been applied to valorize biomass for energy recovery. It can also be composted into a valuable soil conditioners and fertilizers, while raw and fermented citrus residues may exhibit phytoprotective activity. Citrus-derived residues can be converted into materials such as nanoparticles with adsorptive capacity for heavy metals and recalcitrant organic pollutants, and materials with antimicrobial properties against various microbial pathogens, or the potential to remove antibiotic-resistance genes (ARGs) from wastewater. Indeed, citrus residues are an ideal source of industrial biomolecules, like pectin, and the recovery of bioactive compounds with added value in food processing industry. Citrus processing waste can also serve as a source for isolating specialized microbial starter cultures or as a substrate for the growth of bioplastic-producing microorganisms. Solid-state fermentation of citrus residues can enhance the production of hydrolytic enzymes, with applications in food and environmental technology, as well as in animal feed. Certain fermented products also exhibit antioxidant properties. Citrus processing waste may be used as alternative feedstuff that potentially improves the oxidative stability and quality of animal products. Full article

(This article belongs to the Special Issue Earth Systems: Shaped by Microbial Life)

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26 pages, 5840 KiB

Open AccessArticle

Investigating the Alleviating Effects of Dihydromyricetin on Subclinical Mastitis in Dairy Cows: Insights from Gut Microbiota and Metabolomic Analysis

by Jie Yu, Yingnan Ao, Hongbo Chen, Tinxian Deng, Chenhui Liu, Dingfa Wang, Pingmin Wan, Min Xiang and Lei Cheng

Microorganisms 2025, 13(8), 1890; https://doi.org/10.3390/microorganisms13081890 - 13 Aug 2025

Abstract

Mastitis is a common disease for dairy cows that exerts tremendously detrimental impacts on the productivity of cows and economic viability of pasture. Dihydromyricetin (DMY) is a flavonoid monomeric compound that possesses anti-inflammatory and antioxidant activity. This study aimed at dissecting the effects [...] Read more.

Mastitis is a common disease for dairy cows that exerts tremendously detrimental impacts on the productivity of cows and economic viability of pasture. Dihydromyricetin (DMY) is a flavonoid monomeric compound that possesses anti-inflammatory and antioxidant activity. This study aimed at dissecting the effects of DMY on the lactation performance, blood parameters, gut microbiota, and metabolite profiles of dairy cows with subclinical mastitis (SM). The results showed that dietary supplementation with DMY resulted in a reduction in milk somatic cell count, an increase in serum T-AOC and CAT activity, as well as a decrease in serum MDA content. DMY significantly enhanced the prevalence of Coprococcus and Roseburia and reduced the proportion of Cyanobacteria, Proteobacteria, and Dehalobacterium. The amino acid degradation, antibiotic resistance, and O-antigen building blocks biosynthesis (E. coli) capacity of gut microbes were notably diminished by DMY supplementation in cows with SM. Moreover, fecal and plasma metabolomic analysis revealed that DMY intervention reduced the abundance of pro-inflammatory metabolites including arachidonic acid analogues, ω-6 PUFA, and structural components of bacteria. Nevertheless, the levels of anti-inflammatory and antioxidant metabolites involving secondary bile acids, antioxidant vitamins, specific amino acid analogues, etc. were elevated by DMY administration. Overall, DMY might ameliorate SM via enhancing antioxidant capacity and improving the structure of the hindgut microbial community and metabolite profiles in dairy cows. These findings underscore the potential of DMY as a valuable dietary supplement for the improvement of mammary inflammatory diseases in dairy cows. Full article

(This article belongs to the Section Gut Microbiota)

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13 pages, 1965 KiB

Open AccessProtocol

Automated Platform for the Analysis of Multi-Plate Growth and Reporter Data

by Avichay Nahami, Dor Kain, Yonatan Cohen, Yuval Kolodkin-Gal, Yohanan Assouline, Avihu H. Yona, Ilana Kolodkin-Gal and Yuval Dorfan

Microorganisms 2025, 13(8), 1889; https://doi.org/10.3390/microorganisms13081889 - 13 Aug 2025

Abstract

Researchers traditionally calculate growth rates using the natural logarithm of optical density (OD), with existing script packages facilitating this process. Automatic plate readers, capable of simultaneously measuring OD across 384 cultures, significantly enhance data collection efficiency. Furthermore, these readers also measure luminescence and [...] Read more.

Researchers traditionally calculate growth rates using the natural logarithm of optical density (OD), with existing script packages facilitating this process. Automatic plate readers, capable of simultaneously measuring OD across 384 cultures, significantly enhance data collection efficiency. Furthermore, these readers also measure luminescence and fluorescence, providing valuable insights into gene expression. However, current analysis software often struggle with data generated by robotic systems measuring multiple plates, limiting the integration of growth and reporter analyses. This method paper addresses three key challenges: (a) the incompatibility of robotic multi-plate systems with existing analysis software, (b) the integration of growth and reporter analyses, and (c) the development of user-friendly interfaces for non-programmers. To address these challenges, we offer optimized script packages and a relevant case study on matrix expression in response to antibiotics. Our platform facilitates the efficient and integrated analysis of multi-plate growth and reporter data. Full article

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

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23 pages, 3860 KiB

Open AccessArticle

Alteromonas nitratireducens sp. nov., a Novel Nitrate-Reducing Bacterium Isolated from Marine Sediments, and the Evolution of Nitrate-Reducing Genes in the Genus Alteromonas

by Ying-Li Chang, Jia-Xi Li, Xing-Chen Wang, Yang Li, Yun-Fei Cao, Xiang-Wen Duan, Cong Sun, Can Chen and Lin Xu

Microorganisms 2025, 13(8), 1888; https://doi.org/10.3390/microorganisms13081888 - 13 Aug 2025

Abstract

Nitrate reduction serves as a pivotal process in the global nitrogen cycle, playing a crucial role in natural ecosystems and industrial applications. Although the genus Alteromonas is not traditionally regarded as a nitrate reducer, several Alteromonas strains have recently been found to be [...] Read more.

Nitrate reduction serves as a pivotal process in the global nitrogen cycle, playing a crucial role in natural ecosystems and industrial applications. Although the genus Alteromonas is not traditionally regarded as a nitrate reducer, several Alteromonas strains have recently been found to be capable of doing so. However, the evolutionary trajectory of this capability remains undiscovered. In this study, 32 bacterial strains were isolated and cultivated from the tidal flat sediment in Hangzhou Bay and classified into the classes Cytophagia (n = 2), Alphaproteobacteria (n = 2), Gammaproteobacteria (n = 17), Flavobacteriia (n = 5), and Bacilli (n = 6). One nitrate-reducing strain, designated as CYL-A6^T, was identified by polyphasic taxonomy and proposed as a novel Alteromonas species. Genomic analysis reveals that seven Alteromonas genomes encode the dissimilatory nitrate reduction genes narGHI. Evolutionary analysis showed that these three nitrate-reducing genes were present in the early common ancestor of the genus Alteromonas, while gene loss events occurred in the subsequent evolution. With the loss of nitrate-reducing genes in the ancestry nodes, a wide variety of genes related to energy production and conversion, as well as carbohydrate, nucleotide, coenzyme, and inorganic ion metabolism, were gained in those nodes, which enabled Alteromonas members to utilize diverse substrates for increased energy production. This study enhances the understanding of microbial diversity in marine tidal flat sediments, proposes a novel nitrate-reducing species of the genus Alteromonas, and highlights the ecological diversification and ecological niche breadth in the evolution of the microbial metabolic network. Full article

(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition)

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18 pages, 3495 KiB

Open AccessArticle

Structural and Functional Differences in the Gut and Lung Microbiota of Pregnant Pomona Leaf-Nosed Bats

by Taif Shah, Qi Liu, Guiyuan Yin, Zahir Shah, Huan Li, Jingyi Wang, Binghui Wang and Xueshan Xia

Microorganisms 2025, 13(8), 1887; https://doi.org/10.3390/microorganisms13081887 - 13 Aug 2025

Viewed by 17

Abstract

Mammals harbor diverse microbial communities across different body sites, which are crucial to physiological functions and host homeostasis. This study aimed to understand the structure and function of gut and lung microbiota of pregnant Pomona leaf-nosed bats using V3-V4 16S rRNA gene sequencing. [...] Read more.

Mammals harbor diverse microbial communities across different body sites, which are crucial to physiological functions and host homeostasis. This study aimed to understand the structure and function of gut and lung microbiota of pregnant Pomona leaf-nosed bats using V3-V4 16S rRNA gene sequencing. Of the 350 bats captured using mist nets in Yunnan, nine pregnant Pomona leaf-nosed bats with similar body sizes were chosen. Gut and lung samples were aseptically collected from each bat following cervical dislocation and placed in sterile cryotubes before microbiota investigation. Microbial taxonomic annotation revealed that the phyla Firmicutes and Actinobacteriota were most abundant in the guts of pregnant bats, whereas Proteobacteria and Bacteroidota were abundant in the lungs. Family-level classification revealed that Bacillaceae, Enterobacteriaceae, and Streptococcaceae were more abundant in the guts, whereas Rhizobiaceae and Burkholderiaceae dominated the lungs. Several opportunistic and potentially pathogenic bacterial genera were present at the two body sites. Bacillus, Cronobacter, and Corynebacterium were abundant in the gut, whereas Bartonella, Burkholderia, and Mycoplasma dominated the lungs. Alpha diversity analysis (using Chao1 and Shannon indices) within sample groups examined read depth and species richness, whereas beta diversity using unweighted and weighted UniFrac distance metrics revealed distinct clustering patterns between the two groups. LEfSe analysis revealed significantly enriched bacterial taxa, indicating distinct microbial clusters within the two body sites. The two Random Forest classifiers (MDA and MDG) evaluated the importance of microbial features in the two groups. Comprehensive functional annotation provided insights into the microbiota roles in metabolic activities, human diseases, signal transduction, etc. This study contributes to our understanding of the microbiota structure and functional potential in pregnant wild bats, which may have implications for host physiology, immunity, and the emergence of diseases. Full article

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

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18 pages, 1577 KiB

Open AccessArticle

Bacterial Diversity Dynamics in Sandy Loam Soils in Tanzania Under Varying Fertilizer-Derived Uranium Concentrations

by Dennis A. Mwalongo, Jacob B. Lisuma, Nils H. Haneklaus, Ali Maged, Hendrik Brink, Fernando P. Carvalho, Stanisław Wacławek, Nelson Mpumi, Aloyce I. Amasi, Jerome M. Mwimanzi, Furaha M. Chuma, Thomas T. Kivevele and Kelvin M. Mtei

Microorganisms 2025, 13(8), 1886; https://doi.org/10.3390/microorganisms13081886 - 13 Aug 2025

Viewed by 90

Abstract

The presence of radiotoxic uranium (U) in mineral fertilizers is of global concern. A pilot study was conducted in Tabora (Tanzania) to determine the release of U from three brands of phosphate fertilizers and its impact on soil bacteria. The experiment used three [...] Read more.

The presence of radiotoxic uranium (U) in mineral fertilizers is of global concern. A pilot study was conducted in Tabora (Tanzania) to determine the release of U from three brands of phosphate fertilizers and its impact on soil bacteria. The experiment used three types of fertilizer: Minjingu Powder (MP), Nafaka Plus (NP), a mixed and granulated fertilizer made from Minjingu Phosphate Rock (MPR), and YaraMila Cereal (YC) fertilizer. There was also a control treatment that was not fertilized (NF). Alpha diversity and the R tool were used to analyze bacterial diversity in four samples within an average sequencing depth of 74,466 reads, using metrics like ASVs, Shannon index, and Chao1. The results showed that the number of amplicon sequence variants (ASVs) in the DNA from soil bacteria decreased, specifically to 400 ASVs, in the NP treatment, which was in line with the higher U concentration (3.93 mg kg⁻¹) in the soils. In contrast, the MP fertilizer treatment, associated with a lower U concentration (3.06 mg kg⁻¹) in soils, exhibited an increase in ASVs within the DNA of soil bacteria, reaching 795; the highest ASV value (822) was observed in the NF treatment. Higher amounts of U in the soil plots seemed to have resulted in more types of bacteria, with the Actinobacteriota phylum being the most common in all of the treatments. The NP (3.93 mg kg⁻³ U concentration) and MP (3.06 mg kg⁻³ U concentration) treatments were the only ones that showed Halobacteriota and Crenarchaeota phyla. Nonetheless, bacterial diversity may also account for the alterations in soil phosphorus and nitrogen following fertilizer application. The YaraMila Cereal treatment did not seem to be linked to any particular bacterial phylum. This means that in this study it did not have any measurable effect on the soil bacteria species compared to the MP and NP treatments. Full article

(This article belongs to the Special Issue Advances in Agro-Microbiology)

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17 pages, 2037 KiB

Open AccessArticle

Influence of Two Root Media and Three Vermicompost Amendments on Bacterial Communities in a Greenhouse Container Garden Model System

by Sihan Bu, Nikita H. Nel, Alyssa W. Beavers, Kameron Y. Sugino, Katherine Alaimo, John A. Biernbaum and Sarah S. Comstock

Microorganisms 2025, 13(8), 1885; https://doi.org/10.3390/microorganisms13081885 - 13 Aug 2025

Viewed by 61

Abstract

The aim of this study was to determine the impact of two root media and three vermicompost amendments on the root zone bacterial communities and harvest mass of lettuce grown in a greenhouse container garden model system. Lettuce seeds were planted in seven [...] Read more.

The aim of this study was to determine the impact of two root media and three vermicompost amendments on the root zone bacterial communities and harvest mass of lettuce grown in a greenhouse container garden model system. Lettuce seeds were planted in seven root media/amendment conditions. Lettuce was later harvested, and root media DNA was extracted for 16S rRNA sequencing to determine the composition of, as well as the alpha and beta diversity of, the bacterial communities. Fresh weight, dry weight, and percentage dry weight of lettuce were calculated under each treatment. Results indicate that the peat-lite growth media without any additions had the lowest rhizosphere bacterial alpha diversity compared to the other six growth media. Bacterial communities from containers with peat-lite media were significantly different than those from containers with compost-based media as measured by beta diversity. Moreover, the compost-based medium with vermicompost condition tended to result in a higher percentage dry weight lettuce than lettuce grown under the peat-lite condition. The peat-lite treatment condition had the numerically lowest dry weight (%) and bacterial diversity. Addition of vermicompost amendments had varying impacts on bacterial diversity, bacterial community composition, and harvest mass. Overall, this experiment establishes a protocol which can be applied for further understanding of the impact of root media type and vermicompost amendments on rhizosphere bacterial diversity and harvest mass. Full article

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

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20 pages, 8043 KiB

Open AccessArticle

Cervico-Vaginal Microbiome Dynamics Across HPV-Driven Lesion Stages in Moroccan Women

by Malika Allali, Khaoula Errafii, Rachid El Fermi, Karima Fichtali, Sanaa El Majjaoui, Adil El Ghanmi, Hicham El Fazazi, Najib Al Idrissi, Bouchra Ghazi, Youssef Bakri, Hassan Ghazal and Salsabil Hamdi

Microorganisms 2025, 13(8), 1884; https://doi.org/10.3390/microorganisms13081884 - 13 Aug 2025

Viewed by 151

Abstract

Cervical cancer (CC), often caused by persistent high-risk HPV infection, is a major health issue for Moroccan women. This study is the first in Morocco to examine how the cervico-vaginal microbiome differs across HPV-related clinical stages. Using 16S rRNA sequencing, the researchers analyzed [...] Read more.

Cervical cancer (CC), often caused by persistent high-risk HPV infection, is a major health issue for Moroccan women. This study is the first in Morocco to examine how the cervico-vaginal microbiome differs across HPV-related clinical stages. Using 16S rRNA sequencing, the researchers analyzed samples from 247 women—100 healthy controls, 43 hr-HPV⁺ pre-cancer cases, and 104 post-treatment CC cases. In healthy women, Lactobacillus dominated (70%), but it significantly declined in the pre-cancer group (45%, p < 0.01) and remained low post-treatment (50%). Meanwhile, Pseudomonadota and Actinobacteriota increased in pre-cancer samples (up to 25–30%, p < 0.01). Although the alpha diversity remained stable, the beta diversity differed significantly across stages (p = 0.001), but not by HPV status. Post-treatment samples showed a sharp decline in Bacillota (logFC −5, p < 10⁻¹⁵) and increases in Campylobacterota and Fusobacteriota (logFC +6 to +21, p < 10⁻¹⁶). Functionally, chemo-heterotrophy and fermentation declined, while nitrogen fixation and phototrophy rose in pre-cancer cases. Host factors like late menarche, high parity, STIs, and contraceptive use correlated with specific microbiota shifts. Full article

(This article belongs to the Section Medical Microbiology)

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24 pages, 1005 KiB

Open AccessReview

The Potential Role of Helicobacter pylori-Related Mast Cell Activation in the Progression from Gastroesophageal Reflux to Barrett’s Esophagus and Esophageal Adenocarcinoma

by Evangelos I. Kazakos, Efthymia Petinaki, Christos Liatsos, Ioannis S. Papanikolaou, Kyriaki Anastasiadou and Jannis Kountouras

Microorganisms 2025, 13(8), 1883; https://doi.org/10.3390/microorganisms13081883 - 12 Aug 2025

Viewed by 232

Abstract

Helicobacter pylori (Hp), a widespread gastric pathogen, has long been studied for its role in upper gastrointestinal disorders. While its involvement in gastritis, peptic ulcer disease, and gastric cancer is well established, its impact on esophageal diseases remains an area of [...] Read more.

Helicobacter pylori (Hp), a widespread gastric pathogen, has long been studied for its role in upper gastrointestinal disorders. While its involvement in gastritis, peptic ulcer disease, and gastric cancer is well established, its impact on esophageal diseases remains an area of ongoing investigation. Nevertheless, some data indicate that Hp may be involved in the pathogenesis of gastroesophageal reflux disease–Barrett’s esophagus–esophageal adenocarcinoma sequence. Similarly, the Hp-related mast cell activation—an essential immunological event—may also play a crucial role in the progression from gastroesophageal reflux disease to Barrett’s esophagus and esophageal adenocarcinoma. The underlying mechanisms include immune modulation, cytokine cascades, and microbial interactions that collectively shape the esophageal microenvironment. This review provides an in-depth analysis of these pathways, highlighting the potential role of Hp-induced, mast cell-driven inflammation in esophageal disease progression and discussing emerging therapeutic strategies. Full article

(This article belongs to the Special Issue Helicobacter pylori Infection: Detection and Novel Treatment)

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17 pages, 1623 KiB

Open AccessArticle

Sustainable Formulation of Chewing Candies Using Liver Hydrolysates with Antioxidant and Antimicrobial Properties

by Ignė Juknienė, Naga Pavan Kumar Reddy Jonnagiri, Irena Mačionienė, Gintarė Zakarienė, Jūratė Stankevičienė, Ingrida Sinkevičienė, Vitalijs Radenkovs, Vaida Andrulevičiūtė and Gintarė Zaborskienė

Microorganisms 2025, 13(8), 1882; https://doi.org/10.3390/microorganisms13081882 - 12 Aug 2025

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Abstract

This study aimed to develop innovative functional gummy candies enriched with protein hydrolysates derived from porcine liver, enhancing their antioxidant and antimicrobial properties. First, the overall consumer acceptability (OA) was assessed to determine the most suitable combination of gummy matrix components. Selected combinations [...] Read more.

This study aimed to develop innovative functional gummy candies enriched with protein hydrolysates derived from porcine liver, enhancing their antioxidant and antimicrobial properties. First, the overall consumer acceptability (OA) was assessed to determine the most suitable combination of gummy matrix components. Selected combinations were then analyzed for antioxidant activity (ABTS•+, DPPH•), antimicrobial effects, microbiological safety, and physicochemical characteristics. The incorporation of liver hydrolysates significantly increased antioxidant capacity. The highest activity was observed in sample GC5Pa24Ag, hydrolyzed with papain for 24 h and formulated with agar, showing ABTS•+ and DPPH• scavenging activities of (67.6 ± 0.98 µmol/g) and (49.14 ± 1.00%), respectively (p ≤ 0.05). Pepsin hydrolyzed samples (GC2Pe3Gl, GC2Pe6Gl, GC2Pe24Gl) exhibited significantly larger inhibition zones against Listeria monocytogenes ATCC 13932, Escherichia coli ATCC 25922, and Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14028 compared to the control (p < 0.05). Among all, GC5Pa24Ag demonstrated the broadest antimicrobial activity, with a 29.0 ± 0.2 mm inhibition zone against all tested pathogens. These findings suggest that porcine liver hydrolysates can be successfully incorporated into confectionery products to create functional gummies with potential health benefits, offering antioxidant protection and antimicrobial effects in a consumer-friendly form. Full article

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

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14 pages, 1153 KiB

Open AccessArticle

Dynamics and Assembly Mechanisms of Bacterial Communities During Larval Development of Macrobrachium rosenbergii: A High-Frequency Sampling Study Based on 16S rRNA Absolute Quantification Sequencing

by Zhibin Lu, Jingwen Hao, Jilun Meng, Cui Liu, Tiantian Ye, Junjun Yan, Guo Li, Yutong Zheng, Pao Xu and Zhimin Gu

Microorganisms 2025, 13(8), 1881; https://doi.org/10.3390/microorganisms13081881 - 12 Aug 2025

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Abstract

This study aimed to elucidate stage-specific dynamics, assembly mechanisms, and functional roles of bacterial communities during Macrobrachium rosenbergii larval development through high-resolution microbiota profiling. A high-frequency sampling strategy (126 samples across 11 zoeal stages and 1 post-larval stage within 21 days) and 16S [...] Read more.

This study aimed to elucidate stage-specific dynamics, assembly mechanisms, and functional roles of bacterial communities during Macrobrachium rosenbergii larval development through high-resolution microbiota profiling. A high-frequency sampling strategy (126 samples across 11 zoeal stages and 1 post-larval stage within 21 days) and 16S rRNA absolute quantification sequencing were employed. Bacterial succession, persistent taxa, and ecological processes were analyzed using abundance-occupancy modeling, neutral community modeling, and PICRUSt2-based functional prediction. Absolute bacterial abundance exhibited a triphasic abundance trajectory. Initial accumulation: Linear increase (Dph 1–5, peak Δlog10 = +1.7). Mid-stage expansion: Peak abundance (log10 = 7.5 copies/g, Dph 7–8). Late-stage remodeling: Secondary peak (log10 = 7.1 copies/g, Dph 19). Eighty dominant amplicon sequence variants (ASVs) (dominant taxa: Herminiimonas, Maritalea, and Enterobacteriaceae) comprised > 95% of the total abundance and coexisted via niche partitioning. Community construction was dominated by ecological drift/dispersal limitation (neutral model R² = 0.16, p < 0.01). Metabolic pathways (e.g., nutrient metabolism) shifted with dietary transition. “Phylogenetic replacement” underpinned microbiota resilience against environmental perturbations. Optimizing aquaculture environments offers a viable antibiotic-free strategy for microbial management, advancing our understanding of host microbe interactions and ecological niche differentiation in aquatic animals. Full article

(This article belongs to the Topic Diversity of Insect-Associated Microorganisms)

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19 pages, 2657 KiB

Open AccessArticle

Molecular Surveillance of ESBL and Carbapenemase Genes in Gram-Negative Bacterial Pathogens Isolated from Various Clinical Samples Collected from Northern Region of United Arab Emirates

by Premalatha Ragupathi, Vaneezeh Khamisani, Aisha Fadila Sadiq, Mariam Aliyu Mobiddo, Nasir Parwaiz, Sovan Bagchi and Nazeerullah Rahamathullah

Microorganisms 2025, 13(8), 1880; https://doi.org/10.3390/microorganisms13081880 - 12 Aug 2025

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Abstract

The aim of this study was to explore the prevalence of ESBL and carbapenemase genes in Gram-negative bacteria isolated from various clinical samples collected from northern regions of UAE. In total 3670 clinical samples were obtained from patients attending various hospitals and clinics [...] Read more.

The aim of this study was to explore the prevalence of ESBL and carbapenemase genes in Gram-negative bacteria isolated from various clinical samples collected from northern regions of UAE. In total 3670 clinical samples were obtained from patients attending various hospitals and clinics in the northern regions of the UAE. All the samples underwent routine bacterial culture examination, and their antibiotic sensitivity patterns mainly on beta-lactam and carbapenem resistance in Gram-negative bacteria. Molecular detection of ESBL and carbapenemase genes (bla_CTX-M, bla_TEM, bla_SHV, bla_NDM, bla_IMP, and bla_OXA-48) was performed on them. A total of 249 MDR Gram-negative bacteria (E. coli, K. pneumoniae, P. aeruginosa, P. mirabilis and A. baumannii) were isolated. The genes bla_CTX-M, bla_TEM, and bla_SHV were detected in all the MDR isolates. Among them, the bla_CTX-M was predominant especially in E. coli. The bla_NDM and bla_IMP were detected in a few K. pneumoniae and A. baumannii. The genes combination bla_CTX-M+TEM and bla_CTX-M+SHV, bla_CTX-M+SHV, bla_TEM+SHV, and bla_TEM+NDM were detected mostly in K. pneumoniae and E. coli, and few A. baumannii. The gene combination bla_{CTX-M+TEM+SHV} and bla_{CTX-M+TEM+SHV+IMP} were also detected in few E. coli, P. aeruginosa, and A. baumannii. The current findings highlight the importance of molecular detection of ESBL and carbapenemase genes to emphasize monitoring and controlling the development of MDR bacterial pathogens. Full article

(This article belongs to the Special Issue Evolution and Spread of Drug-Resistant Pathogens)

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Microorganisms, Volume 13, Issue 8 (August 2025) – 198 articles

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