Microbiology Research

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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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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