Microbiology Research

13 pages, 1261 KB

Open AccessArticle

Influence of Milking Process and Production System on Raw Goat Milk Bacteriome

by Ezquibel Montesinos Rivera, Estela Garza Brenner, Pascuala Ambriz Morales, Williams Arellano Vera, Rogelio de J. Treviño-Rangel and Ana María Sifuentes Rincón

Microbiol. Res. 2025, 16(10), 218; https://doi.org/10.3390/microbiolres16100218 - 4 Oct 2025

Abstract

The aim of this study was to compare, during milking, the bacteriomes of goat milk from farms in Mexico representing traditional and semi-intensive production systems. Metagenomic DNA was isolated from pooled milk samples collected at different milking stages, and following 16S rRNA-targeted sequencing, [...] Read more.

The aim of this study was to compare, during milking, the bacteriomes of goat milk from farms in Mexico representing traditional and semi-intensive production systems. Metagenomic DNA was isolated from pooled milk samples collected at different milking stages, and following 16S rRNA-targeted sequencing, alpha (Shannon H’ and Simpson D) and beta (Bray–Curtis) diversity indices were calculated. Within the semi-intensive system, fore-stripping showed lower diversity (H’ = 1.5 vs. H’ = 4.0) but greater evenness (D = 0.5 vs. D = 0.8) than the milking stage. In contrast, no differences between stages in the traditional system were observed. The Bray–Curtis index revealed that the use of the semi-intensive system explained 99.4% of the variability, while the traditional system accounted for only 0.5%. In the semi-intensive system, fore-stripping was dominated by Mesoplasma (51.9%) and Staphylococcus (42.1%), whereas Enterococcus (27.2%) and Lactococcus (18.5%) prevailed during milking. Meanwhile, in the traditional system, Pseudomonas (46.9% and 22.7) and Lactococcus (22.7% and 29.2%) predominated in both stages. Management practices strongly influence the microbiological profile of milk, leading to changes in not only the diversity and abundance of pathogenic bacteria but also in the presence of beneficial lactic acid bacteria and, hence, the overall expected milk quality. Full article

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16 pages, 1782 KB

Open AccessArticle

Fungal Functional Level to Describe Soil Fungal Composition at Mediterranean Vineyards

by Yasmin Piñuela, María Hernández, Iván Escudero, Peter Sisseck and Jaime Olaizola

Microbiol. Res. 2025, 16(10), 217; https://doi.org/10.3390/microbiolres16100217 - 2 Oct 2025

Abstract

Understanding the soil fungal community in vineyards sheds light on the interactions between plants and their associated microorganisms. For example, identifying arbuscular mycorrhizal fungi (AMF), which are beneficial to grapevine growth, is a good indicator of soil health. In contrast, other fungi, such [...] Read more.

Understanding the soil fungal community in vineyards sheds light on the interactions between plants and their associated microorganisms. For example, identifying arbuscular mycorrhizal fungi (AMF), which are beneficial to grapevine growth, is a good indicator of soil health. In contrast, other fungi, such as the pathogen group, can be detrimental to vine growth. The present study aimed to characterize the soil fungal community and the fungal diversity present at six Mediterranean vineyards located in Burgos (Spain), delving into fungal functional guilds and focusing on AMF and pathogenic fungal groups. The fungal structure was investigated using DNA metabarcoding in three soil samples taken from each vineyard, and differences in the abundance of functional guilds were assessed. Similar soil fungal community structures were observed among soil sample repetitions within vineyards. In contrast, adjacent vineyards presented differences in their microbial composition. Saprophytes followed by pathogens were the dominant fungal functional guilds across all vineyards. However, no differences in the relative abundance of the different fungal functional groups were observed among sites. The vineyard with the highest relative abundance of AMF (0.5%) also had the lowest pathogen relative abundance from all the sites (29.76%). Also, sites presenting a high relative abundance of pathogens in soil (>35%) had a low relative abundance of AMF (<0.05%). Our results suggest that the fungal community is affected by the intrinsic properties of the soil and the characteristics of each vineyard’s microsite over the effect of the geographical proximity. In addition, to improve our understanding of the soil microbial ecology, we highlight the necessity of prospecting soil fungal analyses into functional groups, interpreting diversity results within taxonomic groups alongside the total abundance of target groups/species. Full article

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14 pages, 279 KB

Open AccessArticle

Molecular Epidemiology of Different Bacterial Pathogens and Their Antimicrobial Resistance Genes Among Patients Suffering from Surgical Site Infections in Lebanon

by Inass Kawtharani, Ghassan Ghssein, Ola Srour, Abdul Amir Chaaban and Pascale Salameh

Microbiol. Res. 2025, 16(10), 216; https://doi.org/10.3390/microbiolres16100216 - 1 Oct 2025

Abstract

Background: Antimicrobial resistance (AMR) is a major global health threat, particularly in surgical site infections (SSIs), where multidrug-resistant (MDR) pathogens complicate treatment. Objective: This study aimed to identify antimicrobial resistance genes and assess their prevalence in bacterial species causing SSIs in Lebanon. Materials [...] Read more.

Background: Antimicrobial resistance (AMR) is a major global health threat, particularly in surgical site infections (SSIs), where multidrug-resistant (MDR) pathogens complicate treatment. Objective: This study aimed to identify antimicrobial resistance genes and assess their prevalence in bacterial species causing SSIs in Lebanon. Materials and Methods: The present research is a multicenter and prospective study that included patients who developed SSIs after surgery in seven hospitals, within the period of January 2024–September 2024. Bacterial isolates from wound swabs or tissue samples were identified using standard microbiological methods. Antimicrobial susceptibility was tested by disk diffusion, and resistance genes were detected by PCR. Data were analyzed using Statistical Package for the Social Sciences (SPSS). Results: Among 6933 surgical patients, 63 developed SSIs (0.91%; 95% CI [0.70–1.15]). Gram-negative bacteria predominated (73%), mainly Escherichia coli and Pseudomonas aeruginosa, while Gram-positive isolates accounted for 27%, mostly Staphylococcus aureus. MDR was observed in 71% of Gram-positive and 61% of Gram-negative isolates. The most frequent genes were mecA in S. aureus (100%) and coagulase-negative staphylococci (83.3%); bla_CTX-M in E. coli, Klebsiella pneumoniae, and Enterobacter cloacae (100%); and bla_NDM in E. cloacae (100%) and Acinetobacter baumannii (60%). bla_KPC was less common, and no isolates carried Imipenemase (IMP), Verona integron-encoded metallo-β-lactamase (VIM), and Oxacillinase-48-like β-lactamase (OXA-48). Conclusions: This study highlights the high prevalence of antibiotic resistance in agents causing SSIs in Lebanese hospitals. Resistance genes, particularly mecA, bla_CTX-M, and blaNDM, were highly prevalent in SSI pathogens, underscoring the urgent need for surveillance and judicious antibiotic use in Lebanese hospitals. Full article

(This article belongs to the Topic Multidrug Resistance Across Pathogens: Fungi, Bacteria, Parasites, and Viruses)

12 pages, 486 KB

Open AccessArticle

Research on the Influence of Enterobius vermicularis on the Composition and Quality of the Intestinal Microbiota, and the Susceptibility to Co-Infections

by Eleonora Kaneva, Rumen Harizanov, Maria Pavlova, Desislava Velcheva, Nina Tsvetkova, Aleksandra Ivanova, Mihaela Videnova, Raina Borisova, Ivailo Alexiev and Reneta Dimitrova

Microbiol. Res. 2025, 16(10), 215; https://doi.org/10.3390/microbiolres16100215 - 30 Sep 2025

Abstract

The present study examined the presence of concomitant intestinal parasites and bacteria in individuals infected with Enterobius vermicularis in Bulgaria, and analyzed its effects on the intestinal microbiome and the risk of co-infection. Fecal samples from people with and without (control group) enterobiasis [...] Read more.

The present study examined the presence of concomitant intestinal parasites and bacteria in individuals infected with Enterobius vermicularis in Bulgaria, and analyzed its effects on the intestinal microbiome and the risk of co-infection. Fecal samples from people with and without (control group) enterobiasis were tested for the presence of concomitant bacterial infection. The results were compared to find out about the intestinal microbiome in these groups. The microbiological examination of the control group showed that 8.3% had only conditionally pathogenic flora. However, in individuals with enterobiasis, 56% had normal intestinal bacterial flora, but 46% had disturbed microbiota: 7% were carriers of pathogenic intestinal bacteria and 24% had opportunistic pathogens. The most prevalent were Klebsiella pneumoniae (49%), followed by Enterobacter spp. (22%), and Proteus mirabilis (12.2%). Our study is the first in the country to investigate the impact of E. vermicularis infection on the composition and quality of the gut microbiome, as well as the potential for co-infections with pathogenic gut bacteria. Although our findings are preliminary, they suggest that this nematode may significantly contribute to a predisposition for dysbiosis or the onset of secondary bacterial infections. Full article

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16 pages, 3572 KB

Open AccessArticle

Genome-Wide Analysis and Expression Profiling of the Cellulase Genes in Aspergillus oryzae

by Danni Hu, Ruoyu Zhao, Yingxu Lin and Chunmiao Jiang

Microbiol. Res. 2025, 16(10), 214; https://doi.org/10.3390/microbiolres16100214 - 26 Sep 2025

Abstract

One of the critical steps in lignocellulosic deconstruction is the hydrolysis of cellulose by cellulases. Aspergillus oryzae can produce and secrete a large amount of various extracellular enzymes, including cellulases. However, due to the lack of a comprehensive characterization of the cellulase genes [...] Read more.

One of the critical steps in lignocellulosic deconstruction is the hydrolysis of cellulose by cellulases. Aspergillus oryzae can produce and secrete a large amount of various extracellular enzymes, including cellulases. However, due to the lack of a comprehensive characterization of the cellulase genes in A. oryzae, the development and application of A. oryzae cellulase are greatly limited. In this study, a total of 219 glycosyl hydrolase genes were systematically identified from the A. oryzae 3.042 genome and classified into 40 glycosyl hydrolase families. Among these glycosyl hydrolase genes, 26 genes encoding the cellulases of endoglucanase, exoglucanase, and β-glucosidase were identified and functionally characterized. The chromosome localizations, gene structures, functional domains, and subcellular localizations of these 26 cellulases were analyzed by bioinformatics. In addition, analysis of the expression patterns revealed that the expression of A. oryzae cellulase genes was time-specific, and most of the cellulase genes were inhibited under low- and high-temperature stress and high salt stress, which had important guiding significance for understanding the transcription patterns of A. oryzae cellulase genes. These findings lay a foundation for our subsequent modification of cellulase activity to realize the industrial applications of A. oryzae cellulase genes in cellulose biorefineries. Full article

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18 pages, 3054 KB

Open AccessArticle

Altitudinal Gradient Drives Rhizosphere Microbial Structure and Functional Potential in Prickly Pear Cactus (Opuntia ficus-indica L.)

by Lorena Jacqueline Gómez-Godínez, José Luis Aguirre-Noyola, Carlos Hugo Avendaño-Arrazate, Sergio de los Santos-Villalobos, Magali Ruiz-Rivas, Ramón Ignacio Arteaga-Garibay and José Martín Ruvalcaba-Gómez

Microbiol. Res. 2025, 16(10), 213; https://doi.org/10.3390/microbiolres16100213 - 26 Sep 2025

Abstract

The prickly pear cactus (Opuntia ficus-indica L.) is an emblematic crop for Mexico’s economy, gastronomy, and culture. Microbial communities play an important role in the health, development, and productivity of crops. This study used 16S rRNA high-throughput sequencing and bioinformatic analyses to [...] Read more.

The prickly pear cactus (Opuntia ficus-indica L.) is an emblematic crop for Mexico’s economy, gastronomy, and culture. Microbial communities play an important role in the health, development, and productivity of crops. This study used 16S rRNA high-throughput sequencing and bioinformatic analyses to evaluate the rhizosphere microbiome of prickly pear cactus across an altitudinal gradient in Milpa Alta (Mexico). A microbial core consisting of Bacillus, Acidibacter, and Sphingomonas was detected, reflecting strong co-adaptation between plants and soil microorganisms under different agroecosystems. However, in the lower-altitude zones, Conexibacter, Agromyces, Domibacillus, Pedomicrobium, and Rokubacteriales predominated, which are associated with humid environments and high organic matter content. In contrast, in the middle-altitude zones, Acidothermus, Gemmatimonas, Mesorhizobium, and Pseudoxanthomonas were enriched, which are involved in carbon and nitrogen cycles. Higher-altitude zones exhibited greater bacterial specialization, with genera adapted to more extreme conditions such as Halocella, Solirubrobacter, Rhodomicrobium, Phenylobacterium, Roseomonas, Pseudarthrobacter, Crossiella, Aquicella, and others. Overall, our data show that altitude acts as an ecological filter structuring soil microbial communities associated with prickly pear cactus, influencing the diversity and functional potential. This study on microbial diversity not only provides insights into the health of the agroecosystem but also represents a valuable source of microorganisms with functional potential for sustainable agriculture. Full article

(This article belongs to the Topic New Challenges on Plant–Microbe Interactions)

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13 pages, 3043 KB

Open AccessArticle

Phylogenetic Incongruence of Cyclic di-GMP-Activated Glycosyltransferase nfrB with 16S rRNA Gene Tree Reflects In Silico-Predicted Protein Structural Divergence in Diaphorobacter nitroreducens Isolated from Estero de Paco, Manila, Philippines

by Ram Julius L. Marababol and Windell L. Rivera

Microbiol. Res. 2025, 16(10), 212; https://doi.org/10.3390/microbiolres16100212 - 26 Sep 2025

Abstract

Diaphorobacter nitroreducens is a Gram-negative bacterium ubiquitously found in wastewater, recognized for its ecological adaptability and potential applications in environmental, biomedical, and industrial processes. Central to its adaptability is the nfrB gene, which encodes a cyclic di-3′,5′-guanylate (c-di-GMP)-activated glycosyltransferase. This enzyme facilitates the [...] Read more.

Diaphorobacter nitroreducens is a Gram-negative bacterium ubiquitously found in wastewater, recognized for its ecological adaptability and potential applications in environmental, biomedical, and industrial processes. Central to its adaptability is the nfrB gene, which encodes a cyclic di-3′,5′-guanylate (c-di-GMP)-activated glycosyltransferase. This enzyme facilitates the secretion of biofilm-associated extracellular polymeric substances (EPS), essential for its survival and functionality in diverse environments. Using complete EMJH media as a selective medium, D. nitroreducens was successfully isolated from soil and water samples from Estero de Paco, Manila, Philippines, enabling downstream analyses of its nfrB gene. Phylogenetic analyses revealed that the nfrB gene tree deviates significantly from the canonical 16S rRNA gene tree, with D. nitroreducens clustering alongside members of the Enterobacteriaceae family. This deviation suggests the potential influence of horizontal gene transfer, adaptive evolution, or lineage-specific pressures on nfrB evolution. Structural analysis of NfrB through Alphafold 3 prediction demonstrated a conserved N-terminal region across taxa, except for the outgroup Zymomonas mobilis. Conversely, the C-terminal region, housing the catalytic domain, showed considerable diversity, reflecting adaptive modifications across bacterial lineages. Despite this variability, the putative binding site for cyclic di-3′,5′-guanylate remained conserved, indicating a balance between functional conservation and adaptive diversification. These findings not only deepen the existing understanding of bacterial signaling and glycosylation mechanisms but also provide insights into the evolutionary dynamics of glycosyltransferases. Furthermore, the study underscores the potential of NfrB as a target for innovative applications, including the design of novel biocatalysts and the development of informed strategies for bacterial management in environmental, industrial, and biotechnological contexts. Full article

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17 pages, 2778 KB

Open AccessArticle

Bacillus Probiotic Strains Induce Gonadal Maturation and Sex Differentiation in Red Abalone Haliotis rufescens Using a Plant-Based Diet

by Jorge Olmos, Manuel Acosta-Ruiz, Fabiola Lafarga-De la Cruz and Jeremie Bauer

Microbiol. Res. 2025, 16(10), 211; https://doi.org/10.3390/microbiolres16100211 - 24 Sep 2025

Abstract

This study examined the effects of Bacillus probiotic strains on red abalone Haliotis rufescens reproductive performance. We supplemented plant- and fish-based feeds and compared them to fresh giant kelp Macrocystis pyrifera as a control diet. Over 180 days, abalone fed the plant–probiotic diet [...] Read more.

This study examined the effects of Bacillus probiotic strains on red abalone Haliotis rufescens reproductive performance. We supplemented plant- and fish-based feeds and compared them to fresh giant kelp Macrocystis pyrifera as a control diet. Over 180 days, abalone fed the plant–probiotic diet reached higher female gonadal maturation, with 56% of females attaining the maximum Visual Gonad Index (VGI 3). Additionally, plant-based treatment showed a female-biased sex ratio (1.5:1 female-to-male ratio, F:M) compared with the kelp control treatment (0.8:1 F:M). These results suggest that probiotics can improve nutrient utilization from soybean meal and may enhance the bioavailability of phytoestrogens and other bioactive compounds, contributing to reproductive outcomes. Although the mechanisms remain to be confirmed, this approach provides a promising strategy to reduce reliance on fishmeal and wild macroalgae while supporting faster reproductive cycles in abalone aquaculture. Future research should focus on biochemical validation, molecular pathways, and multigenerational trials to ensure the long-term safety and sustainability of probiotic–plant-based feeds. Full article

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17 pages, 2176 KB

Open AccessCommunication

Gut Microbiome Analysis Reveals Core Microbiota Variation Among Allopatric Populations of the Commercially Important Euryhaline Cichlid Etroplus suratensis

by Jilu Alphonsa Jose, Anoop Alex and Siby Philip

Microbiol. Res. 2025, 16(10), 210; https://doi.org/10.3390/microbiolres16100210 - 23 Sep 2025

Abstract

The gut microbiome plays a critical role in host physiology and adaptation, shaped by both intrinsic host factors and extrinsic environmental conditions. In this study, we investigated the influence of habitat type and geographical isolation on gut microbial communities in habitat-isolated populations of [...] Read more.

The gut microbiome plays a critical role in host physiology and adaptation, shaped by both intrinsic host factors and extrinsic environmental conditions. In this study, we investigated the influence of habitat type and geographical isolation on gut microbial communities in habitat-isolated populations of the euryhaline cichlid Etroplus suratensis, which inhabit freshwater and brackish water environments. Using 16S rRNA gene amplicon sequencing, we compared microbial assemblages in fish guts and their corresponding habitats to assess patterns of community divergence. Alpha and beta diversity analyses revealed significant differences in microbial composition between gut and water samples, with limited overlap, particularly in brackish water, indicating strong host-mediated filtering of environmental microbiota. Notably, brackish and freshwater habitats harbored 2244 and 3136 unique water-associated taxa, respectively, while only 36 and 426 taxa were shared between water and gut in each habitat. Despite habitat divergence, 59 microbial taxa were consistently shared across gut samples from both populations, indicating the existence of a conserved core microbiome that likely fulfills essential functional roles. These findings support the notion that the fish gut serves as a selective ecological niche, enabling the persistence of functionally relevant microbes while restricting the entry of environmental transients. Moreover, the observed divergence in gut microbiota across habitats, coupled with a shared core, highlights the interplay between local adaptation and conserved host–microbe associations, with potential implications for understanding microbial contributions to vertebrate ecological diversification and allopatric speciation. Full article

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16 pages, 1442 KB

Open AccessArticle

Comparative Virulence Gene Profiling of Campylobacter jejuni and Campylobacter coli Isolates from Avian and Human Sources in Egypt

by Amr Mekky, Mohamed R. Issa, Amro Hashish, Wafaa Hassan, Ali Wahdan, Islam Hisham, Shymaa Enany and Mohamed Enany

Microbiol. Res. 2025, 16(9), 209; https://doi.org/10.3390/microbiolres16090209 - 18 Sep 2025

Abstract

Campylobacter species are considered to be the leading bacterial cause of human gastroenteritis globally. Consumption of undercooked or contaminated food, such as chicken, is the main cause of human campylobacteriosis. Despite this significant zoonotic link, comparative data on virulence determinants in Campylobacter isolates [...] Read more.

Campylobacter species are considered to be the leading bacterial cause of human gastroenteritis globally. Consumption of undercooked or contaminated food, such as chicken, is the main cause of human campylobacteriosis. Despite this significant zoonotic link, comparative data on virulence determinants in Campylobacter isolates across avian and human sources remain limited. This study aimed to characterize the prevalence and expression of virulence determinants in Campylobacter jejuni and Campylobacter coli isolates from chicken and human sources in Ismailia governorate, Egypt. A total of twenty C. jejuni and C. coli isolates (ten of each species) were screened for 14 virulence genes using PCR. All isolates harbored virB11, iam, racR, and tetO. Chicken isolates exhibited a significantly higher prevalence: C. jejuni (chicken): pldA, dnaJ, flaA (100%), cdtB (80%), ciaB (60%), and wlaN (0%); C. coli (chicken): pldA, dnaJ (100%), flaA (60%), cdtB (60%), ciaB (40%), and wlaN (20%). In contrast, human isolates showed a markedly lower prevalence: C. jejuni (human): dnaJ, flaA, and cdtB (20%); C. coli (human): dnaJ, flaA, and cdtB (40%). Crucially, pldA, ciaB, and wlaN were absent in all human isolates. plda and dnaJ genes showed statistically significant prevalence differences. qPCR revealed a significant upregulation (p < 0.05) of dnaJ, virB11, flaA, and iam in chicken isolates compared to human isolates, with log₂ fold changes of 3.52, 2.84, 2.43, and 1.90 for C. jejuni and 3.06, 2.38, 1.51, and 1.32 for C. coli. Differential expressions of racR, cdtB, and tetO were not significant, with log2 fold changes ranging from −0.51 to 0.14. Ganglioside mimicry genes (Cst11, wlaN, Waac, ggt, and cgtB) and the carbon storage regulator gene (csrA) were absent in all human isolates. These findings underscore the significant variability in virulence gene profiles in chicken and human C. jejuni and C. coli isolates and highlight the importance of molecular characterization in the risk assessment and epidemiological surveillance of Campylobacter infections. Full article

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9 pages, 542 KB

Open AccessCommunication

Herd-Level Prevalence of Hepatitis E Virus in Greek Pig Farms

by Efthymia Stamelou, Konstantinos Papageorgiou, Aikaterini Stoikou, Dimitrios Chatzopoulos, Dimitrios Papadopoulos, Ioannis A. Giantsis, Charalambos Billinis, Evanthia Petridou and Spyridon K. Kritas

Microbiol. Res. 2025, 16(9), 208; https://doi.org/10.3390/microbiolres16090208 - 18 Sep 2025

Abstract

Hepatitis E virus (HEV) is an emerging zoonotic pathogen, with swine identified as a major reservoir. Despite the global significance of HEV, epidemiological data regarding its presence in Greek pig farms remain limited. This study investigated the presence of HEV RNA in swine [...] Read more.

Hepatitis E virus (HEV) is an emerging zoonotic pathogen, with swine identified as a major reservoir. Despite the global significance of HEV, epidemiological data regarding its presence in Greek pig farms remain limited. This study investigated the presence of HEV RNA in swine populations across Greece. In 2019, a total of 280 fecal samples from finishing pigs were collected from 28 pig farms in diverse geographic regions. Pooled samples were analyzed by real-time RT-PCR targeting the conserved ORF3 region of the HEV genome (without genotyping). HEV RNA was detected in 42.9% (12/28) of farms, with positive farms identified in five of the six surveyed regions, suggesting widespread viral circulation. These findings confirm, for the first time, the presence of HEV in the Greek swine population, while the observed prevalence aligns with intermediate to high levels reported in other European countries. Considering the zoonotic potential of HEV, especially via occupational exposure or consumption of contaminated pork products, these results highlight the need for continued surveillance and further investigation into potential public health implications. Full article

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20 pages, 1223 KB

Open AccessArticle

Characterization of New Yeast Strains Isolated from Local Grape Varieties of the Soufli Region in Northern Greece

by Anastasios Nikolaou, Ioanna Prapa, Ioanna Karapantzou, Vasiliki Kompoura, Niki Proxenia, Yorgos Kotseridis and Yiannis Kourkoutas

Microbiol. Res. 2025, 16(9), 207; https://doi.org/10.3390/microbiolres16090207 - 18 Sep 2025

Abstract

Over the past few years, consumers’ preference for wines with a distinct regional identity has shifted producers to adopt traditional grape varieties and has increased interest in the indigenous grapevine microbiome, due to its potential influence on the wine quality characteristics. In the [...] Read more.

Over the past few years, consumers’ preference for wines with a distinct regional identity has shifted producers to adopt traditional grape varieties and has increased interest in the indigenous grapevine microbiome, due to its potential influence on the wine quality characteristics. In the present study, indigenous Saccharomyces cerevisiae strains were isolated from 3 local grape varieties (“Keratsouda”, “Karnachalas”, and “Bogialamas”) of the Soufli region in northern Greece. After molecular identification, all strains were evaluated for key oenological traits (ethanol resistance, SO₂ resistance, H₂S production, and aminoacid decarboxylation). Three representative strains (one per grape variety) were further evaluated for their long-term survival after freeze-drying and their fermentation potential at 12 °C and 22 °C. Ethanol content ranged in similar values (11.9–12.5%) for all wines, but kinetic parameters were significantly affected by the strain used and the fermentation temperature. Principal component analysis revealed that the volatile composition as well as practical wine attributes were affected by both the strain used and the fermentation temperature and resulted in distinct sensory profiles in the new products. Full article

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

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16 pages, 385 KB

Open AccessArticle

Extended-Spectrum β-Lactamase-/AmpC-Producing Escherichia coli and Associated Risk Factors in Shelter Dogs: A Baseline Study in North Macedonia

by Ivana Shikoska, Sanja Duvnjak, Tom Koritnik, Bojana Chapkunovska, Jane Vlahov, Marija Ratkova Manovska, Aleksandar Cvetkovikj and Iskra Cvetkovikj

Microbiol. Res. 2025, 16(9), 206; https://doi.org/10.3390/microbiolres16090206 - 17 Sep 2025

Abstract

Antimicrobial resistance (AMR) is a significant public health concern in companion animals, yet systematic surveillance in North Macedonia is lacking. This study investigated the prevalence of resistance in Escherichia coli isolated from 112 fecal samples from dogs in six shelters in North Macedonia [...] Read more.

Antimicrobial resistance (AMR) is a significant public health concern in companion animals, yet systematic surveillance in North Macedonia is lacking. This study investigated the prevalence of resistance in Escherichia coli isolated from 112 fecal samples from dogs in six shelters in North Macedonia and evaluated the associated risk factors, providing the first baseline dataset for this population. High resistance was observed for sulfamethoxazole (68.75%), ampicillin (52.68%), and ciprofloxacin (41.07%). Multidrug resistance was present in 50% of the isolates, with 17 (15.17%) confirmed as ESBL producers. Additionally, 18 isolates (16.1%) were identified as AmpC producers, 16 of which carried the blaCMY-2 gene. Notably, 72.2% of ESBL/AmpC isolates were resistant to ertapenem despite the absence of carbapenemase genes, a finding that warrants further investigation. Risk factors such as shared housing, longer shelter stays, and frequent empirical antimicrobial use were identified as probable contributors to the carriage of ESBL-/AmpC-producing E. coli. None of the shelters had antimicrobial stewardship protocols or routine diagnostic testing, revealing critical gaps in infection control and antimicrobial practices. These findings underscore the urgent need for antimicrobial stewardship and surveillance in North Macedonia’s companion animal populations within the One Health framework. Full article

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16 pages, 2638 KB

Open AccessArticle

Microbial Diversity and Metabolite Changes in Greenhouse Soil Continuously Cropped with Morchella

by Ping Yu, Nan Tao, Weimin Chen, Jie Zhang, Chunxin Yao and Guoting Tian

Microbiol. Res. 2025, 16(9), 205; https://doi.org/10.3390/microbiolres16090205 - 15 Sep 2025

Abstract

True morels (Morchella spp., Morchellaceae, Ascomycota) are a rare and highly valuable edible fungus. As the morel cultivation scale has expanded, obstacles to continuous cropping have come to the fore. This study investigates the specific biological mechanisms that may hinder the continuous [...] Read more.

True morels (Morchella spp., Morchellaceae, Ascomycota) are a rare and highly valuable edible fungus. As the morel cultivation scale has expanded, obstacles to continuous cropping have come to the fore. This study investigates the specific biological mechanisms that may hinder the continuous cropping of Morchella by means of microbiome and metabolome analysis of the soil. Using amplicon sequencing-based microbiome analysis, 5288 bacterial operational taxonomic units (OTUs) and 1847 fungal OTUs were identified. Bacterial genera such as Arthrobacter, Tychonema, Rhodanobacter, Luteimonas, and Streptomyces, along with pathogenic fungi, likely play specific roles in hindering continuous cropping of Morchella. Metabolomic analysis revealed 368 metabolites, including lipids and lipid-like molecules, organic acids and derivatives, benzene-containing compounds, and heterocyclic compounds. Eighteen metabolites showed significant differences between Morchella continuous cropping and control soil, including toxic compounds such as 2,4,5-Trichloro-6-Hydroxybenzene-1,3-Dicarbonitrile, 2,4-Dichloro-6-nitrophenol, and Aflatoxin B2. These results indicate that alterations in soil microbial structure and toxic metabolites secreted by Morchella collectively contribute to the hindrance of continuous cropping. Full article

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14 pages, 2791 KB

Open AccessArticle

Asterocapsa thermalis sp. nov. from the Unique European Continental Geyser in Sapareva Banya (Bulgaria)

by Maya Stoyneva-Gärtner, Georg Gärtner and Blagoy Uzunov

Microbiol. Res. 2025, 16(9), 204; https://doi.org/10.3390/microbiolres16090204 - 13 Sep 2025

Abstract

Thermal algae are extremophilic organisms that live in one of the harshest environments in the world and thrive in waters with temperatures of up to 90 °C. They have gained attention due to their special ecological adaptations, their great biotechnological potential and their [...] Read more.

Thermal algae are extremophilic organisms that live in one of the harshest environments in the world and thrive in waters with temperatures of up to 90 °C. They have gained attention due to their special ecological adaptations, their great biotechnological potential and their recently recognised role in combating global climate change and achieving sustainable development. However, the biodiversity of these algae is far from being fully explored. The article presents the first finding of the prokaryotic genus Asterocapsa (Chroococcales, Cyanophyceae, Cyanoprokaryota/Cyanobacteria) in thermal waters and describes a new species from the fountain basins in the thermal system of the only continental European geyser (101 °C) in the town of Sapareva Banya (south-west Bulgaria). This species is not only one of the few aquatic representatives of this generally aeroterrestrial genus, but is also characterised by its extremophilic lifestyle and differs clearly from the type species and other aquatic species of the genus due to its morphological characteristics. These include the smaller dimensions of the cells and colonies, as well as the colourless, transparent, but always lamellar and regularly verrucous mucilage envelopes. The unique locality of this alga is highly endangered and was included in the first Red List of Bulgarian wetlands. Due to human activities and changes in the geyser system, we have detected some unfavourable changes in the algal habitat and therefore propose to add the newly described species to the Red List of Bulgarian Microalgae with the status Critically Endangered. Full article

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15 pages, 1658 KB

Open AccessArticle

Emerging Resistance in Klebsiella pneumoniae: CTX-M Prevalence, Biofilm Formation, and Efficacy of Platanus orientalis Extract

by Ahmed Najm Abed and Basma Mnif

Microbiol. Res. 2025, 16(9), 203; https://doi.org/10.3390/microbiolres16090203 - 7 Sep 2025

Abstract

CTX-M beta-lactamases have become the predominant extended-spectrum beta-lactamases (ESBLs) globally, contributing to increased patient morbidity, mortality, and healthcare costs. This study investigated the prevalence of biofilm formation and CTX-M genes in Klebsiella pneumoniae strains isolated from Baghdad hospitals, aiming to better understand antimicrobial [...] Read more.

CTX-M beta-lactamases have become the predominant extended-spectrum beta-lactamases (ESBLs) globally, contributing to increased patient morbidity, mortality, and healthcare costs. This study investigated the prevalence of biofilm formation and CTX-M genes in Klebsiella pneumoniae strains isolated from Baghdad hospitals, aiming to better understand antimicrobial resistance mechanisms and support the development of targeted interventions. A total of 300 samples were collected from various clinical and hospital sources, and antibiotic susceptibility testing was performed using the Kirby–Bauer disc diffusion method. ESBL production was also confirmed using specifically designed primers. Platanus orientalis Linn extract was evaluated for its antimicrobial and antibiofilm activity against K. pneumoniae isolates. The results showed significant resistance to the majority of antibiotics, including cefotaxime, gentamicin, levofloxacin, ceftazidime, and ceftriaxone. A high prevalence of the CTX-M gene (100%) was detected in the isolates, with the most frequent alleles being blaCTX-M-15 (65.2%) and blaCTX-M-1 (30%). Furthermore, 95.6% of the isolates were capable of forming biofilms. However, when treated with P. orientalis Linn extract, most isolates exhibited reduced biofilm production, becoming weak biofilm producers. Phytochemical analysis of P. orientalis Linn revealed significant amounts of phenolic compounds, tannins, and glycosides, as well as the presence of alkaloids and carbohydrates. Overall, this study demonstrates a correlation between CTX-M production and biofilm-forming ability in K. pneumoniae and highlights the potential role of P. orientalis Linn extract in combating antibiotic-resistant infections. Full article

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23 pages, 2707 KB

Open AccessArticle

Sentinel or Disperser? The Role of White Storks (Ciconia ciconia) in the Spread of Antibiotic-Resistant Bacteria

by Teresa Cardona-Cabrera, Sandra Martínez-Álvarez, Yolanda Muela-Trujillo, Alberto Sánchez-Cano, Juan Carlos Montero, Juan Manuel Fernández-Gallego, Carmen Torres and Ursula Höfle

Microbiol. Res. 2025, 16(9), 202; https://doi.org/10.3390/microbiolres16090202 - 6 Sep 2025

Abstract

Antimicrobial resistance (AMR) represents a threat to human, animal, and environmental health. This study evaluated the potential role of birds as AMR dispersers in white storks as a model species investigating dispersal between locations connected by their movements. Throughout a year, 346 samples [...] Read more.

Antimicrobial resistance (AMR) represents a threat to human, animal, and environmental health. This study evaluated the potential role of birds as AMR dispersers in white storks as a model species investigating dispersal between locations connected by their movements. Throughout a year, 346 samples were collected from two landfills (225 fecal samples) and two wetlands (93 fecal/28 water samples) based on satellite tracking data that confirmed continuous stork movements between foraging (landfill) and nighttime roosting (wetlands) locations. Samples were seeded in selective media with antibiotics for the isolation of antibiotic-resistant bacteria. A total of 313 isolates from 35 different bacterial species were obtained, with an AMR prevalence of 43.1% in fecal samples from landfills, 7.5% in fecal samples from wetlands, and 21.4% in water from wetlands. Multidrug resistant bacteria were only found in fecal samples (19.6% landfills/4.3% wetlands) and extended-spectrum beta-lactamase producing-bacteria were found exclusively in fecal samples from landfills with a marked presence during the fall migration period. Our study reveals marked differences in AMR prevalence and resistance phenotypes between study locations and fecal and water samples throughout the year, thus not supporting a clear role of storks as AMR dispersers. Nevertheless, similar changes in AMR phenotype prevalences during fall migration in stork faecal samples from one of the tested landfills and its paired wetland, and the significant increase in ESBL-producing Enterobacterales prevalence matching the arrival of migratory white storks in fall, underline the need for more in-depth genome-based studies to elucidate the role of white storks as dispersers or sentinels of AMR. Full article

(This article belongs to the Special Issue Diagnostics and Molecular Epidemiology of Infectious Diseases in Veterinary Medicine)

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41 pages, 826 KB

Open AccessReview

The Prevalence of ESKAPE Pathogens and Their Drug Resistance Profiles in Aquatic Environments Around the World

by Tunde Olarinde Olaniyan, Ana Verónica Martínez-Vázquez, Cesar Marcial Escobedo-Bonilla, Cristina López-Rodríguez, Patricia Huerta-Luévano, Oziel Castrejón-Sánchez, Wendy Lizeth de la Cruz-Flores, Manuel J. Cedeño-Castillo, Erick de Jesús de Luna-Santillana, Maria Antonia Cruz-Hernández, Gildardo Rivera and Virgilio Bocanegra-García

Microbiol. Res. 2025, 16(9), 201; https://doi.org/10.3390/microbiolres16090201 - 4 Sep 2025

Abstract

Antimicrobial-resistant bacteria (ARB) in the ESKAPE group include Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These pathogens continue to pose a global threat to human health. Urban and non-urban rivers affected by [...] Read more.

Antimicrobial-resistant bacteria (ARB) in the ESKAPE group include Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These pathogens continue to pose a global threat to human health. Urban and non-urban rivers affected by anthropogenic activities such as farming can act as reservoirs for ARB. The influx of wastewater from animal farms and irrigation processes can affect the normal microbiota in surrounding waterbodies. New bacteria, such as those in the ESKAPE family, may be introduced into these waterbodies, since most ESKAPE pathogens are domiciled in humans and animals. There is a dearth of information on the persistence of ESKAPE isolates and their associated health hazards in non-nosocomial settings. Therefore, this review aimed to collect data on the global distribution of ESKAPE pathogens in aquatic systems. PubMed and Google Scholar were searched for articles published from 2009 to 2025. A total of 76 studies published in peer-reviewed journals were included. Data were collected from 21 papers for E. faecium/faecalis, 12 for S. aureus, 15 for K. pneumoniae, 11 for A. baumannii, 8 for P. aeruginosa, and 9 for Enterobacter spp. The findings in this review will increase public health awareness on the significance of ESKAPE pathogens in aquatic systems. Full article

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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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