Microorganisms

12 pages, 2399 KiB

Open AccessCase Report

Chronic Leptospirosis in a Breeding Bull: A Case Report

by Gabrita De Zan, Antonio Carminato, Monia Cocchi, Giacomo Catarin, Irene Pascuci, Laura Lucchese, Laura Bellinati, Letizia Ceglie, Elisa Mazzotta, Mario D’Incau, Martina Ustulin, Laura Grassi and Alda Natale

Microorganisms 2025, 13(7), 1695; https://doi.org/10.3390/microorganisms13071695 (registering DOI) - 18 Jul 2025

Abstract

Leptospirosis is a (re-)emerging and global zoonotic disease. Given the complex host-pathogen interaction and the numerous environmental risk factors related to the transmission, a One Health approach to both disease prevention and control is needed. Occurring at the human–cattle–environment interfaces, bovine leptospirosis represents [...] Read more.

Leptospirosis is a (re-)emerging and global zoonotic disease. Given the complex host-pathogen interaction and the numerous environmental risk factors related to the transmission, a One Health approach to both disease prevention and control is needed. Occurring at the human–cattle–environment interfaces, bovine leptospirosis represents a zoonotic risk for the professionals in the field, besides being a potential cause of significant economic losses due to the bovine reproductive disorders. Although climatic change is a potential factor in exacerbating the risk of leptospirosis in Europe, this disease remains largely neglected, with several knowledge gaps in research, investigations, and diagnosis of bovine genital leptospirosis syndrome across the continent. The present report describes the results of the diagnostic investigations on a case of chronic bovine leptospirosis in a breeding bull. Following the seroconversion to Leptospira Sejroe var Hardjo after the arrival of the animal in a quarantine facility, a monitoring plan including both serological/molecular analyses and a therapeutic protocol was undertaken. The bull exhibited a persistent seroconversion and a repeated positivity for Leptospira to real-time PCR in urine samples, indicative of a chronic shedder pattern. This report emphasizes the diagnostic and management challenges in the context of such a complex but frequently overlooked disease. Full article

(This article belongs to the Special Issue Advances in the Research on Leptospira and Leptospirosis)

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30 pages, 8114 KiB

Open AccessArticle

Effects of Italian Mediterranean Organic Diet on the Gut Microbiota: A Pilot Comparative Study with Conventional Products and Free Diet

by Laura Di Renzo, Giulia Frank, Barbara Pala, Rossella Cianci, Giada La Placa, Glauco Raffaelli, Roselisa Palma, Daniele Peluso, Antonino De Lorenzo and Paola Gualtieri

Microorganisms 2025, 13(7), 1694; https://doi.org/10.3390/microorganisms13071694 - 18 Jul 2025

Abstract

The human exposome, including dietary exposures such as pesticides, additives, and environmental contaminants, plays a critical role in shaping the gut microbiota (GM) and long-term health outcomes. While the Mediterranean Diet is known for its health-promoting effects, the role of food quality, specifically [...] Read more.

The human exposome, including dietary exposures such as pesticides, additives, and environmental contaminants, plays a critical role in shaping the gut microbiota (GM) and long-term health outcomes. While the Mediterranean Diet is known for its health-promoting effects, the role of food quality, specifically organic vs. conventional products, in modulating GM within this dietary pattern remains underexplored. The aim of this study was to evaluate (1) whether an Italian Mediterranean Organic Diet (IMOD) confers additional benefits compared to an Italian Mediterranean non-Organic Diet (IMnOD), and (2) the impact of IMOD and IMnOD versus a free diet (No Diet) on GM and anthropometric parameters. A randomized, controlled trial was conducted on 39 healthy subjects. Eligible subjects were divided into the following groups: (1) 4 weeks No Diet, (2) 4 weeks IMOD, and (3) 4 weeks IMnOD. Microbiota profiling (16S rRNA sequencing), body composition (BIA), and dietary adherence (MEDAS, FFQ) were evaluated. Distinct microbial shifts following both IMOD and IMnOD compared to No Diet were revealed. Several taxa previously associated with short-chain fatty acid (SCFA) biosynthesis (i.e., Anaerobutyricum hallii, Anaerostipes hadrus, and Dorea longicatena) were increased after both Mediterranean Diet interventions, while Parabacteroides distasonis showed a specific increase in the IMOD group. No significant changes in body weight or composition were observed. These findings suggest that adherence to a Mediterranean Diet, regardless of food source, reshapes the gut microbiota, while organic food intake may influence specific microbial trajectories. Our results support the relevance of food quality in dietary interventions. Full article

(This article belongs to the Special Issue Discovering the Human Holobiont: How the Microbiome Affects Human Health)

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12 pages, 2374 KiB

Open AccessArticle

The Complete Genomes of Microcystis ichthyoblabe Kützing and Microcystis protocystis (Crow) Komárek & Anagnostidis Reveal the Complexity and Plasticity of Microcystis Genomes

by Jina Kim, Hyaekang Kim, Jaeduk Goh, Seung Won Nam, Eu Jin Chung, Miyoung Shin, Donghyeok Seol, Ki Hwan Kim and Woori Kwak

Microorganisms 2025, 13(7), 1693; https://doi.org/10.3390/microorganisms13071693 - 18 Jul 2025

Abstract

Microcystis is a genus of cyanobacteria responsible for harmful algal blooms (HABs) in freshwater ecosystems, posing significant ecological and public health risks. Despite its importance, current genomic resources are heavily biased toward Microcystis aeruginosa, limiting comprehensive understanding of genomic diversity within the [...] Read more.

Microcystis is a genus of cyanobacteria responsible for harmful algal blooms (HABs) in freshwater ecosystems, posing significant ecological and public health risks. Despite its importance, current genomic resources are heavily biased toward Microcystis aeruginosa, limiting comprehensive understanding of genomic diversity within the genus. In this study, we present the first complete genome sequences of two morphospecies, M. ichthyoblabe FBCC-A1114 and M. protocystis FBCC-A270. Using long-read sequencing, both genomes were assembled into single circular chromosomes of 5.84 Mb and 5.76 Mb, respectively. Phylogenetic analyses placed both strains within genospecies G, alongside M. aeruginosa and M. viridis. Comparative analysis of biosynthetic gene clusters revealed that, while most genospecies G members harbor aeruginosin, cyanobactin, and microviridin gene clusters, the two newly sequenced strains lack cyanobactin and microcystin clusters but retain the microginin cluster. Synteny analysis demonstrated high structural conservation between the two genomes, while notable structural variations were observed when compared with M. aeruginosa NIES-298. These findings reveal both functional and structural plasticity within the genospecies, suggesting ecotype diversification driven by environmental adaptation. The newly assembled genomes provide critical resources to refine classification frameworks and advance our understanding of Microcystis genomic diversity. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 4791 KiB

Open AccessArticle

Diversity and Metabolic Potential of Gut Bacteria in Dorcus hopei (Coleoptera: Lucanidae): Influence of Fungus and Rotten Wood Diets

by Pan Wang, Xiaoyan Bin, Xingjia Xiang and Xia Wan

Microorganisms 2025, 13(7), 1692; https://doi.org/10.3390/microorganisms13071692 - 18 Jul 2025

Abstract

Stag beetles are saproxylic insects, essential for decomposing rotten wood and maintaining the carbon cycle. Their gut bacteria contribute significantly to nutrient digestion and energy acquisition, making them crucial for understanding host-microbe interactions. Despite the fungivorous behavior of stag beetle larvae, research on [...] Read more.

Stag beetles are saproxylic insects, essential for decomposing rotten wood and maintaining the carbon cycle. Their gut bacteria contribute significantly to nutrient digestion and energy acquisition, making them crucial for understanding host-microbe interactions. Despite the fungivorous behavior of stag beetle larvae, research on how diet influences gut bacterial diversity remains scarce. Therefore, this study was conducted to compare the diversity and metabolic functions of gut bacteria in Dorcus hopei larvae fed on fungus (Pleurotus geesteranus) and rotten wood diets using high-throughput sequencing technology. Significant differences (p < 0.05) were observed in gut bacterial community composition between two diets, highlighting diet as a key factor shaping bacterial diversity. Additionally, gut bacterial communities varied across larval developmental stages (p < 0.05), indicating the influence of host age. Dominant bacterial phyla included Firmicutes, Bacteroidetes, and Proteobacteria. Bacteroidetes were more abundant in rotten-wood-fed larvae (7.61%) than fungus-fed larvae (0.15%), while Proteobacteria were more abundant in fungus-fed larvae. Functional analysis revealed that rotten-wood-fed larvae were primarily related to carbohydrate and amino acid metabolism, whereas fungus-fed larvae exhibited enhanced membrane transport function. This study enhances the understanding of gut bacterial diversity and functions in stag beetles, providing a theoretical foundation for their conservation and sustainable utilization. Full article

(This article belongs to the Section Gut Microbiota)

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19 pages, 746 KiB

Open AccessReview

Endophytic Bioactive Compounds for Wound Healing: A Review of Biological Activities and Therapeutic Potential

by Octavio Calvo-Gomez, Farkhod Eshboev, Kamilla Mullaiarova and Dilfuza Egamberdieva

Microorganisms 2025, 13(7), 1691; https://doi.org/10.3390/microorganisms13071691 - 18 Jul 2025

Abstract

Endophytic microorganisms inhabiting plant tissues constitute a unique and largely untapped reservoir of bioactive metabolites, including phenolics, terpenoids, alkaloids, polysaccharides, and anthraquinones, among others. This review focuses on the potential of these compounds to modulate the complex processes of wound repair, such as [...] Read more.

Endophytic microorganisms inhabiting plant tissues constitute a unique and largely untapped reservoir of bioactive metabolites, including phenolics, terpenoids, alkaloids, polysaccharides, and anthraquinones, among others. This review focuses on the potential of these compounds to modulate the complex processes of wound repair, such as hemostasis, inflammation, proliferation, and remodeling. Uniquely, this review delineates the specific mechanisms supported not only by indirect evidence but by primary research directly linking endophytic metabolites to wound repair. We synthesized and evaluated evidence from 18 studies, of which over 75% directly assessed wound healing effects through in vitro and in vivo models. Metabolites from endophytic microorganisms promoted wound contraction, suppressed biofilm formation by key pathogens (e.g., MRSA, P. aeruginosa), and accelerated tissue re-epithelialization in animal models. Other compounds demonstrated >99% wound closure in rats, while several extracts showed anti-inflammatory and cytocompatible profiles. Nevertheless, the majority of studies applied unstandardized methods and used crude extracts, hindering precise structure–activity assessment. The originality of this review lies in drawing attention to direct evidence for wound healing from diverse endophytic sources and systematically identifying gaps between preclinical promise and clinical translation, positioning endophytes as a sustainable platform for next-generation wound therapeutics. Full article

(This article belongs to the Section Medical Microbiology)

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12 pages, 225 KiB

Open AccessArticle

Microbiological Sampling in Total Knee Arthroplasty After Post-Traumatic Osteoarthritis: Rate of Periprosthetic Joint Infection and the Debate Around Sampling Unremarkable Tissue

by Felix Erne, Leonard Grünwald, Tina Histing and Philipp Hemmann

Microorganisms 2025, 13(7), 1690; https://doi.org/10.3390/microorganisms13071690 - 18 Jul 2025

Abstract

Background: Proximal tibial fractures can lead to post-traumatic osteoarthritis (PTOA), and subsequent total knee arthroplasty (TKA) in such patients is associated with elevated complication rates. A two-stage approach, involving the elective removal of osteosynthetic hardware prior to TKA, is recommended. The utility of [...] Read more.

Background: Proximal tibial fractures can lead to post-traumatic osteoarthritis (PTOA), and subsequent total knee arthroplasty (TKA) in such patients is associated with elevated complication rates. A two-stage approach, involving the elective removal of osteosynthetic hardware prior to TKA, is recommended. The utility of microbiological sampling from macroscopically unremarkable tissue during TKA implantation remains controversial. Objective: To retrospectively evaluate the rate of periprosthetic joint infection (PJI) following TKA after PTOA and to assess the potential benefit of intraoperative microbiological sampling. The secondary objective was to evaluate the presence of prior colonization in osteosynthetic hardware among the affected cases. Patients and Methods: A retrospective screening of the hospital database was conducted between 2008 and 2022, including only AO/OTA type 41-B and 41-C fractures. Patients were assigned to a sampling group (with microbiological sampling during TKA) or a control group (without sampling). All patients received structured follow-up to assess postoperative complications. Results: A total of 40 patients met the screening criteria. In the sampling group (n = 29), 17.24% required surgical revision, and the rate of PJI was 3.45%. In the control group (n = 11), 18.14% underwent revision surgery, with a PJI rate of 9.09%. The average follow-up period was 4.35 years (range 2–11.6 years). Discussion: TKA in patients with PTOA is associated with a heightened risk of complications. A noteworthy possible correlation between systematic microbiological sampling and reduced PJI incidence was observed. While the small sample size limits definitive conclusions regarding causality, the findings support the potential value of consistent intraoperative sampling. Full article

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

15 pages, 4647 KiB

Open AccessArticle

Adaptability and Sensitivity of Trichoderma spp. Isolates to Environmental Factors and Fungicides

by Allinny Luzia Alves Cavalcante, Andréia Mitsa Paiva Negreiros, Naama Jéssica de Assis Melo, Fernanda Jéssica Queiroz Santos, Carla Sonale Azevêdo Soares Silva, Pedro Sidarque Lima Pinto, Sabir Khan, Inês Maria Mendes Sales and Rui Sales Júnior

Microorganisms 2025, 13(7), 1689; https://doi.org/10.3390/microorganisms13071689 - 18 Jul 2025

Abstract

Biological control employs beneficial microorganisms to suppress phytopathogens and mitigate the incidence of associated plant diseases. This study investigated the in vitro development and survival of Trichoderma spp. isolates derived from commercial formulations under different temperatures, pH levels, and sodium chloride (NaCl) concentrations [...] Read more.

Biological control employs beneficial microorganisms to suppress phytopathogens and mitigate the incidence of associated plant diseases. This study investigated the in vitro development and survival of Trichoderma spp. isolates derived from commercial formulations under different temperatures, pH levels, and sodium chloride (NaCl) concentrations and with synthetic fungicides with distinct modes of action. Three isolates were analyzed: URM-5911 and TRA-0048 (T. asperellum) and TRL-0102 (T. longibrachiatum). The results revealed substantial variability among the isolates, with the optimal mycelial growth temperatures ranging from 24.56 to 29.42 °C. All the isolates exhibited broad tolerance to the tested pH (5–9) and salinity levels (250–1000 mM), with TRL-0102 demonstrating the highest salt resistance. The fungicide treatments negatively affected mycelial growth across all the isolates, with Azoxystrobin + Difenoconazole and Boscalid causing growth reductions of up to 50%. Notably, Boscalid enhanced conidial production more compared to the control (126.0% for URM-5911, 13.7% for TRA-0048, and 148.5% for TRL-0102) and decreased the percentage of inactive conidia to less than 10% in all the isolates. These results provide strategic information for the application of Trichoderma spp. in agricultural systems, supporting the selection of more adapted and suitable isolates for integrated disease management programs. Full article

(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)

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10 pages, 558 KiB

Open AccessCommunication

Carbon Sink Potential of Sulfur-Oxidizing Bacteria in Groundwater at Petroleum-Contaminated Sites

by Pingping Cai, Zhuo Ning and Min Zhang

Microorganisms 2025, 13(7), 1688; https://doi.org/10.3390/microorganisms13071688 - 18 Jul 2025

Abstract

Groundwater at petroleum-contaminated sites typically exhibits elevated dissolved inorganic carbon (DIC) levels due to hydrocarbon biodegradation; however, our prior field investigations revealed an enigmatic DIC depletion anomaly that starkly contradicts this global pattern and points to an unrecognized carbon sink. In a breakthrough [...] Read more.

Groundwater at petroleum-contaminated sites typically exhibits elevated dissolved inorganic carbon (DIC) levels due to hydrocarbon biodegradation; however, our prior field investigations revealed an enigmatic DIC depletion anomaly that starkly contradicts this global pattern and points to an unrecognized carbon sink. In a breakthrough demonstration, this study provides the first experimental confirmation that sulfur-oxidizing bacteria (SOB) drive substantial carbon sequestration via a coupled sulfur oxidation autotrophic assimilation process. Through integrated hydrochemical monitoring and 16S rRNA sequencing in an enrichment culture system, we captured the complete DIC transformation trajectory: heterotrophic acetate degradation initially increased DIC to 370 mg/L, but subsequent autotrophic assimilation by SOB dramatically reduced DIC to 270 mg/L, yielding a net consumption of 85 mg/L. The distinctive pH dynamics (initial alkalization followed by acidification) further corroborated microbial regulation of carbon cycling. Critically, Pseudomonas stutzeri and P. alcaliphila were identified as the dominant carbon-fixing agents. These findings definitively establish that chemolithoautotrophic SOB convert DIC into organic carbon through a “sulfur oxidation-carbon fixation” coupling mechanism, overturning the conventional paradigm of petroleum-contaminated sites as perpetual carbon sources. The study fundamentally redefines natural attenuation frameworks by introducing microbial carbon sink potential as an essential assessment metric for environmental sustainability. Full article

(This article belongs to the Section Environmental Microbiology)

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24 pages, 3099 KiB

Open AccessArticle

Comprehensive Assessment of Health Risks Associated with Gram-Negative Bacterial Contamination on Healthcare Personnel Gowns in Clinical Settings

by Daniela Moreno-Torres, Carlos Alberto Jiménez-Zamarripa, Sandy Mariel Munguía-Mogo, Claudia Camelia Calzada-Mendoza, Clemente Cruz-Cruz, Emilio Mariano Durán-Manuel, Antonio Gutiérrez-Ramírez, Graciela Castro-Escarpulli, Madeleine Edith Vélez-Cruz, Oscar Sosa-Hernández, Araceli Rojas-Bernabé, Beatriz Leal-Escobar, Omar Agni García-Hernández, Enzo Vásquez-Jiménez, Gustavo Esteban Lugo-Zamudio, María Concepción Tamayo-Ordóñez, Yahaira de Jesús Tamayo-Ordóñez, Dulce Milagros Razo Blanco-Hernández, Benito Hernández-Castellanos, Julio César Castañeda-Ortega, Marianela Paredes-Mendoza, Miguel Ángel Loyola-Cruz and Juan Manuel Bello-López Show full author list Hide full author list

Microorganisms 2025, 13(7), 1687; https://doi.org/10.3390/microorganisms13071687 - 18 Jul 2025

Abstract

Microbiological contamination of healthcare workers’ gowns represents a critical risk for the transmission of healthcare-associated infections (HAIs). Despite their use as protective equipment, gowns can act as reservoirs of antibiotic-resistant bacteria, favouring the spread of pathogens between healthcare workers and patients. The presence [...] Read more.

Microbiological contamination of healthcare workers’ gowns represents a critical risk for the transmission of healthcare-associated infections (HAIs). Despite their use as protective equipment, gowns can act as reservoirs of antibiotic-resistant bacteria, favouring the spread of pathogens between healthcare workers and patients. The presence of these resistant bacteria on healthcare workers’ gowns highlights the urgent need to address this risk as part of infection control strategies. The aim of this work was to assess the microbiological risks associated with the contamination of healthcare staff gowns with Gram-negative bacteria, including the ESKAPE group, and their relationship with antimicrobial resistance. An observational, cross-sectional, prospective study was conducted in 321 hospital workers. The imprinting technique was used to quantify the bacterial load on the gowns, followed by bacterial identification by MALDI-TOF mass spectrometry. In addition, antimicrobial resistance profiles were analysed, and tests for carbapenemases and BLEE production were performed. The ERIC-PCR technique was also used for molecular analysis of Pantoea eucrina clones. Several Gram-negative bacteria were identified, including bacteria of the ESKAPE group. The rate of microbiological contamination of the gowns was 61.05% with no association with the sex of the healthcare personnel. It was observed that critical areas of the hospital, such as intensive care units and operating theatres, showed contamination by medically important bacteria. In addition, some strains of P. eucrina showed resistance to carbapenemics and cephalosporins. ERIC-PCR analysis of P. eucrina isolates showed genetic heterogeneity, indicating absence of clonal dissemination. Healthcare personnel gowns are a significant reservoir of pathogenic bacteria, especially in critical areas of Hospital Juárez de México. It is essential to implement infection control strategies that include improving the cleaning and laundering of gowns and ideally eliminating them from clothing to reduce the risk of transmission of nosocomial infections. Full article

(This article belongs to the Section Medical Microbiology)

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11 pages, 798 KiB

Open AccessArticle

Endophytic Bacteria with Potential Antimicrobial Activity Isolated from Theobroma cacao in Brazilian Amazon

by Lívia Freitas da Silva Pinto, Taynara Cristina Santos Tavares, Oscar Victor Cardenas-Alegria, Elaine Maria Silva Guedes Lobato, Cristina Paiva de Sousa and Adriana Ribeiro Carneiro Nunes

Microorganisms 2025, 13(7), 1686; https://doi.org/10.3390/microorganisms13071686 - 18 Jul 2025

Abstract

Endophytic bacteria inhabit plant tissues without damaging them and have specialized adaptation capabilities that allow them to establish themselves in this ecological niche. Endophytes produce numerous secondary metabolites with antimicrobial, anticancer, and pesticide properties, among others. In this study, endophytic bacteria were isolated [...] Read more.

Endophytic bacteria inhabit plant tissues without damaging them and have specialized adaptation capabilities that allow them to establish themselves in this ecological niche. Endophytes produce numerous secondary metabolites with antimicrobial, anticancer, and pesticide properties, among others. In this study, endophytic bacteria were isolated and characterized from cocoa plants in a Brazilian municipality, with the view to evaluate their potential antagonistic activity on clinical bacterial strains. The isolates were identified through phenotypic analysis and molecular characterization. After bacterial isolation, it was possible to verify the presence of 11 different endophytic strains, with a bacterial load of up to 6.3 × 10³ CFU/g in each plant. The morphological and biochemical profile of the isolates varied. At the taxonomic level, these bacteria showed 99% similarity with the genera Microbacterium, Curtobacterium, Pseudomonas, Bacillus, Ralstonia, and Methylobacterium. The strains of the phylum Actinobacteria, which are known for producing natural bioactive compounds with high biotechnological potential, were effective in inhibiting Staphylococcus aureus ATCC and multidrug-resistant clinical strains. This work aims to expand knowledge about endophytes, with the aim of applying them in other sectors, such as the production of compounds against resistant human pathogens. Full article

(This article belongs to the Special Issue Microbial Biotechnology: The Biodiversity, Properties and Benefits of Microorganisms in Medical, Clinical, Food and Environmental Fields)

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16 pages, 5000 KiB

Open AccessArticle

High-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap Mushroom Stropharia rugosoannulata

by Fei Liu, Bin Cao, Hongmei Dai, Guojie Li, Shoumian Li, Wei Gao and Ruilin Zhao

Microorganisms 2025, 13(7), 1685; https://doi.org/10.3390/microorganisms13071685 - 17 Jul 2025

Abstract

Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains [...] Read more.

Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains and identified over 2.7 million SNPs, unveiling substantial genetic diversity within the species. Using core gene-associated multiple nucleotide polymorphism (cgMNP) markers, we developed an efficient and transferable framework for strain discrimination. The analysis revealed pronounced genetic differentiation among cultivars, clustering them into two distinct phylogenetic groups. Nucleotide diversity (π) across 83 core genes varied significantly, highlighting both highly conserved loci under purifying selection and highly variable loci potentially associated with adaptive evolution. Phylogenetic analysis of the most variable gene, Phosphatidate cytidylyltransferase mitochondrial, identified 865 SNPs, enabling precise differentiation of all 85 cultivars. Our findings underscore the utility of cgMNP markers in addressing challenges posed by horizontal gene transfer and phylogenetic noise, demonstrating their robustness in cross-species applications. By providing insights into genetic diversity, evolutionary dynamics, and marker utility, this study establishes a foundation for advancing breeding programs, conservation strategies, and functional genomics in S. rugosoannulata. Furthermore, the adaptability of cgMNP markers offers a universal tool for high-resolution strain identification across diverse fungal taxa, contributing to broader fungal phylogenomics and applied mycology. Full article

(This article belongs to the Special Issue Fungal Biology and Interactions—3rd Edition)

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11 pages, 263 KiB

Open AccessArticle

Prevalence and Diagnostic Comparison of Helicobacter pylori and Non-Helicobacter pylori Helicobacter Infections in Patients Undergoing Upper Gastrointestinal Endoscopy with Gastric Biopsy in Algarve, Portugal

by Francisco Cortez Nunes, Teresa Letra Mateus, Catarina Aguieiras, Ricardo Louro, Bruno Peixe, Mauro Calhindro, Patrícia Queirós and Pedro Castelo-Branco

Microorganisms 2025, 13(7), 1684; https://doi.org/10.3390/microorganisms13071684 - 17 Jul 2025

Abstract

H. pylori infects over half of the global population and is associated with various gastric and extra-gastric diseases. Other species, such as zoonotic non-Helicobacter pylori Helicobacters (NHPHs), have shown similar associations with gastritis and MALT lymphoma and H. pylori-negative cases with [...] Read more.

H. pylori infects over half of the global population and is associated with various gastric and extra-gastric diseases. Other species, such as zoonotic non-Helicobacter pylori Helicobacters (NHPHs), have shown similar associations with gastritis and MALT lymphoma and H. pylori-negative cases with gastric disease have been identified, including gastric MALT lymphoma, chronic gastritis, and gastroduodenal ulcers. Accurate identification of these species is of great relevance but remains challenging using conventional diagnostic methods. This cross-sectional study aimed to determine the prevalence of H. pylori and NHPH infections, comparing standard histological protocols with molecular techniques. Between December 2024 and February 2025, 54 adult patients undergoing upper gastrointestinal endoscopy (UGE) with gastric biopsy in three hospitals in Algarve, Portugal were recruited. Endoscopic assessment was performed, and gastric biopsies were collected for histological and molecular analysis. DNA was extracted from antral biopsies and analyzed by conventional PCR to detect H. pylori and NHPH. H. pylori diagnostic techniques were compared, descriptive plus statistical analysis was performed, and p-values < 0.05 were considered to be statistically significant. Fifty-four patients were included in the study, with 51.9% of them presenting symptoms. Endoscopic gastritis was observed in 66.7% of patients, while histological gastritis was present in 88.9%, with statistically significant differences between the two diagnostic techniques (p = 0.004). Helicobacter spp. were identified in 44.4% (24/54) of the patients. H. pylori was detected in 42.6% of the patients by Modified Giemsa stain and in 33.3% by PCR. H. bizzozeronii was found in 35.9% of the patients, with 22.2% showing mixed infections. This study reveals a significant prevalence of Helicobacter spp. in patients from the Algarve region, with both H. pylori and zoonotic H. bizzozeronii detected. This is the first report of H. bizzozeronii DNA detection in gastric biopsies via PCR from patients undergoing UGE in Portugal, highlighting the need to consider NHPH in clinical diagnosis. It is important to include molecular methods in routine diagnostics and the need for broader studies to assess regional and national trends in Helicobacter infections besides H. pylori. Full article

(This article belongs to the Section Public Health Microbiology)

18 pages, 3226 KiB

Open AccessArticle

Isolation, Identification, and Antibiotic Resistance, CRISPR System Analysis of Escherichia coli from Forest Musk Deer in Western China

by Kaiwei Yang, Xi Wu, Hui Ding, Bingcun Ma, Zengting Li, Yin Wang, Zexiao Yang, Xueping Yao and Yan Luo

Microorganisms 2025, 13(7), 1683; https://doi.org/10.3390/microorganisms13071683 - 17 Jul 2025

Abstract

Escherichia coli (E. coli) is an opportunistic pathogen widely distributed in nature, and multi-drug resistance (MDR) E. coli has been widely recognized as a critical reservoir of resistance genes, posing severe health threats to humans and animals. A total of 288 [...] Read more.

Escherichia coli (E. coli) is an opportunistic pathogen widely distributed in nature, and multi-drug resistance (MDR) E. coli has been widely recognized as a critical reservoir of resistance genes, posing severe health threats to humans and animals. A total of 288 E. coli strains were isolated and purified from fresh fecal samples of forest musk deer collected from farms in Sichuan, Shaanxi, and Yunnan Provinces of China between 2013 and 2023. This study aimed to conduct antibiotic susceptibility testing and resistance gene detection on the isolated forest musk deer-derived E. coli, analyze the correlations between them, investigate the presence of CRISPR systems within the strains, and perform bioinformatics analysis on the CRISPR systems carried by the strains. Results showed that 138 out of 288 E. coli strains were MDR, with the highest resistance to tetracycline (48.3%), cefalexin (45.1%), and doxycycline (41.7%). Prevalent genes were tetA (41.0%), sul2 (30.2%), blaTEM (27.1%), with 29 gene–phenotype pairs correlated. CRISPR system-negative strains had higher resistance rates to 16 antibiotics and lower detection rates only for aac (6′)-Ib-cr, qnrA, and qnrB compared to CRISPR system-positive strains. Regional analysis showed that the problem of drug resistance in Sichuan and Shaanxi was more serious, and that the detection rate of antibiotic resistance genes was relatively high. This study guides E. coli infection control in forest musk deer and enriches resistance research data. Full article

(This article belongs to the Special Issue Bacterial Infections and Antimicrobial Resistance in Animal Populations)

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18 pages, 1646 KiB

Open AccessArticle

Initial Analysis of Plant Soil for Evidence of Pathogens Associated with a Disease of Seedling Ocotea monteverdensis

by William D. Eaton, Debra A. Hamilton, Alexander Lemenze and Patricia Soteropoulos

Microorganisms 2025, 13(7), 1682; https://doi.org/10.3390/microorganisms13071682 - 17 Jul 2025

Abstract

Seedlings of the ecologically important, critically endangered tree Ocotea monteverdensisis experience high mortality in the Monteverde, Costa Rica, cloud forests at the onset of the wet season, yet there are no studies suggesting the disease etiology. Here, healthy and diseased plant root and [...] Read more.

Seedlings of the ecologically important, critically endangered tree Ocotea monteverdensisis experience high mortality in the Monteverde, Costa Rica, cloud forests at the onset of the wet season, yet there are no studies suggesting the disease etiology. Here, healthy and diseased plant root and bulk soils were analyzed for various carbon and nitrogen (N) metrics and respiration levels, and DNA sequence-based bacterial and fungal community compositions. All nitrogen metric levels were greater in diseased vs. healthy plant root soils, which could enhance pathogen growth and pathogenic mechanisms. Greater DNA percentages from several potential pathogens were found in diseased vs. healthy plant root soils, suggesting this disease may be associated with a root pathogen. The DNA of the fungus Mycosphaerella was at greater levels in diseased vs. healthy plant root soils than other potential pathogens. Mycosphaerella causes similar diseases in other plants, including coffee, after onset of the wet season. The O. monteverdensis disease also occurs in seedlings planted within or near former coffee plantations at wet season onset. Distance-based linear model analyses indicated that NO₃⁻ levels best predicted the pattern of fungal pathogens in the soils, and Mycosphaerella and Tremella best predicted the patterns of the different N metrics in the soils, supporting their possible roles in this disease. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions Revisited: Emerging Concepts and Biotechnological Innovations)

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5 pages, 201 KiB

Open AccessEditorial

Peri-Implantitis Treatment on Microbial Decontamination

by Maria Pia Di Palo

Microorganisms 2025, 13(7), 1681; https://doi.org/10.3390/microorganisms13071681 - 17 Jul 2025

Abstract

Peri-implantitis, as defined by the 2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions, is a pathological condition affecting the tissues around dental implants, with inflammation in the outer peri-implant tissues and bone loss [...] Full article

(This article belongs to the Special Issue Exploring Microbial Dynamics in Oral Health and Disease: Periodontics, Implant Dentistry and Endodontics)

15 pages, 4191 KiB

Open AccessArticle

Whole-Genome Sequencing of a Potentially Novel Aeromonas Species Isolated from Diseased Siberian Sturgeon (Acipenser baerii) Using Oxford Nanopore Sequencing

by Akzhigit Mashzhan, Izat Smekenov, Serik Bakiyev, Kalamkas Utegenova, Diana Samatkyzy, Asset Daniyarov, Ulykbek Kairov, Dos Sarbassov and Amangeldy Bissenbaev

Microorganisms 2025, 13(7), 1680; https://doi.org/10.3390/microorganisms13071680 - 17 Jul 2025

Abstract

Aeromonas spp. are opportunistic pathogens that are widely distributed in water sources, with several species being associated with fish and human diseases. We have previously identified an Aeromonas AB005 isolate from diseased Acipencer baerii. This isolate was identified as A. hydrophila based [...] Read more.

Aeromonas spp. are opportunistic pathogens that are widely distributed in water sources, with several species being associated with fish and human diseases. We have previously identified an Aeromonas AB005 isolate from diseased Acipencer baerii. This isolate was identified as A. hydrophila based on the 16S rRNA and gyrB gene sequences. However, this novel strain does not produce indole and tested negative for ornithine decarboxylase and d-xylose fermentation—differences that set it apart from typical A. hydrophila strains. In the present study, this strain was subjected to whole-genome sequencing and compared with the genomes of the type strain (Aeromonas hydrophila ATCC 7966^T) and other Aeromonas spp. Comprehensive genome analysis suggests that AB005 represents a distinct species within the genus. The draft genome of the AB005 strain comprises 4,780,815 base pairs with a GC content of 61.2% and contains 6104 predicted protein-coding sequences along with numerous genes implicated in antibiotic resistance. The core/pan-genome analysis reveals extensive genetic diversity, indicative of a dynamic genomic structure. These findings collectively underscore the taxonomic distinction of the AB005 strain as a novel species and highlight its potential pathogenic implications in aquaculture and public health settings. Full article

(This article belongs to the Section Microbial Biotechnology)

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12 pages, 217 KiB

Open AccessArticle

Polymicrobial Prosthetic Joint Infections: Unraveling Risk Factors and Outcomes in a Single-Center Study

by Álvaro Auñón, Ignacio Ortiz, Salvador Peñarrubia, Carmen Álvaro, Estíbaliz Torrecilla-Sádaba, Joaquin Garcia-Cañete and Jaime Esteban

Microorganisms 2025, 13(7), 1679; https://doi.org/10.3390/microorganisms13071679 - 16 Jul 2025

Abstract

Periprosthetic joint infection (PJI) is a serious complication after joint arthroplasty, with polymicrobial PJIs representing a distinct subset associated with worse outcomes. This study aims to characterize the risk factors, microbiological profiles, and clinical outcomes of polymicrobial PJIs in a single tertiary care [...] Read more.

Periprosthetic joint infection (PJI) is a serious complication after joint arthroplasty, with polymicrobial PJIs representing a distinct subset associated with worse outcomes. This study aims to characterize the risk factors, microbiological profiles, and clinical outcomes of polymicrobial PJIs in a single tertiary care center. A retrospective analysis was conducted on 499 patients diagnosed with PJI between 2010 and 2023. Polymicrobial infection was defined by isolation of ≥2 distinct pathogens from intraoperative samples. Demographic, microbiological, and clinical data were analyzed. Treatment success was defined as infection eradication without recurrence or chronic suppressive therapy. Polymicrobial PJIs accounted for 18.2% of cases. Patients with polymicrobial infections had higher rates of obesity, insulin-dependent diabetes, and higher Charlson comorbidity scores. Coagulase-negative staphylococci and gram-negative bacilli were more frequently isolated in polymicrobial infections, while S. aureus predominated in monomicrobial cases. Treatment success rates were significantly lower in polymicrobial infections, both in acute (61.5% vs. 94.5%, p = 0.003) and chronic settings (51.3% vs. 75.3%, p = 0.02). Polymicrobial PJIs are associated with distinct microbiological patterns, increased comorbidity burden, and significantly worse clinical outcomes. Recognition of specific risk factors and pathogen profiles is essential to optimize management strategies for this complex condition. Full article

(This article belongs to the Special Issue Challenges of Biofilm-Associated Bone and Joint Infections)

11 pages, 809 KiB

Open AccessCommunication

Application of Real-Time PCR Syndromic Panel on Lower Respiratory Tract Samples: Potential Use for Antimicrobial De-Escalation

by Christian Leli, Paolo Bottino, Lidia Ferrara, Luigi Di Matteo, Franca Gotta, Daria Vay, Elisa Cornaglia, Mattia Zenato, Chiara Di Bella, Elisabetta Scomparin, Cesare Bolla, Valeria Bonato, Laura Savi, Annalisa Roveta, Antonio Maconi and Andrea Rocchetti

Microorganisms 2025, 13(7), 1678; https://doi.org/10.3390/microorganisms13071678 - 16 Jul 2025

Abstract

Molecular methods allow for a rapid identification of the main causative agents of pneumonia along with the most frequent resistance genes. Prolonged broad-spectrum antibiotic therapy without microbiological evidence of infection drives antimicrobial resistance. We evaluated if the result provided by the molecular method [...] Read more.

Molecular methods allow for a rapid identification of the main causative agents of pneumonia along with the most frequent resistance genes. Prolonged broad-spectrum antibiotic therapy without microbiological evidence of infection drives antimicrobial resistance. We evaluated if the result provided by the molecular method is helpful for antimicrobial de-escalation. All respiratory samples collected and directly processed via Real-Time PCR from patients with suspected pneumonia, of whom clinical data were available, were included in this study. In 82 patients out of a total of 174 (47.1%), antimicrobial therapy was modified after the molecular test, and in 28/82 (34.1%), antimicrobial de-escalation was carried out. Among the 92 patients in whom therapy was not modified, 33 (35.9%) were did not receive any antimicrobial therapy before the molecular test and no antibiotics were prescribed after the test. Therefore, in 61 (28 + 33) out of the 174 (35%) patients, unnecessary antimicrobials were discontinued or avoided. The syndromic panel used at our institution can be of help in better choosing when empiric antibiotic de-escalation therapy could be feasible. Full article

(This article belongs to the Special Issue Novel Approaches in the Diagnosis and Control of Emerging Pathogens)

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16 pages, 1620 KiB

Open AccessArticle

Oral Dysbiosis Is Associated with the Pathogenesis of Aortic Valve Diseases

by Erika Yaguchi, Yuske Komiyama, Shu Inami, Ikuko Shibasaki, Tomoaki Shintani, Ryo Shiraishi, Toshiki Hyodo, Hideki Shiba, Shinsuke Hamaguchi, Hirotsugu Fukuda, Shigeru Toyoda, Chonji Fukumoto, Sayaka Izumi, Takahiro Wakui and Hitoshi Kawamata

Microorganisms 2025, 13(7), 1677; https://doi.org/10.3390/microorganisms13071677 - 16 Jul 2025

Abstract

The involvement of oral bacteria in the pathogenesis of distant organs, such as the heart, lungs, brain, liver, and intestine, has been shown. We analyzed the distribution of bacterial species in the resected aortic valve by 16S rRNA metagenomic analysis and directly compared [...] Read more.

The involvement of oral bacteria in the pathogenesis of distant organs, such as the heart, lungs, brain, liver, and intestine, has been shown. We analyzed the distribution of bacterial species in the resected aortic valve by 16S rRNA metagenomic analysis and directly compared their gene sequences with those in the oral cavity. Thirty-two patients with aortic stenosis or aortic regurgitation who underwent aortic valve replacement were enrolled in this study. Antibody titer against periodontal pathogenic bacteria in the patient’s serum was analyzed. The genetic background and distribution of bacterial species on subgingival plaque, the dorsal surface of the tongue, and the resected aortic valve were analyzed. Patients with aortic valve disease were shown to have more severe periodontal disease by the detection of antibodies against Socransky’s red-complex bacteria of periodontitis. Bacterial DNA was detected in the aortic valves of 12 out of 32 patients. The genomic sequences of the V3-V4 region of the 16S rRNA in some bacteria isolated from the aortic valves of six patients who underwent metagenomic analysis were identical to those found in the oral cavity. The findings indicate that bacteria detected in the aortic valve may be introduced through oral dysbiosis, a condition characterized by an imbalance in the oral microbiota that increases the risk of periodontal disease and dental caries. Oral dysbiosis and the resulting potential bacteremia are associated with the pathogenesis of aortic valve diseases. Full article

(This article belongs to the Section Medical Microbiology)

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