Microbiology Research

18 pages, 1358 KB

Open AccessArticle

Microbiological Analysis of Traditional Sausage in Prishtina, Republic of Kosovo, During Production and Storage

by Flutura C. Ajazi, Rreze M. Gecaj, Matthias A. Ehrmann, Sarah Shaqiri, Idriz Vehapi, Veton Haziri, Namik Durmishi, Xhavit Bytyçi and Violeta Lajqi-Makolli

Microbiol. Res. 2025, 16(9), 200; https://doi.org/10.3390/microbiolres16090200 - 3 Sep 2025

Abstract

Traditional sausage in the Republic of Kosovo has been produced for centuries as a traditional method of preserving the nutritional value of meat. In sausage fermentation, natural microbiota such as lactic acid bacteria (LAB) and Micrococcaceae usually participate; these are not only critical [...] Read more.

Traditional sausage in the Republic of Kosovo has been produced for centuries as a traditional method of preserving the nutritional value of meat. In sausage fermentation, natural microbiota such as lactic acid bacteria (LAB) and Micrococcaceae usually participate; these are not only critical for ensuring product safety and flavor development but also represent significant biotechnological potential. The purpose of this study was to analyze traditional fermented sausage, in terms of production practices and hygiene, throughout the production and storage phases. Samples in three stages of production and maturation were analyzed for microbiota, pH, and water activity level. Our results show that the main changes in the bacterial populations from 0 to 7 days of storage included increases in the total numbers of viable mesophilic aerobic bacteria (LAB) and Micrococcaceae (MC). However, the Enterobacteriaceae and coliforms (EC) count showed a significant decrease (p < 0.05) in 1.60 ± 1.62 lg cfu/g by day 14. In conclusion, the number of EC in the traditional sausage was decreased during storage, while LAB and MC were stable, data that indicate the safety and quality of this product. No differences regarding the production practices and storage of traditional sausage were observed, based on the data from the butchers who participated in this study. Full article

(This article belongs to the Collection Microbiology and Technology of Fermented Foods)

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12 pages, 589 KB

Open AccessArticle

Application of MALDI-TOF Protein Profiles for Rapid Detection of Streptococcus agalactiae Highly Virulent Strains: ST1

by Kwanchai Onruang, Panan Rattawongjirakul and Pitak Santanirand

Microbiol. Res. 2025, 16(9), 199; https://doi.org/10.3390/microbiolres16090199 - 1 Sep 2025

Abstract

Expanding the capacity of Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) beyond species identification to strain typing becomes a new challenge in clinical microbiology. This study demonstrated a specific identification of Streptococcus agalactiae sequence type 1 (ST1) by a [...] Read more.

Expanding the capacity of Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) beyond species identification to strain typing becomes a new challenge in clinical microbiology. This study demonstrated a specific identification of Streptococcus agalactiae sequence type 1 (ST1) by a manual decision tree and automatically ranking from the newly added MTPPs library, which has not been previously reported. The mass spectra of 25 STs (277 isolates) were generated. The presence and absence of specific peaks were combined to create a decision tree for manual identification. Three peaks at 3127, 5914, and 6252 in combination with m/z 3368 and 6281 were used for primary identification of ST1. However, to differentiate ST1 and ST314, five additional peaks were required. For the automatic system, the MTPP of all isolates was divided into three training–testing ratios of 40:60, 50:50, and 60:40. All categories revealed excellent accuracy rates of above 90% for ST1 identification. The 60:40 group showed the highest overall performance, in which sensitivity was observed at 83.9 to 96.8%, and specificity reached up to 100.0% for both the top two and the top three matches. In conclusion, we propose that the MTPP from MALDI-TOF is a potential model for speedy bacterial typing, crucial in epidemiology, prevention, and patient management. Full article

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22 pages, 2681 KB

Open AccessArticle

Genome Sequence and Characterization of Bacillus cereus Endophytes Isolated from the Alectra sessiliflora and Their Biotechnological Potential

by Khuthadzo Tshishonga and Mahloro Hope Serepa-Dlamini

Microbiol. Res. 2025, 16(9), 198; https://doi.org/10.3390/microbiolres16090198 - 1 Sep 2025

Abstract

Bacillus cereus AS_3 and Bacillus cereus AS_5 are bacterial endophytes isolated from sterilized leaves of the medical plant Alectra sessiliflora, which were previously identified using 16S rRNA sequencing. Here, we present the whole-genome sequencing and annotation of strains AS_3 and AS_5, the [...] Read more.

Bacillus cereus AS_3 and Bacillus cereus AS_5 are bacterial endophytes isolated from sterilized leaves of the medical plant Alectra sessiliflora, which were previously identified using 16S rRNA sequencing. Here, we present the whole-genome sequencing and annotation of strains AS_3 and AS_5, the first genome report of Bacillus cereus strains from A. sessiliflora. The genome of strain AS_3 has 59 contigs, 5 503 542 bp draft circular chromosome, an N₅₀ of 211,274 bp, and an average G+C content of 35.2%; whereas strain AS_5 has 38 contigs, 5,510,121 bp draft circular chromosome, an N₅₀ of 536,033 bp, and an average G+C content of 35.2%. A total of 5679 protein-coding genes, 62 genes coding for RNAs, and 122 pseudogenes in the strain AS_3 genome were identified by the National Center for Biotechnology Information Prokaryotic Annotation pipeline, whereas a total of 5688 gene protein-coding genes were identified in AS_5, with 60 genes coding for RNAs and 120 pseudogenes. Phenotypic analysis and whole-genome sequencing analysis showed that AS_3 and AS_5 share similar characteristics, including Gram-positive, motile, rod-shaped, and endospore-forming have shown a high sequence similarity with Bacillus cereus, type strain ATCC 14579^T. Strains AS_3 and AS_5 had genomic digital DNA–DNA hybridization (dDDH) with the type strain Bacillus cereus ATCC 14579^T of 85.8% and 86%, respectively, and average nucleotide identities (ANIs) of 98% and 98.01%, respectively. Phylogenomic analysis confirmed that strains AS_3 and AS_5 share very similar genomic and phenotypic characteristics, and are closely related to the type strain Bacillus cereus type strain ATCC 14579^T, supporting their classification within the Bacillus cereus species. A total of 10 secondary metabolite gene clusters, including siderophore type petrobactin, terpene type molybdenum cofactor, non-ribosomal peptide synthetase (NRPS) type bacillibactin, and β-lactone type fengycin, were predicted using AntiSMASH software (version 5.0). Putative genes potentially involved in bioremediation and endophytic lifestyle were identified in the genome analysis. Genome sequencing of Bacillus cereus AS_3 and Bacillus cereus AS_5 has provided genomic information and demonstrated potential biotechnological applications. Full article

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15 pages, 4268 KB

Open AccessArticle

Metagenomic Insights into the Impact of Nutrition on Human Gut Microbiota and Associated Disease Risk

by Preethi Balasundaram, Kirti Dubli, Rinku Chaudhari, Sarvesh Vettrivelan, Amrita Kaur, Raman Kapoor, Raja Singh, Anmol Kapoor and Minal Borkar Tripathi

Microbiol. Res. 2025, 16(9), 197; https://doi.org/10.3390/microbiolres16090197 - 1 Sep 2025

Abstract

Metagenomic investigation of gut microbiome is a comprehensive and rapid technique for the analysis and diagnosis of numerous diseases. The gut microbiome is an intricate ecosystem, coordinated by the interaction of various microbes and the metabolites produced by them, which helps in developing [...] Read more.

Metagenomic investigation of gut microbiome is a comprehensive and rapid technique for the analysis and diagnosis of numerous diseases. The gut microbiome is an intricate ecosystem, coordinated by the interaction of various microbes and the metabolites produced by them, which helps in developing and sustaining immunity and homeostasis. A healthy gut microbiome is driven by different factors, such as nutrition, lifestyle, etc. The current study examines the association of diet to gut microbiome dysbiosis and its role in various disease conditions. Gut microbiome data was collected from 73 patients and tested at BioAro Inc. lab, using shotgun metagenomics through next generation sequencing. It was then analyzed and compared with data from 20 healthy subjects from HMP database. An in-house bioinformatics pipeline (PanOmiQ) and Pathogen Fast Identifier were utilized for secondary analysis, while tertiary analysis was accomplished using R software. Results showed a higher number of opportunistic pathogen microorganisms in the gut microbiome of subjects consuming a meat diet, as compared to those consuming a plant diet. These opportunistic pathogens included Ruminococcus torques (>3.34%), Ruminococcus gnavus (>2.22%), and Clostridium symbiosum (>1.87%). The study also found a higher relative abundance of these pathogens in cancer patients, as compared to healthy subjects. We also observed a highly significant (p < 0.0001) correlation of a meat diet with obesity in comparison to the subjects on a plant diet and the healthy subjects. Our findings suggest that patients following a plant diet have a lower relative abundance of pathogens that are associated with cancer and obesity. These findings provide critical insight into how we can use shotgun metagenomics to study the composition and diversity of the gut microbiome and the effects of a diet on the gut microbiome and its role in metabolic diseases. This is the first report investigating gut microbiota using shotgun metagenomics, correlating with different diseases and diet followed, which might impact the presence of opportunistic pathogens or keystones species. Additionally, it can provide valuable insights to physicians and dietetic practitioners for providing personalized treatment or customizing a diet plan. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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24 pages, 2945 KB

Open AccessArticle

Comprehensive Investigation of Qatar Soil Bacterial Diversity and Its Correlation with Soil Nutrients

by Muhammad Riaz Ejaz, Kareem Badr, Farzin Shabani, Zahoor Ul Hassan, Nabil Zouari, Roda Al-Thani and Samir Jaoua

Microbiol. Res. 2025, 16(9), 196; https://doi.org/10.3390/microbiolres16090196 - 1 Sep 2025

Abstract

Arid and semi-arid regions show distinctive bacterial groups important for the sustainability of ecosystems and soil health. This study aims to investigate how environmental factors across five Qatari soils influence the taxonomic composition of bacterial communities and their predicted functional roles using 16S [...] Read more.

Arid and semi-arid regions show distinctive bacterial groups important for the sustainability of ecosystems and soil health. This study aims to investigate how environmental factors across five Qatari soils influence the taxonomic composition of bacterial communities and their predicted functional roles using 16S rRNA amplicon sequencing and soil chemical analysis. Soil samples from five different locations in Qatar (three coastal and two inland) identified 26 bacterial phyla, which were dominated by Actinomycetota (35–43%), Pseudomonadota (12–16%), and Acidobacteriota (4–13%). Species-level analysis discovered taxa such as Rubrobacter tropicus, Longimicrobium terrae, Gaiella occulta, Kallotenue papyrolyticum, and Sphingomonas jaspsi, suggesting the presence of possible novel microbial families. The functional predictions showed development in pathways related to amino acid metabolism, carbohydrate metabolism, and stress tolerance. In addition, heavy-metal-related taxa, which are known to harbor genes for metal resistance mechanisms including efflux pumps, metal chelation, and oxidative stress tolerance. The presence of Streptomyces, Pseudomonas, and Bacillus highlights their roles in stress tolerance, biodegradation, and metabolite production. These findings improve the understanding of microbial roles in dry soils, especially in nutrient cycling and ecosystem resilience. They highlight the importance of local bacteria for sustaining desert soil functions. Further research is needed to validate these relationships, using metabolomic approaches while monitoring microbial-community-changing aspects under fluctuating environmental conditions. Full article

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15 pages, 1166 KB

Open AccessArticle

Anti-Listerial Effects of Satureja hortensis Essential Oils in Ready-to-Eat Poultry Meat Stored at Different Temperatures

by Yüsra Toplu and Harun Önlü

Microbiol. Res. 2025, 16(9), 195; https://doi.org/10.3390/microbiolres16090195 - 1 Sep 2025

Abstract

Listeria monocytogenes presents a considerable threat in cooked chicken products, especially those that are ready-to-eat, like deli meats. The aim of this study was to evaluate the antimicrobial efficacy of oregano essential oil (Satureja hortensis: SHEO) against L. monocytogenes contamination of [...] Read more.

Listeria monocytogenes presents a considerable threat in cooked chicken products, especially those that are ready-to-eat, like deli meats. The aim of this study was to evaluate the antimicrobial efficacy of oregano essential oil (Satureja hortensis: SHEO) against L. monocytogenes contamination of ready-to-eat cooked chicken meat during storage. The chemical content of SHEO was identified using GC-MS, with its antimicrobial properties confirmed through Kirby–Bauer disk diffusion tests. GC analyses of the SHEO used in the study showed that it contained 14.69% carvacrol and 10.61% thymol. L. monocytogenes strain NCTC 5348 was inoculated into chicken meat through a dipping technique at concentration levels of 2 × 10⁷ CFU/mL before and after application of SHEO solution (2 μL/mL). Inoculated and SHEO-treated meat samples were stored −20 °C, +4 °C, and +10 °C under both traditional and vacuum packaging conditions for 28 days. Results indicated that SHEO significantly suppressed the growth of L. monocytogenes (approximately 1 log CFU/g), especially during the first 5–7 days at +4 °C in both packaging types. Vacuum packaging prolonged the antimicrobial effect of SHEO compared to conventional packaging at +4 °C and +10 °C, approximately 1.1–1.3 log CFU/g for 14 days. The antimicrobial activity of SHEO was limited to a range of approximately 0.1–0.5 log CFU/g at −20 °C compared to the control. These results suggest that combining essential oils with modern packaging methods can provide an effective approach to controlling cold-tolerant pathogens such as L. monocytogenes, thereby improving the shelf life and safety of ready-to-eat meat products. Full article

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21 pages, 7386 KB

Open AccessArticle

The Oral Bacteriome

by Soukaina Ghaouas and Sanaa Chala

Microbiol. Res. 2025, 16(9), 194; https://doi.org/10.3390/microbiolres16090194 - 1 Sep 2025

Abstract

The oral microbiome has garnered significant interest in recent years. Its profound implications for oral and systemic diseases have led to a considerable amount of research and analysis aimed at providing deeper insights into its composition. This study aimed to characterize oral bacterial [...] Read more.

The oral microbiome has garnered significant interest in recent years. Its profound implications for oral and systemic diseases have led to a considerable amount of research and analysis aimed at providing deeper insights into its composition. This study aimed to characterize oral bacterial communities comprehensively based on microorganisms indexed in the Human Oral Microbiome Database, which was systematically analyzed, and its taxonomic classification was used to describe the diversity of indexed bacteria in the oral cavity. A total of 522 bacteria were considered for the analysis. Among these, 49.04% were named, whereas 29.12% represent uncultivated phylotypes. The taxonomic characterization revealed that more than 80% of total taxa are distributed across five phyla: Bacillota, Bacteroidota, Actinomycetota, Pseudomonadota, and Fusobacteriota. Of these, Bacillota and Bacteroidota are the dominant ones with, respectively, 166 (31.80%) and 96 (18.39%) bacterial taxa. With the recent advances in genomics and bioinformatics, the HOMD is constantly updated, further enhancing our understanding of the bacterial community of the oral microbiome. However, the considerable diversity of the oral microbiome may present analytical challenges and the possible misperception of the implications of closely related species/subspecies in oral and systemic health. Full article

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13 pages, 1864 KB

Open AccessArticle

Broad Spectrum Antagonistic Activity of Streptomyces sp. CACIS-1.16CA Against Phytopathogenic Fungi

by Karen A. Vargas-Gómez, Zahaed Evangelista-Martínez, Élida Gastélum-Martínez, Alberto Uc-Varguez, Evangelina E. Quiñones-Aguilar and Gabriel Rincón-Enríquez

Microbiol. Res. 2025, 16(9), 193; https://doi.org/10.3390/microbiolres16090193 - 1 Sep 2025

Abstract

The most common reason for a decrease in the quantity and quality of produced crops is microbial diseases. The aims of this study were to evaluate the antagonistic activity of Streptomyces sp. CACIS-1.16CA against plant pathogenic fungi and to assess its bioactive metabolites [...] Read more.

The most common reason for a decrease in the quantity and quality of produced crops is microbial diseases. The aims of this study were to evaluate the antagonistic activity of Streptomyces sp. CACIS-1.16CA against plant pathogenic fungi and to assess its bioactive metabolites to inhibit fungal conidial germination. Antagonistic evaluations of fungal phytopathogens were performed using dual and multiple confrontation assays. Additionally, the inhibitory effect of the bioactive extract (BE) containing secondary metabolites produced by the CACIS-1.16CA strain on the germination of conidia from some fungi was tested. The results indicate that Streptomyces sp. CACIS-16CA inhibited the growth of all tested pathogens (16 strains) with percentages of inhibition (PIs) ranging from 43.3% to 72%, while S. lydicus inhibited 13 of the 16 fungi, with PI values from 35.6% to 68.5%. Moreover, CACIS-1.16CA exerted superior PI values (significant differences at p < 0.05) than S. lydicus against the damping-off fungi consortia with Phytophthora capsici, Fusarium oxysporum, and Rhizoctonia solani. Otherwise, an inhibitory effect was observed on the germination of conidial cells due to the interaction with the BE in Alternaria sp., Botrytis cinerea, and Colletotrichum spp. In conclusion, Streptomyces sp. CACIS-1.16CA may serve as an effective and natural alternative for managing several fungal plant diseases. Full article

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20 pages, 6239 KB

Open AccessArticle

Mechanisms by Which Soil Microbial Communities Regulate Ecosystem Multifunctionality in Tea Gardens of Longnan City, China

by Lili Nian, Juan Li, Ying Tang, Fasih Ullah Haider, Zining Wang, Liuwen Dong, Jie Zhang, Qian Long, Wenli Wang and Xu Zhao

Microbiol. Res. 2025, 16(9), 192; https://doi.org/10.3390/microbiolres16090192 - 27 Aug 2025

Abstract

Soil microbial communities are fundamental to soil health and ecosystem functioning in agricultural landscapes. This study assessed how soil nutrient variation influences microbial community structure and ecosystem multifunctionality in tea gardens across three counties in Longnan, China. Key findings revealed that Kangxian tea [...] Read more.

Soil microbial communities are fundamental to soil health and ecosystem functioning in agricultural landscapes. This study assessed how soil nutrient variation influences microbial community structure and ecosystem multifunctionality in tea gardens across three counties in Longnan, China. Key findings revealed that Kangxian tea garden soils exhibited 18–25% higher bacterial and fungal richness and diversity indices than Wenxian, which had the lowest values among the three counties. Co-occurrence network analysis indicated a 32% higher proportion of positive (cooperative) interactions among microbial taxa in Wenxian soils. Null model analysis showed that bacterial community assembly was primarily driven by deterministic heterogeneous selection, whereas fungal assembly was governed by stochastic ecological drift. Functionally, Wenxian soils demonstrated 22% higher carbon sequestration, 19% higher nutrient storage, and 17% higher nutrient supply than the other counties (p < 0.05), while Kangxian soils had 21% greater nutrient cycling and overall ecosystem multifunctionality. Soil C/P and N/P ratios significantly influenced carbon sequestration, nutrient storage, and multifunctionality (explaining up to 48% of the variance), while soil pH was a key driver of carbon sequestration, nutrient supply, and cycling. Both bacterial and fungal community structures significantly impacted nutrient storage and multifunctionality. Regional differences in soil nutrients, shaped by tea garden management, directly influence microbial community traits and ecosystem multifunctionality. Targeted nutrient management and enhanced microbial diversity are key to improving soil multifunctionality and sustainability in tea agroecosystems. Full article

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17 pages, 1034 KB

Open AccessReview

Prevalence and Factors Associated with Tuberculosis Among Healthcare Workers: A Systematic Review with Meta-Analysis

by Alessandro Rolim Scholze, Paola Obreli Bersi, Mariane Cândido da Silva, Júlia Trevisan Martins, Emiliana Cristina Melo, Maria José Quina Galdino, Flávia Meneguetti Pieri, Felipe Mendes Delpino, Yan Mathias Alves, Thais Zamboni Berra, Oclaris Lopes Munhoz, Josilene Dália Alves, Mellina Yamamura and Ricardo Alexandre Arcêncio

Microbiol. Res. 2025, 16(8), 191; https://doi.org/10.3390/microbiolres16080191 - 16 Aug 2025

Abstract

Background: Healthcare workers are exposed to an unhealthy environment that increases the risk of developing tuberculosis. Objective: To analyze the prevalence and factors associated with tuberculosis among healthcare workers. Methods: A systematic review with meta-analysis was conducted using six databases. [...] Read more.

Background: Healthcare workers are exposed to an unhealthy environment that increases the risk of developing tuberculosis. Objective: To analyze the prevalence and factors associated with tuberculosis among healthcare workers. Methods: A systematic review with meta-analysis was conducted using six databases. Methodological quality was assessed according to JBI recommendations. A random-effects meta-analysis was performed. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines were followed for reporting. Results: Thirty-two articles were included in the evidence synthesis. The prevalence of tuberculosis among healthcare workers was found to be 15.92% [95% CI 8.49–27.88|I² = 99% | p = 0]. Female sex was associated with 1.37 times higher odds of infection [95% CI 0.68–2.38, I² = 80%, p = 0.01]. Advanced age increased the odds by 1.47 times [95% CI 1.33–4.62, I² = 76%, p = 0.01]. Conclusions: Early diagnosis of tuberculosis in the workplace and the implementation of continuing education programs with preventive strategies are essential to control contamination and the spread of the disease: CRD42022320153. Full article

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26 pages, 1099 KB

Open AccessArticle

Effects of Obesity and Feeding Avocado Extract on Gut Microbiota and Fecal Metabolomic Profile in Overweight/Obese Cats

by Roman Husnik, Jon Fletcher, Rachel Pilla, Donald Ingram, Frederic Gaschen, George Roth, Chih-Chun Chen and Jan Suchodolski

Microbiol. Res. 2025, 16(8), 190; https://doi.org/10.3390/microbiolres16080190 - 14 Aug 2025

Abstract

Background/Objectives: Obesity is a growing problem in the feline population worldwide. An extract of unripe avocado (AvX) has been shown to attenuate gains in body weight and body fat in mice fed a high-fat diet. The aim of this study was to evaluate [...] Read more.

Background/Objectives: Obesity is a growing problem in the feline population worldwide. An extract of unripe avocado (AvX) has been shown to attenuate gains in body weight and body fat in mice fed a high-fat diet. The aim of this study was to evaluate the effects of overweight/obesity and AvX on gut microbiota (GM) and fecal metabolomics in cats with natural overweight/obesity. Methods: Ten naturally overweight/obese and ten lean purpose-bred domestic shorthair cats were included in this study. In a prospective, randomized, double-blind study, one group of overweight/obese cats received AvX, while the second group received maltodextrin for 16 weeks. Fecal samples were collected after spontaneous defecation at specific time points and submitted for analysis. Fecal samples of overweight/obese cats collected before administration of AvX/maltodextrin were also compared to fecal samples of lean cats. Results: There was a significant difference in the clustering of GM over time in the AvX group and between lean and overweight/obese cats. The abundance of Firmicutes in the group of cats receiving AvX decreased compared to baseline. AvX induced a trend toward an increased abundance of Dialister sp. and a trend of decreased abundances of SMB53, Roseburia sp., Blautia producta, Acidaminococcus sp., Akkermansia sp., Adlercreutzia sp., and Collinsella aerofaciens. The metabolites that significantly differed after AvX administration included tryptophan, indole-3-acetate, nicotinamine, and glycyl-proline. At the species level, abundances of Prevotella sp., Turicibacter sp., Clostridium sp., Veillonella sp., Dialister sp., Catenibacterium sp., Eubacterium biforme, Desulfovibrio sp., and Campylobacter sp. were significantly higher in lean cats. Abundances of Coriobacterium sp. and Ruminococcus gnavus were significantly higher in overweight/obese cats. Additionally, LEfSe analysis identified Dialister as the genus associated with AvX administration and Dialister, Prevotella, Ruminococcus, Campylobacter, Catenibacterium, Clostridium, Helicobacter, Eubacterium, Pseudoramibacter, Veillonella, S247, Turicibacter, and Phascolarctobacterium as bacteria associated with the lean state. Genus Coriobacterium and Enterococcus were associated with overweight/obesity. A correlation between the concentration of metabolites significantly different between the AvX/placebo groups and the abundances of detected bacterial taxa at the genus level was assessed and described. Conclusions: There are significant differences in the GM between lean and overweight/obese cats. AvX consumption appears to affect the composition of GM and fecal metabolite concentrations in naturally overweight/obese cats. Full article

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23 pages, 5810 KB

Open AccessArticle

Oral Intake of Klebsiella oxytoca Disrupts Murine Intestinal Bacteriota and Anti-K. oxytoca Compound Baicalin by In Silico and In Vitro Analysis

by Yuming Ma, Xinchi Qin, Yongjie Wang, Lu Xie and Lanming Chen

Microbiol. Res. 2025, 16(8), 189; https://doi.org/10.3390/microbiolres16080189 - 14 Aug 2025

Abstract

Klebsiella oxytoca originating from shellfish Scapharca subcrenata contains a number of virulence-related genes. In this study, we investigated its pathogenicity using a murine intestinal infection model and predicted its antibacterial compounds and targets via molecular docking analysis. The results revealed that the intake [...] Read more.

Klebsiella oxytoca originating from shellfish Scapharca subcrenata contains a number of virulence-related genes. In this study, we investigated its pathogenicity using a murine intestinal infection model and predicted its antibacterial compounds and targets via molecular docking analysis. The results revealed that the intake of K. oxytoca 8-2-11 strain (10⁹ CFU/day) via oral gavage for 7 days reduced the average body weight of the mice. The bacterium was present in fecal samples but absent from blood, lung, and liver samples from the mice. The intake of K. oxytoca 8-2-11 significantly altered colon bacteriota, with reduced abundance of Firmicutes, Lachnospiraceae, Lactobacillaceae, Lactobacillus, and Lactobacillus murinus, and increased in Bacteroidota, Muribaculaceae, and Alistipes (p < 0.05). Forty-four bioactive compounds in Scutellaria baicalensis and Forsythia suspensa were screened for docking with 117 potential virulence factors (VFs) in K. oxytoca 8-2-11. The compound baicalin displayed higher binding affinity toward these VFs, with the lowest mean binding energy (−8.4 kcal/mol). Baicalin was able to bind to key VFs in biofilm formation and adherence/motility (e.g., Mrks and EcpA) via forming stable hydrogen bonds, π-stacking, and π-cation interaction. In vitro, baicalin inhibited the bacterial growth and biofilm formation. This study establishes the first murine infection model using aquatic animal-derived K. oxytoca, and it provides candidate antibacterial compounds and targets for control of K. oxytoca infections. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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16 pages, 2407 KB

Open AccessArticle

Mechanisms of Cultivation Chronosequence on Distribution Characteristics of Arbuscular Mycorrhizal Fungi in Tea Plantations, South Henan, China

by Xiangchao Cui, Dongmeng Xu, Shuping Huang, Wei Wei, Ge Ma, Mengdi Li and Junhui Yan

Microbiol. Res. 2025, 16(8), 188; https://doi.org/10.3390/microbiolres16080188 - 12 Aug 2025

Abstract

The vital role of arbuscular mycorrhizal (AM) fungi in tea plant growth is well established; however, the mechanisms underlying how increasing cultivation chronosequence (CC) influences AM fungal distribution remain unclear. An investigation was conducted to investigate the temporal dynamics of AM fungal indices [...] Read more.

The vital role of arbuscular mycorrhizal (AM) fungi in tea plant growth is well established; however, the mechanisms underlying how increasing cultivation chronosequence (CC) influences AM fungal distribution remain unclear. An investigation was conducted to investigate the temporal dynamics of AM fungal indices and soil properties across a 100-year tea CC (10-, 30-, 60-, and 100-year CC) in Xinyang Maojian tea (Camellia sinensis L.) plantations (Xinyang, Henan Province, China). Principal coordinate analysis was conducted to reveal the significant reorganization of AM fungal indices during early-to-mid stages (PCoA1: 89.2%, p < 0.05), with triphasic development. Mycorrhizal colonization (MC), hypha biomass (hypha), and spore density (SD) surged by 100% during 10–30 years; SD peaked at 60 years (164 spores g⁻¹) before declining, while glomalin-related soil protein (GRSP) accumulated significantly only at 100 years (p < 0.05). Concurrently, soil acidification (pH decreased from 6.37 to 4.84) and phosphorus depletion (AP from 119.6 mg kg⁻¹ to 32 mg kg⁻¹) intensified by 60 years, contrasting with the significant accumulations of soil organic organisms (SOM) (from 10.6 g kg⁻¹ to 36.4 g kg⁻¹), electrical conductivity (EC) (from 0.019 to 0.050 mS·cm⁻¹), and microaggregate accumulation (MAR) (from 25.8% to 40.3%) during the period. The linear regression model was performed to validate the significant effects (p < 0.05) of CC on the AM indices (MC, SD, hypha, and GRSP) and soil physiochemical characteristics (EC, moisture, and SOM). Variance partitioning attributed 97.4% of the total variation, while interactions among cultivation ages, nutrient characteristics (SOM and AP), and non-nutrient characteristics (pH, EC, moisture, and aggregates) accounted for 23.0%. To identify the driving factors of AM fungi indices, Pearson correlation and redundancy analysis (RDA) were performed, and EC (26.5%) and pH (20.9%) were identified as the paramount regulators of hyphal integrity and colonization efficiency. It was found that 60 years worked as a critical transition point for targeted interventions (e.g., organic amendments and pH buffering) to mitigate rhizosphere dysfunction and optimize mycorrhizal services in perennial monocultures. Full article

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19 pages, 6210 KB

Open AccessArticle

Novel Reoviruses of Waterfowl Origin in Northern Vietnam: A Laboratory Investigation

by Thi-Ngoc Vu, Van-Truong Le, Thi-Bich-Phuong Cao, Van-Giap Nguyen and Thi-My-Le Huynh

Microbiol. Res. 2025, 16(8), 187; https://doi.org/10.3390/microbiolres16080187 - 12 Aug 2025

Abstract

Novel waterfowl reoviruses (nWRVs) have been reported in several countries, but their circulation and genetic characteristics in Vietnam remain poorly understood. In this study, we investigated nWRVs in northern Vietnam through molecular detection, virus isolation, experimental infection in ducklings, and molecular analysis of [...] Read more.

Novel waterfowl reoviruses (nWRVs) have been reported in several countries, but their circulation and genetic characteristics in Vietnam remain poorly understood. In this study, we investigated nWRVs in northern Vietnam through molecular detection, virus isolation, experimental infection in ducklings, and molecular analysis of the sigma C-encoding (sC) gene. We also applied immunoinformatic tools to explore the antigenic and structural features of the sC protein. nWRVs were detected in 15.6% of tested samples across ten provinces. Three isolates were successfully recovered, all showing a characteristic cytopathic effect—syncytium formation—in Vero cells. When tested in ducklings (n = 72), the isolates caused disease of varying severity, but all induced characteristic gross and microscopic lesions, particularly ecchymotic hemorrhages and large necrotic foci in the liver and spleen. Phylogenetic analysis based on sC sequences placed the Vietnamese isolates (n = 14) within the nWRV clade, with evidence of two genetically distinct groups. Our immunoinformatic analysis identified four predicted B-cell epitopes located in the head and body domains of the sC protein, with little variation. Full article

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15 pages, 2999 KB

Open AccessArticle

Evaluation of Antibiotic Resistance in Escherichia coli Isolated from a Watershed Section of Ameca River in Mexico

by Mariana Díaz-Zaragoza, Sergio Yair Rodriguez-Preciado, Lizeth Hernández-Ventura, Alejandro Ortiz-Covarrubias, Gustavo Castellanos-García, Sonia Sifuentes-Franco, Ana Laura Pereira-Suárez, José Francisco Muñoz-Valle, Margarita Montoya-Buelna and Jose Macias-Barragan

Microbiol. Res. 2025, 16(8), 186; https://doi.org/10.3390/microbiolres16080186 - 12 Aug 2025

Abstract

Antibiotic resistance (AR) in environmental Escherichia coli represents a growing public health challenge. This study evaluated the prevalence of AR among E. coli isolates recovered from surface water bodies within the Ameca River basin in Jalisco, Mexico, and examined associations with anthropogenic influence [...] Read more.

Antibiotic resistance (AR) in environmental Escherichia coli represents a growing public health challenge. This study evaluated the prevalence of AR among E. coli isolates recovered from surface water bodies within the Ameca River basin in Jalisco, Mexico, and examined associations with anthropogenic influence and seasonal variation. Over a 1-year period, water samples were collected monthly from 16 sites, including tributaries, wetlands, and main river channels with differing degrees of urban impact. E. coli isolates were confirmed by malB gene PCR and tested for susceptibility to six antibiotics using the Kirby–Bauer disk diffusion method. High resistance frequencies were observed for ampicillin (93.9%), tetracycline (92.4%), and streptomycin (89.6%), while gentamicin exhibited the lowest resistance rate (48.1%). Resistance prevalence was significantly higher at sites adjacent to urban settlements and during the rainy season (p < 0.05). These findings underscore the influence of land use and seasonal dynamics on AR dissemination in aquatic environments and highlight the need for improved wastewater management strategies to mitigate the spread of resistant bacteria. Full article

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13 pages, 1098 KB

Open AccessArticle

Risk Factors and Seroprevalence of Infection by Corynebacterium pseudotuberculosis in Goats from Espírito Santo State, Southeastern Brazil

by Letícia Pereira Pedrini Vicentini, Thiago Doria Barral, Marcus Alexandre Vaillant Beltrame, Luiz Filippe Simão Soares, Ricardo Wagner Portela and Blima Fux

Microbiol. Res. 2025, 16(8), 185; https://doi.org/10.3390/microbiolres16080185 - 8 Aug 2025

Abstract

Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis, a significant infectious disease that affects small ruminants and poses economic challenges to livestock production. This study aimed to assess the seroprevalence of C. pseudotuberculosis in goats from Espírito Santo state, Brazil, and identify [...] Read more.

Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis, a significant infectious disease that affects small ruminants and poses economic challenges to livestock production. This study aimed to assess the seroprevalence of C. pseudotuberculosis in goats from Espírito Santo state, Brazil, and identify risk factors associated with infection by the bacterium. Serum samples from 145 goats were analyzed using an indirect enzyme-linked immunosorbent assay (ELISA). The overall seroprevalence was found to be 34.5%. The risk factors significantly associated with infection included the presence of abscesses and the absence of veterinary assistance on farms. The findings emphasize the need for improved management practices and veterinary oversight to mitigate caseous lymphadenitis transmission. This research provides critical insights into the epidemiology of caseous lymphadenitis in goats from Espírito Santo, informing effective disease control strategies. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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18 pages, 7277 KB

Open AccessArticle

Comprehensive Analysis of the Molecular Epidemiological Characteristics of Duck-Derived Salmonella in Certain Regions of China

by Jiawen Chen, Xiangdi Li, Yanling Liu, Wenjia Rong, Laiyu Fu, Shuhua Wang, Yan Li, Xiaoxiao Duan, Yongda Zhao and Lili Guo

Microbiol. Res. 2025, 16(8), 184; https://doi.org/10.3390/microbiolres16080184 - 7 Aug 2025

Abstract

Salmonella is a major foodborne pathogen, yet real-time data on duck-derived strains in China remain scarce. This study investigated the epidemiology, antimicrobial resistance (AMR), gene profiles, and PFGE patterns of 114 Salmonella isolates recovered from 397 deceased ducks (2021–2024) across nine provinces (isolation [...] Read more.

Salmonella is a major foodborne pathogen, yet real-time data on duck-derived strains in China remain scarce. This study investigated the epidemiology, antimicrobial resistance (AMR), gene profiles, and PFGE patterns of 114 Salmonella isolates recovered from 397 deceased ducks (2021–2024) across nine provinces (isolation rate: 28.72%). Fourteen serotypes were identified, with S. Typhimurium (23.68%), S. Indiana (21.93%), S. Kentucky (18.42%), and S. Enteritidis (12.28%) being predominant. Most isolates showed high resistance to β-lactams, tetracyclines, quinolones, and sulfonamides, with extensive multidrug resistance (MDR) observed—especially in S. Indiana, S. Typhimurium, and S. Kentucky. Among the 23 detected resistance genes, tet(B) had the highest prevalence (75.44%), particularly in S. Indiana. Biofilm formation was observed in 99.12% of isolates, with 84.21% demonstrating moderate to strong capacity. Eighteen virulence genes were detected; S. Enteritidis carried more spvB/C, sipB, and sodC1, while S. Indiana had higher cdtB carriage. PFGE revealed substantial genetic diversity among strains. This comprehensive analysis highlights the high AMR and biofilm potential of duck-derived Salmonella in China, emphasizing the urgent need for enhanced surveillance and control measures to mitigate public health risks. Full article

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24 pages, 957 KB

Open AccessReview

Biofilm and Antimicrobial Resistance: Mechanisms, Implications, and Emerging Solutions

by Bharmjeet Singh, Manju Dahiya, Vikram Kumar, Archana Ayyagari, Deepti N. Chaudhari and Jayesh J. Ahire

Microbiol. Res. 2025, 16(8), 183; https://doi.org/10.3390/microbiolres16080183 - 6 Aug 2025

Abstract

Biofilms are a spontaneously formed slimy matrix of extracellular polymeric substances (EPS) enveloping miniature bacterial colonies, which aid in pathogen colonization, shielding the bacteria from antibiotics, as well as imparting them resistance towards the same. Biofilms employ a robust communication mechanism called quorum [...] Read more.

Biofilms are a spontaneously formed slimy matrix of extracellular polymeric substances (EPS) enveloping miniature bacterial colonies, which aid in pathogen colonization, shielding the bacteria from antibiotics, as well as imparting them resistance towards the same. Biofilms employ a robust communication mechanism called quorum sensing that serves to keep their population density constant. What is most significant about biofilms is that they contribute to the development of bacterial virulence by providing protection to pathogenic species, allowing them to colonize the host, and also inhibiting the activities of antimicrobials on them. They grow on animate surfaces (such as on teeth and intestinal mucosa, etc.) and inanimate objects (like catheters, contact lenses, pacemakers, endotracheal devices, intrauterine devices, and stents, etc.) alike. It has been reported that as much as 80% of human infections involve biofilms. Serious implications of biofilms include the necessity of greater concentrations of antibiotics to treat common human infections, even contributing to antimicrobial resistance (AMR), since bacteria embedded within biofilms are protected from the action of potential antibiotics. This review explores various contemporary strategies for controlling biofilms, focusing on their modes of action, mechanisms of drug resistance, and innovative approaches to find a solution in this regard. This review interestingly targets the extracellular polymeric matrix as a highly effective strategy to counteract the potential harm of biofilms since it plays a critical role in biofilm formation and significantly contributes to antimicrobial resistance. Full article

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20 pages, 3465 KB

Open AccessArticle

Inhibitory Effects of Selected Chemical Substances on the Growth of Filamentous Fungi Occurring in Cellar Management

by Karolina Kostelnikova, Romana Heralecka, Anna Krpatova, Filip Matousek, Jiri Sochor and Mojmir Baron

Microbiol. Res. 2025, 16(8), 182; https://doi.org/10.3390/microbiolres16080182 - 4 Aug 2025

Abstract

This study evaluated the inhibitory efficacy of sulphur dioxide, hydrogen peroxide, copper sulphate pentahydrate, chlorine-based formulations, a chlorine-free formulation, ethanol, and acetic acid against Cladosporium cladosporioides, Aspergillus niger, and Penicillium expansum. An in vitro inhibition test was employed to investigate [...] Read more.

This study evaluated the inhibitory efficacy of sulphur dioxide, hydrogen peroxide, copper sulphate pentahydrate, chlorine-based formulations, a chlorine-free formulation, ethanol, and acetic acid against Cladosporium cladosporioides, Aspergillus niger, and Penicillium expansum. An in vitro inhibition test was employed to investigate the inhibitory properties. The results demonstrated different sensitivities of filamentous fungi to the inhibitors. All tested substances displayed fungicidal properties. Sulphur dioxide (40% NH₄HSO₃ solution) inhibited growth at a 4% v/v concentration. No minimum effective concentration was established for H₂O₂; only a 30% w/v solution inhibited P. expansum. CuSO₄·5H₂O completely inhibited fungal growth at 5% w/v solution, with 2.5% w/v also proving effective. For the chlorine-based product, 40% w/v solution (48 g∙L⁻¹ active chlorine) had the most substantial effect, though it only slowed growth, and NaClO solution completely inhibited growth at 2.35 g NaClO per 100 g of product (50% w/v solution). FungiSAN demonstrated fungicidal effects; however, the recommended dose was insufficient for complete inhibition. Ethanol exhibited the lowest efficacy, while the inhibitory threshold for CH₃COOH was found to be a 5% v/v solution. The findings of this study may serve as a basis for informed decision-making when selecting the most suitable product, depending on specific application conditions. Full article

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