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Beyond the Tropics: Clinical Presentation and Epidemiology of Travel-Associated Dengue Fever in a Non-Endemic European Setting -
Methane Production on Mars-Relevant Clay Minerals -
Identification and Genomic Localization of the cpe Gene in Clostridium perfringens -
A Structural View of Influenza Virus Ribonucleoprotein Complex and Its Functions
Journal Description
Microorganisms
Microorganisms
is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with Microorganisms, and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Microbiology) / CiteScore - Q1 (Virology)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.5 days after submission; acceptance to publication is undertaken in 3.3 days (median values for papers published in this journal in the first half of 2026).
- Recognition of Reviewers: Reviewers whose reports are timely and of high quality receive an APC discount voucher for a future publication in an MDPI journal. Become a reviewer.
- Companion journal for Microorganisms include: Applied Microbiology and Bacteria.
- Journal Cluster of Microbiology: Acta Microbiologica Hellenica, Applied Microbiology, Bacteria, Journal of Fungi, Microorganisms, Microbiology Research, Pathogens, Viruses, Fermentation and Germs.
Impact Factor:
4.7 (2025);
5-Year Impact Factor:
5.1 (2025)
Latest Articles
Divergent Association Pathways of Soil Organic Carbon Variation Under Grazing Exclusion Across Three Grassland Sites: Relationships with Microbial Network Structure and Community Assembly
Microorganisms 2026, 14(9), 2023; https://doi.org/10.3390/microorganisms14092023 (registering DOI) - 11 Sep 2026
Abstract
Grazing exclusion is a widely implemented restoration strategy for degraded grasslands, but its effects on soil organic carbon (SOC) remain highly variable, and the ecological pathways associated with these changes—particularly the roles of soil microorganisms—are still insufficiently understood. To investigate context-dependent SOC responses,
[...] Read more.
Grazing exclusion is a widely implemented restoration strategy for degraded grasslands, but its effects on soil organic carbon (SOC) remain highly variable, and the ecological pathways associated with these changes—particularly the roles of soil microorganisms—are still insufficiently understood. To investigate context-dependent SOC responses, we conducted a 12-year grazing exclusion study across three contrasting grassland sites representing an environmental gradient (temperate desert, temperate steppe, and mountain meadow) on the northern slope of the Tianshan Mountains. By integrating multidimensional vegetation–soil–microbe observations with microbial network analysis and community assembly approaches, we examined how plant, soil, and microbial characteristics were associated with SOC variation under grazing exclusion. Our results showed that grazing exclusion was associated with significant increases in surface SOC content across all three investigated sites (16–81%), but these increases corresponded to distinct site-specific ecological association patterns. At the temperate desert site, SOC variation was mainly associated with soil conditions and microbial characteristics, where soil moisture and nutrient availability, together with fungal network complexity, showed significant associations with SOC content. At the temperate steppe site, vegetation recovery represented an important ecological component associated with SOC variation, while bacterial community assembly patterns were also related to SOC differences. At the mountain meadow site, plant, soil, and microbial characteristics showed multiple associations with SOC variation. Across all sites, grazing exclusion was consistently associated with changes in microbial network structure and community assembly processes, and these microbial ecological characteristics showed significant statistical relationships with SOC content. Our findings indicate that SOC responses to grazing exclusion are context-dependent and involve different ecological association pathways across contrasting grassland ecosystems, highlighting the importance of considering local environmental conditions when evaluating grassland restoration outcomes and carbon management strategies.
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(This article belongs to the Section Environmental Microbiology)
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Open AccessReview
Mechanisms and Research Progress of Phosphate-Solubilizing Microorganisms in Promoting Sustainable Crop Production
by
Junfang Wang, Xin Yu, Peiqun Dong, Yifan Li, Ying Zhang and Gang Wang
Microorganisms 2026, 14(9), 2022; https://doi.org/10.3390/microorganisms14092022 (registering DOI) - 11 Sep 2026
Abstract
Phosphorus is an essential macronutrient for crop growth, but soil-available phosphorus is commonly lacking. Conventional chemical P fertilizers suffer from low utilization efficiency and dependence on finite phosphate rock reserves, necessitating the urgent development of green and efficient alternative strategies for phosphorus management.
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Phosphorus is an essential macronutrient for crop growth, but soil-available phosphorus is commonly lacking. Conventional chemical P fertilizers suffer from low utilization efficiency and dependence on finite phosphate rock reserves, necessitating the urgent development of green and efficient alternative strategies for phosphorus management. Phosphate-solubilizing microorganisms (PSMs) are capable of converting insoluble inorganic and organic phosphorus in soils into plant-available forms, thereby serving as key biological resources for enhancing phosphorus use efficiency, reducing dependence on chemical fertilizers, and promoting sustainable agricultural development. This review systematically covers the taxonomic diversity and multifaceted applications of PSMs, elucidates the mechanisms of inorganic P solubilization and organic P mineralization, and separately summarizes recent advances in functional genes involved in inorganic and organic P degradation. It further identifies key bottlenecks restricting PSM development and envisions the use of emerging technologies to transition PSM inoculants from empirical screening toward rationally designed precision deployment, thereby strengthening the scientific and technological foundation for enhancing phosphorus use efficiency and promoting green agricultural sustainability.
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(This article belongs to the Section Environmental Microbiology)
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Open AccessArticle
Root-Associated Bacterial Community Assembly and Functional Divergence of Four Native Halophytes in the Yellow River Delta Coastal Wetland
by
Yunpeng Liu, Jingyi Yu, Bo Zhou, Shichang Liu, Xinping Yu, Jun Wang and Shuai Shang
Microorganisms 2026, 14(9), 2021; https://doi.org/10.3390/microorganisms14092021 - 11 Sep 2026
Abstract
Coastal salt-marsh wetlands sustain diverse native halophytes whose root-associated microbiomes mediate plant adaptation to saline-alkaline environments. Host filtering and niche differentiation between rhizosphere soil and root endosphere jointly shape bacterial community assembly, yet comparative information for co-existing native halophytes in the northern Yellow
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Coastal salt-marsh wetlands sustain diverse native halophytes whose root-associated microbiomes mediate plant adaptation to saline-alkaline environments. Host filtering and niche differentiation between rhizosphere soil and root endosphere jointly shape bacterial community assembly, yet comparative information for co-existing native halophytes in the northern Yellow River Delta remains limited. Here, we collected 80 rhizosphere soil and root tissue samples from replicated plots in the Binzhou coastal salt-marsh wetland (northern Yellow River Delta), and applied Illumina MiSeq 16S rRNA sequencing to compare bacterial communities of four native pioneer halophytes (Phragmites australis, Suaeda salsa, Tamarix chinensis, Cynanchum chinense). Rhizosphere soils had markedly higher alpha diversity than root endospheres, with C. chinense rhizosphere reaching the highest diversity; Proteobacteria dominated roots, whereas Actinobacteriota, Bacteroidota and Chloroflexi accumulated in rhizosphere habitats. Root bacterial communities displayed greater interspecific divergence, and rhizospheres of S. salsa and P. australis possessed enhanced nitrogen metabolism and hydrocarbon degradation. LEfSe identified host-specific biomarkers, and Chloroflexi Subgroup_10 functioned as a core hub whereas no shared keystone genus existed across root endosphere networks, underscoring stronger host filtering in endophytic habitats. This study advances our understanding of host-driven bacterial assembly of native halophytes and provides baseline references for microbiome-assisted wetland restoration in the northern Yellow River Delta.
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(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions, 2nd Edition)
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Open AccessArticle
Deployment Readiness of Anammox for Wastewater Treatment with Potential Carbon-Saving Benefits: Environmental Risks, Monitoring Requirements and Implementation Pathways
by
Ya Zhou, Yi-Fei Liu, Ye Yu, Kai Wan, Yun Fang, Guo-Wei Wang, Jun-Xia Yu, Ru-An Chi and Chun-Qiao Xiao
Microorganisms 2026, 14(9), 2020; https://doi.org/10.3390/microorganisms14092020 - 11 Sep 2026
Abstract
Wastewater treatment systems are under increasing pressure to improve nitrogen removal while reducing carbon emissions, yet the deployment of anaerobic ammonium oxidation (anammox) remains constrained by uncertainty about technical readiness, operational robustness, nitrous oxide (N2O) emissions, life-cycle carbon performance, monitoring capacity,
[...] Read more.
Wastewater treatment systems are under increasing pressure to improve nitrogen removal while reducing carbon emissions, yet the deployment of anaerobic ammonium oxidation (anammox) remains constrained by uncertainty about technical readiness, operational robustness, nitrous oxide (N2O) emissions, life-cycle carbon performance, monitoring capacity, and transferability across wastewater contexts. This study uses dynamic topic modelling and trend assessment of 998 publications from 2001 to 2025 to synthesize deployment-relevant evidence for anammox-based wastewater treatment. The results indicate that the field has shifted from reactor start-up and process-parameter optimization toward microbial regulation, mainstream process integration, coupled nitrogen-removal strategies, and intelligent control. Building on these topic-evolution patterns and reported engineering evidence, this study provides an evidence-based qualitative appraisal of deployment-readiness signals and evidence gaps, distinguishing comparatively mature side-stream applications from mainstream systems that still require monitored demonstrations, transparent N2O accounting, life-cycle assessment, and locally validated operating data. The study argues that anammox should be evaluated as a technology with potential but conditional carbon-saving benefits: its potential carbon-saving benefits depend on operational evidence specific to each application stage, carbon-accounting credibility, and implementation capacity, rather than assuming that research activity alone justifies broad deployment.
Full article
(This article belongs to the Special Issue Microbial Solutions for Sustainable Resource Recovery and Environmental Remediation, 2nd Edition)
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Open AccessArticle
Sequential Screening of Lactic Acid Bacteria from Fermented Sour Bamboo Shoots and Their Effects on Patient-Derived Fecal Microbiota In Vitro
by
Junjie Li, Lianxian Ma, Rui Shi, Yuanrui Yu, Wenyan Zhang, Peng Zhu, Kaijie Kang and Liwen Jiang
Microorganisms 2026, 14(9), 2019; https://doi.org/10.3390/microorganisms14092019 - 11 Sep 2026
Abstract
Naturally fermented sour bamboo shoots represent a potential source of functionally active lactic acid bacteria (LAB). This study screened LAB from sour bamboo shoots and evaluated their potential to modulate patient-derived fecal microbiota in vitro. A total of 42 candidate isolates were obtained
[...] Read more.
Naturally fermented sour bamboo shoots represent a potential source of functionally active lactic acid bacteria (LAB). This study screened LAB from sour bamboo shoots and evaluated their potential to modulate patient-derived fecal microbiota in vitro. A total of 42 candidate isolates were obtained by morphological and physiological/biochemical screening. Five isolates showing intermediate antibiotic resistance were excluded, and the remaining 37 isolates were evaluated for gastrointestinal tolerance, antagonistic activity against enteric pathogens, and adhesion-related properties. Principal component analysis (PCA) identified nine strains for further evaluation. These strains were individually introduced into an in vitro colonic fermentation system prepared from pooled fecal samples of patients with bacterial diarrheal enteritis. After 48 h of fermentation, microbial community composition was assessed by 16S rRNA gene sequencing, and short-chain fatty acids (SCFAs) were quantified. LAB treatment was associated with a higher relative abundance of Firmicutes and a lower relative abundance of Proteobacteria. Compared with the mixed fecal suspension (MFS) control, the relative abundance of Escherichia–Shigella decreased to below 1% in the MRS-6, MRS-12, MRS-36, and MRS-46 groups, accompanied by increases in health-associated commensal genera including Blautia, Bifidobacterium, Faecalibacterium, and Bacteroides. Total SCFA concentrations reached 14.51, 13.55, and 12.16 mmol/L in the MRS-36, MRS-46, and MRS-6 groups, respectively, with the highest butyrate concentrations observed in the MRS-36 and MRS-46 groups. These findings establish a sequential screening framework linking in vitro functional phenotypes with validation in a complex fecal microbial community and identify candidate strains with promising microbiota- and SCFA-modulating potential.
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(This article belongs to the Special Issue Microbial Safety and Beneficial Microorganisms in Foods, 2nd Edition)
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Open AccessArticle
Agricultural Pesticide Exposure and Antimicrobial Resistance in Escherichia coli Across 28 European Countries: A Panel and Spatial Data Analysis
by
Meryem Toprak Tuncer, Tuba Bayir and Ahmet Atessahin
Microorganisms 2026, 14(9), 2018; https://doi.org/10.3390/microorganisms14092018 - 11 Sep 2026
Abstract
Antimicrobial resistance (AMR) is a growing global health threat, and agricultural pesticide exposure has been proposed as an environmental driver of resistance alongside antibiotic consumption. However, long-term, multi-country evidence linking pesticide use to AMR in Escherichia coli remains limited. Panel data analysis was
[...] Read more.
Antimicrobial resistance (AMR) is a growing global health threat, and agricultural pesticide exposure has been proposed as an environmental driver of resistance alongside antibiotic consumption. However, long-term, multi-country evidence linking pesticide use to AMR in Escherichia coli remains limited. Panel data analysis was applied to data from 28 European countries between 2013 and 2023 to examine lagged associations between agricultural pesticide use and E. coli resistance to fluoroquinolones, third-generation cephalosporins, aminoglycosides, and aminopenicillins, alongside spatial analysis of resistance distribution. Country-level panel data on E. coli resistance, antibiotic consumption, and pesticide use per cultivated area were compiled for 28 European countries, except for the aminopenicillin resistance model, for which Sweden was excluded owing to insufficient longitudinal data, yielding a 27-country panel for that indicator. Four random-effects generalized least squares (GLS) panel regression models were constructed for each resistance indicator, incorporating same-year and one-, two-, and three-year lagged pesticide use, adjusted for the corresponding antibiotic consumption. Global Moran’s I and Local Indicators of Spatial Association (LISA) analyses assessed spatial autocorrelation and clustering of resistance across countries. Pesticide use was significantly and positively associated only with fluoroquinolone resistance at a three-year lag; no significant associations were found for third-generation cephalosporin, aminoglycoside, or aminopenicillin resistance at any lag. Antibiotic consumption was consistently and positively associated with resistance across all models. All four resistance indicators showed statistically significant positive spatial autocorrelation, with persistent high-resistance clusters in Southeast Europe and low-resistance clusters in Northern Europe. Antibiotic consumption remains the dominant determinant of E. coli resistance, whereas pesticide use shows only a delayed, class-specific association restricted to fluoroquinolone resistance.
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(This article belongs to the Section Antimicrobial Agents and Resistance)
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Open AccessEditorial
Editorial for the Special Issue “Advances in Plant–Soil–Microbe Interactions”
by
Lily X. Zelaya-Molina and Sergio de los Santos-Villalobos
Microorganisms 2026, 14(9), 2017; https://doi.org/10.3390/microorganisms14092017 - 11 Sep 2026
Abstract
Plant–soil–microbe interactions are central to terrestrial ecosystems and are important for agriculture and environmental management [...]
Full article
(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)
Open AccessArticle
Seasonal Variations in Microbial Community Structure and Function in the Waters Along the Yangtze-to-Huaihe Water Diversion Project According to Metagenomics
by
Hezhou Chen, Bohan Xu, Qidi Xie, Zhen Gu, Shaozhuang Guo and Shuqin Chen
Microorganisms 2026, 14(9), 2016; https://doi.org/10.3390/microorganisms14092016 - 10 Sep 2026
Abstract
Water diversion projects can alleviate the uneven spatiotemporal distribution of water resources, but they may also impact functions of aquatic ecosystems in the waters along the route. Despite their importance, the temporal and spatial changes in multi-domain microbial community structure and function along
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Water diversion projects can alleviate the uneven spatiotemporal distribution of water resources, but they may also impact functions of aquatic ecosystems in the waters along the route. Despite their importance, the temporal and spatial changes in multi-domain microbial community structure and function along the route remain poorly understood. Metagenomics was employed to investigate the community structure and function of bacteria, archaea, and fungi in the aquatic environments along the Yangtze-to-Huaihe water diversion project in winter and summer seasons. The results showed that seasonal variations may drive a trade-off in the species diversity of bacterial and fungal communities. Seasonal variations altered microbial communities (especially for the bacteria), and exerted a greater influence on community structure than spatial factors. Microbial community composition was more sensitive to seasonal fluctuations than functional genes. The species spatial turnover played a dominant role in shaping microbial communities (especially for winter) in both seasons. Archaea, bacteria, fungi and KEGG functional genes all exhibited a positive correlation with some environmental factors in summer but not in winter. PLS-SEM indicated that water quality and microbial composition directly significantly impacted functional genes. This study offers a theoretical basis for maintaining the stability of water ecological microorganisms in water transfer projects.
Full article
(This article belongs to the Section Environmental Microbiology)
Open AccessArticle
Metagenomic Insights into Microbial Functional Potential Associated with Soil Carbon, Nitrogen, and Phosphorus Cycling Along an Elevational Gradient in a Warm-Temperate Forest
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Jingjing Wang, Siyuan Huangfu, Ruochen Li, Haibo Li, Hongyi He, Biaobing Chang, Huinan Ma, Haoqin Ma, Jiaxin Zhang, Ruohong Hou, Houjuan Song and Xiuqing Yang
Microorganisms 2026, 14(9), 2015; https://doi.org/10.3390/microorganisms14092015 - 10 Sep 2026
Abstract
Soil microbial functional potential is crucial to maintaining forest productivity and ecosystem functions. However, how microbially mediated soil nutrient cycling responds to environmental changes, particularly those caused by variations in elevation, remains poorly understood. Using the natural temperature gradient in a temperate mountain
[...] Read more.
Soil microbial functional potential is crucial to maintaining forest productivity and ecosystem functions. However, how microbially mediated soil nutrient cycling responds to environmental changes, particularly those caused by variations in elevation, remains poorly understood. Using the natural temperature gradient in a temperate mountain forest, this study investigated the differences in functional microbial groups and functional genes involved in soil carbon, nitrogen and phosphorus cycling along the elevation gradient, and analyzed the associations between environmental factors and these differences. The results showed that the low-elevation gradient (LE) had significantly higher abundances of genes involved in carbon degradation (pfkC, pgi1, and LSC1) but significantly lower abundances of those involved in carbon fixation (K18602, K18603, and K18604). Compared with the high-elevation gradient (HE), the LE had a significantly higher abundance of the nitrogen-cycle gene involved in organic degradation and synthesis (nao), but significantly lower abundances of denitrification (norB) and dissimilatory nitrate reduction genes (narG, narI, and napC). The abundances of the key genes involved in phosphorus metabolism (aphA and purO) were significantly higher at HE than at LE, whereas the abundance of the key gene associated with phosphorus transport (phnT) was significantly lower. The composition of the microbial community at the phylum level involved in carbon, nitrogen and phosphorus cycling at different elevations was similar, but the relative abundance of Thermoproteota and Nitrospirota increased significantly at HE. The annual average temperature, pH and carbon acquisition enzymes (β-glucosidase and β-D-cellobiosidase) were significantly associated with microbial community composition and functional genes related to carbon, nitrogen and phosphorus cycles. Additionally, genes involved in the carbon, nitrogen and phosphorus cycles were closely related through synergy and antagonism, especially the metabolic pathways encoded by purO, phnT and nrfA. These results provide metagenomic insights into the response patterns of microbial functional potential associated with soil carbon, nitrogen, and phosphorus cycling along an elevational gradient in a warm-temperate forest.
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(This article belongs to the Section Environmental Microbiology)
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Open AccessFeature PaperArticle
Growth-Phase-Dependent Shift in GABA Biosynthetic Pathways Under Temperature Stress in Isochrysis zhanjiangensis
by
Jiansen Luo, Lin Zhang, Jichang Han, Yumeng Wang, Jiaxin Yu, Jingbo Fan, Lulu Wang, Jiayi Cao, Kehou Pan and Jilin Xu
Microorganisms 2026, 14(9), 2014; https://doi.org/10.3390/microorganisms14092014 - 10 Sep 2026
Abstract
Temperature stress is a major constraint on the productivity of microalgae used in aquaculture. γ-Aminobutyric acid (GABA) is well-established as a key player in the stress tolerance of higher plants, yet its role in microalgae remains largely unexplored. Here, we examined the effects
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Temperature stress is a major constraint on the productivity of microalgae used in aquaculture. γ-Aminobutyric acid (GABA) is well-established as a key player in the stress tolerance of higher plants, yet its role in microalgae remains largely unexplored. Here, we examined the effects of low (15 °C), optimal (25 °C), and high (35 °C) temperatures on the GABA shunt in Isochrysis zhanjiangensis during the initial and mid-exponential growth phases. The results demonstrated that temperature stress significantly inhibited cell growth and photosynthetic efficiency (assessed by Fv/Fm and Fv’/Fm’), with soluble protein decreasing and soluble sugar accumulating. During the initial exponential phase, both low and high temperature stress triggered marked GABA accumulation, accompanied by coordinated increases in glutamate decarboxylase (GAD) and diamine oxidase (DAO) activities. Interestingly, the transcript levels of IzGAD and IzDAO decreased under these conditions, suggesting that GABA accumulation at this stage is predominantly governed by post-translational activation rather than transcriptional upregulation. Upon entry into the mid-exponential phase, a distinct phase-dependent shift in GABA biosynthetic regulation emerged. Under low temperature stress, GAD activity and IzGAD expression were both suppressed, whereas DAO activity and IzDAO transcripts increased significantly, indicating the transition to DAO-mediated GABA production as the dominant route. Under high temperature stress, both GAD and DAO activities increased, yet their corresponding gene transcription remained repressed, revealing a persistent asynchrony between enzyme activities and gene expression across both phases. Meanwhile, the expression of catabolic genes (IzGABA-T, IzSSADH1, and IzSSADH2) was consistently downregulated, further facilitating the net accumulation of GABA. Promoter analysis revealed multiple stress- and hormone-responsive cis-elements in these genes, implying a complex regulatory network. Collectively, our findings uncover a growth-phase-dependent reconfiguration of GABA biosynthetic pathways in I. zhanjiangensis under temperature stress. These insights provide a mechanistic basis for strain-specific temperature management in aquaculture applications.
Full article
(This article belongs to the Special Issue Molecular Mechanisms of Algal and Microbial Adaptation to Extreme Temperature Conditions)
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Open AccessReview
Innovative Applications of Artificial Intelligence in Bacteriophage Research: A New Chapter in Future Medicine
by
Dapeng Yang, Xin Yuan and Yubao Li
Microorganisms 2026, 14(9), 2013; https://doi.org/10.3390/microorganisms14092013 - 10 Sep 2026
Abstract
As the crisis of antibiotic resistance escalates, phage therapy has regained attention as an alternative strategy. Artificial intelligence (AI) technologies offer new avenues to overcome the bottlenecks inherent in traditional bacteriophage research. This review summarizes the multi-dimensional innovative applications of machine learning, deep
[...] Read more.
As the crisis of antibiotic resistance escalates, phage therapy has regained attention as an alternative strategy. Artificial intelligence (AI) technologies offer new avenues to overcome the bottlenecks inherent in traditional bacteriophage research. This review summarizes the multi-dimensional innovative applications of machine learning, deep learning, and large biological models in phage studies. In the fields of phage recognition and genomics, support vector machines (SVMs), convolutional neural networks (CNNs), and pre-trained protein language models can all achieve recognition accuracy rates of over 90%. Furthermore, tools such as DeepHost and VirSorter2 can efficiently identify phage sequences, annotate functional genes, and predict hosts at the species or strain levels. For clinical translation, AI integrates patient characteristics, bacterial phenotypes, and phage profiles to customize cocktail regimens for individualized phage therapy. Graph neural network-based models like DeepPBI-KG integrate multi-omics knowledge graphs to precisely predict phage-host interactions (PHIs), whereas agent-based simulation and defense protein predictors forecast phage resistance evolution. Additionally, generative AI can support the de novo design of functional phage genomes and mine massive unannotated virome dark matter. Nevertheless, this cross-disciplinary field faces significant constraints, including uneven and biased sequencing datasets, insufficient model interpretability, and dual-use biosafety ethical risks accompanied by unclear algorithm accountability and incomplete global supervision systems. Future research should optimize standardized multimodal databases, develop explainable AI algorithms, and establish cross-disciplinary ethical governance frameworks to facilitate closed-loop verification between computational prediction and wet-lab experiments. In conclusion, the deep integration of AI and phage biology provides revolutionary strategies to tackle multidrug-resistant infections and advances the clinical transformation of phage precision medicine.
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(This article belongs to the Special Issue Artificial Intelligence as a Tool for Combating Antimicrobial Resistance)
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Open AccessArticle
Seasonal Dynamics of ‘Candidatus Phytoplasma prunorum’ in Selected Prunus Species Revealed by Quantitative PCR
by
Peter Morvay, Tomáš Kiss, Ivo Ondrášek, Erika Slámová, Eliška Zezulová and Tomáš Nečas
Microorganisms 2026, 14(9), 2012; https://doi.org/10.3390/microorganisms14092012 - 10 Sep 2026
Abstract
The distribution of ‘Candidatus Phytoplasma prunorum’, a phloem-limited pathogen, varies among plant tissues during the year, but knowledge about quantitative comparisons of its presence in roots and above-ground tissues across Prunus species remains limited. The variation in ‘Ca. P. prunorum’ in four
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The distribution of ‘Candidatus Phytoplasma prunorum’, a phloem-limited pathogen, varies among plant tissues during the year, but knowledge about quantitative comparisons of its presence in roots and above-ground tissues across Prunus species remains limited. The variation in ‘Ca. P. prunorum’ in four Prunus species was monitored monthly during 2025 using quantitative PCR-based absolute quantification. Roots, one-year-old shoots and annual shoots were sampled monthly from 21 infected trees of Prunus armeniaca, Prunus domestica, Prunus persica and Prunus salicina. Phytoplasma titer varied with plant part and sampling month, and differences were also observed among the examined host groups. Because cultivar and rootstock were linked to species, these differences cannot be attributed to species alone. Roots provided the most consistent year-round detection, whereas above-ground tissues showed stronger monthly variation during the studied period. P. domestica displayed the most distinct pattern: roots remained frequently positive, while one-year-old shoots and particularly annual shoots had lower detection rates and lower phytoplasma titers. Multilocus genotyping detected ten multilocus profiles, but their uneven distribution among only 21 trees precluded a reliable evaluation of their relationship with phytoplasma titer or symptom expression.
Full article
(This article belongs to the Special Issue Phytoplasmas and Phytoplasma Diseases)
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Open AccessArticle
Multicentre Evaluation of Cepheid Xpert® Research-Use-Only Panel for Molecular Rapid Detection of Gastrointestinal Pathogens
by
Olivier Dauwalder, Jan Kehrmann, Stéphane Corvec, Maroussia Roelens, Tiphaine Roussel-Gaillard, Edoardo Bixio, Jan Buer, Elisa Baillemont, Martin Prodel, Christophe Martinaud and Valeria Cento
Microorganisms 2026, 14(9), 2011; https://doi.org/10.3390/microorganisms14092011 - 10 Sep 2026
Abstract
Rapid and accurate identification of enteric pathogens is essential for the management of acute infectious diarrhoeal diseases. Multiplex PCR panels have emerged as first-line screening tools to conventional stool culture by providing broad pathogen coverage and shorter turnaround times. This study evaluated the
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Rapid and accurate identification of enteric pathogens is essential for the management of acute infectious diarrhoeal diseases. Multiplex PCR panels have emerged as first-line screening tools to conventional stool culture by providing broad pathogen coverage and shorter turnaround times. This study evaluated the diagnostic performance of the Cepheid Xpert gastrointestinal (GI) research-use-only (RUO) panel in routine clinical practice across multiple European centres. A multicentre study was conducted in four hospitals across France, Germany and Italy. Stool specimens collected as part of routine care were tested using local standard-of-care (SoC) methods, including conventional stool culture, BDMax® Enteric Panels, or BioFire FilmArray® GI Panel, and subsequently analysed using the Cepheid Xpert GI RUO panel. A total of 11 bacterial, viral and parasitic enteropathogens were targeted. Discordant results underwent additional testing, and a consensus result based on a two-out-of-three agreement rule was used as the reference standard. Diagnostic performance metrics, agreement with SoC methods, microbiological findings and turnaround times were assessed. Of 508 samples, 115 (22.6%) were identified as positive for at least one pathogen according to the consensus result, including 12 samples with co-detection of more than one pathogen (10.4% of positive samples), resulting in a total of 128 pathogens detected. The most frequently detected pathogens were Campylobacter spp. (37 specimens), Norovirus (26 specimens), and Salmonella spp. (25 specimens). Compared with the consensus reference standard, Xpert achieved an overall sensitivity of 98% (95% CI: 94–100%), specificity of 100% (95% CI: 100–100%), positive predictive value of 95% (95% CI: 90–98%), and negative predictive value of 100% (95% CI: 100–100%). Sensitivity was ≥95% and specificity ≥99% for all evaluable targets. Agreement with routine diagnostic methods was high, with overall positive and negative percent agreements exceeding 90% and a Cohen’s kappa coefficient of 0.91. Median analytical turnaround time was 1 h 18 min for Xpert, compared with 3 h for BDMax, 1 h 15 min for BioFire and 48 h for conventional stool culture. The Cepheid Xpert GI (RUO) panel provided highly accurate detection of enteric pathogens across heterogeneous European diagnostic settings and reduced turnaround time by more than 95% compared with conventional stool culture. A future IVD version of this test could provide rapid and accurate detection of enteric pathogens for potential routine management of patients with suspected acute infectious gastroenteritis.
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(This article belongs to the Section Gut Microbiota)
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Open AccessArticle
Synergistic Antimicrobial and Antibiofilm Activity Optimization of a Thymus vulgaris–Moringa oleifera–Echinacea purpurea Ternary Ethanolic Extract Blend Against Candida albicans and Streptococcus mutans Using L-Optimal Mixture Design
by
Khadijah A. Altammar
Microorganisms 2026, 14(9), 2010; https://doi.org/10.3390/microorganisms14092010 - 10 Sep 2026
Abstract
Antimicrobial resistance and biofilm-associated oral infections require multi-target therapeutic strategies beyond single-extract herbal testing. Using the L-optimal mixture design approach, we optimized a ternary combination of Thymus vulgaris, Moringa oleifera, and Echinacea purpurea ethanolic extracts against Candida albicans and Streptococcus mutans
[...] Read more.
Antimicrobial resistance and biofilm-associated oral infections require multi-target therapeutic strategies beyond single-extract herbal testing. Using the L-optimal mixture design approach, we optimized a ternary combination of Thymus vulgaris, Moringa oleifera, and Echinacea purpurea ethanolic extracts against Candida albicans and Streptococcus mutans, then characterized the optimized blend’s phytochemistry, antimicrobial and antibiofilm efficacy, time–kill pharmacodynamics, antioxidant capacity, and cytotoxic safety. Through HPLC, apigenin, chlorogenic acid, resorcinol, and ferulic acid were identified as dominant constituents. The optimal blend (Run 14: T. vulgaris 0.331, M. oleifera 0.318, E. purpurea 0.352) achieved a fractional inhibitory concentration index of 0.50 against both organisms, maximum inhibition zones of 3.10 cm (C. albicans) and 4.10 cm (S. mutans), biofilm inhibition of up to 93.2 ± 2.1% for C. albicans and 78.4 ± 2.8% for S. mutans, and confirmed fungicidal and bactericidal activity within 48 and 24 h, respectively. DPPH scavenging ranged from 55.19 to 68.73%, and oral epithelial cells (OEC) viability exceeded 83% at 300 µg/mL. All assays included three independent biological replicates; statistical significance was defined as p < 0.05. These findings identify the T. vulgaris–M. oleifera–E. purpurea blend as a synergistic, multi-target antimicrobial candidate with a favorable preliminary safety profile, supporting further development and evaluation against clinical isolates for oral fungal and bacterial infections.
Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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Open AccessArticle
Integrating Microbial Indicators from High-Throughput Sequencing into Soil Quality Index: A Case Study in a Restored Mining Area
by
Zhengjun Feng, Chaolong Ma, Shengxin Yan, Wenhui Liu, Peiyin Li, Yan Zou, Dashdorj Munkhbat and Huiping Song
Microorganisms 2026, 14(9), 2009; https://doi.org/10.3390/microorganisms14092009 - 10 Sep 2026
Abstract
The Soil Quality Index (SQI) is a vital tool for evaluating soil quality; however, traditional approaches seldom integrate microbial data from high-throughput sequencing—commonly used to characterize soil microbial communities—into the SQI framework. This study enhances the SQI by incorporating microbial indicators derived from
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The Soil Quality Index (SQI) is a vital tool for evaluating soil quality; however, traditional approaches seldom integrate microbial data from high-throughput sequencing—commonly used to characterize soil microbial communities—into the SQI framework. This study enhances the SQI by incorporating microbial indicators derived from high-throughput sequencing, establishing a more comprehensive evaluation system. We collected soil samples from mining areas and analyzed their fundamental physicochemical properties and microbial indicators. Four SQI models were constructed using different indicator sets: (1) only physicochemical properties (T-SQI); (2) physicochemical properties and bacterial α-diversity (α-SQI); (3) physicochemical properties, α-diversity, and relative abundances of the top five abundant bacteria (αMA-SQI); and (4) physicochemical properties, α-diversity, and relative abundances of the top five bacteria based on LDA scores (αBM-SQI). Results demonstrated that integrating multi-level microbial indicators improved the rationality of soil quality rankings and significantly strengthened correlations with α-diversity. Gemmatimonadota was consistently selected in the Minimum Data Set (MDS) for both αMA-SQI and αBM-SQI, highlighting its ecological importance. Statistically, microbial indicators at the order and family levels were most suitable for inclusion in the MDS, as their results deviated least from the total dataset. In conclusion, incorporating microbial diversity across taxonomic levels refines the SQI, enabling a more accurate and holistic assessment of soil health.
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(This article belongs to the Section Environmental Microbiology)
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Open AccessArticle
Lactococcus G423 Improves Lipid Metabolism in Broilers Through the Gut Microbiota and AMPK Signaling Pathway
by
Bo Pang, Ruixiang Li, Xinyu Wang, Weitong Guan, Wei Ma, Chunqiang Wang, Desheng Li and Mi Wang
Microorganisms 2026, 14(9), 2008; https://doi.org/10.3390/microorganisms14092008 - 10 Sep 2026
Abstract
This study aimed to elucidate the role of Lactococcus G423 in regulating the AMPK (AMP-activated protein kinase) signaling pathway and gut microbiota, and to investigate the mechanisms underlying its potential to improve lipid metabolism in broilers. In this trial, 960 one-day-old Arbor Acres
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This study aimed to elucidate the role of Lactococcus G423 in regulating the AMPK (AMP-activated protein kinase) signaling pathway and gut microbiota, and to investigate the mechanisms underlying its potential to improve lipid metabolism in broilers. In this trial, 960 one-day-old Arbor Acres (AA) broilers were randomly assigned to one of three groups: a control group (CON), a low-dose Lactococcus G423 group (Lac-L), and a high-dose Lactococcus G423 group (Lac-H). Each group consisted of eight replicates, with 40 individuals per replicate. Compared with the CON group, the Lac-L and Lac-H groups showed no significant differences in ADFI (Average Daily Feed Intake), ADG (Average Daily Gain), FCR (Feed Conversion Ratio), breast muscle yield, leg muscle yield, or abdominal fat yield (p > 0.05). Compared with the control group, neither Lac-L nor Lac-H affected serum TG (Triglyceride) or LDL (Low-Density Lipoprotein) levels (p > 0.05). However, both Lac-L and Lac-H significantly decreased serum CHO (Cholesterol) and increased serum HDL (High-Density Lipoprotein) (p < 0.05). Regarding the AMPK signaling pathway, both the Lac-L and Lac-H groups significantly downregulated the hepatic mRNA expression of Acetyl-CoA carboxylase (ACC) (p < 0.05). The Lac-L groups significantly increased the mRNA expression of AMP-activated protein kinase (AMPK) and Sterol Regulatory Element-Binding Protein 1 (SREBP1) (p < 0.05), and the Lac-H groups significantly increased the mRNA expression of Apolipoprotein A1 (APOA1) and Protein kinase B (PKB) (p < 0.05) and significantly reduced the mRNA expression of Fatty acid-binding protein 1 (FABP1) (p < 0.05), compared to the CON group. Gut microbiota analysis indicated that both treatment groups exhibited significantly increased α-diversity indices (p < 0.05) and altered microbial composition at an order level comparable with that of the CON group. Specifically, the abundances of beneficial families such as Lachnospirales and Lactobacillales were elevated, while significant changes were observed in other taxa including Ruminococcaceae and Akkermansiaceae (p < 0.05). These changes corresponded with significant differences in the MDI and GMHI (p < 0.05). In conclusion, Lactococcus G423 may regulate lipid metabolism in broilers through the combined modulation of the AMPK signaling pathway and the gut microbiota. Specifically, Lactococcus G423 appears to regulate broiler lipid metabolism by modulating the gut microbiota–hepatic lipid metabolism axis.
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(This article belongs to the Section Food Microbiology)
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Open AccessArticle
Th1 and Th17 Responses to LTB and Colonization Factors Following Oral ETEC Vaccination
by
Joanna Kaim and Anna Lundgren
Microorganisms 2026, 14(9), 2007; https://doi.org/10.3390/microorganisms14092007 - 10 Sep 2026
Abstract
T helper cells (Th) are central to mucosal IgA induction and key targets for modulation by vaccine adjuvants. To improve understanding of cellular mechanisms underlying mucosal vaccine-induced immunity, we analyzed antigen-specific peripheral blood Th responses elicited by the oral enterotoxigenic Escherichia coli (ETEC)
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T helper cells (Th) are central to mucosal IgA induction and key targets for modulation by vaccine adjuvants. To improve understanding of cellular mechanisms underlying mucosal vaccine-induced immunity, we analyzed antigen-specific peripheral blood Th responses elicited by the oral enterotoxigenic Escherichia coli (ETEC) vaccine ETVAX, administered with or without the double mutant heat-labile toxin (dmLT) adjuvant. ETVAX, consisting of inactivated E. coli overexpressing colonization factors CFA/I, CS3, CS5, and CS6 with a heat-labile toxin B-subunit toxoid, was given orally in two doses to adult volunteers, either alone or with 10 or 25 µg dmLT. Antigen-specific Th-associated cytokine responses were assessed in stimulated peripheral blood mononuclear cells isolated from 15 to 18 individuals/group using ELISA and electrochemiluminescence assays. ETVAX predominantly induced Th1 (IFN-γ) and Th17 (IL-17A) responses, with minimal Th2-associated cytokines. Responses were markedly reduced after CD4+ T-cell depletion, supporting a Th cell origin. The strongest responses targeted LTB and CS3, with IFN-γ responses detected in 60–80% and IL-17A in 40–60% across all vaccinees. Responses to CFA/I, CS5 and CS6 were generally weaker. Exploratory comparisons suggested broader IFN-γ responses and more consistent IFN-γ and IL-17A responses to lower-dose antigens, particularly CS6, in recipients receiving vaccine plus 10 µg dmLT. These trends paralleled IgA antibody-secreting cell response patterns, with significantly enhanced IgA responses to CS6 in the vaccine plus 10 µg dmLT group. In conclusion, ETVAX induces antigen-specific Th1- and Th17-type responses in peripheral blood, supporting a role for cellular immunity in mucosal responses to oral ETEC vaccines.
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(This article belongs to the Special Issue Advancement in Enterotoxigenic Escherichia coli (ETEC) Vaccines)
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Open AccessArticle
Inoculation with Stenotrophomonas maltophilia LIMN and Enterobacter roggenkampii LCMG Enhances Maize (Zea mays L.) Yield and Reduces Nitrogen Fertilizer Dependence in Nutrient-Limited Soils of Semi-Arid Regions
by
Odilón Gayosso Barragán, Griselda Chávez Aguilar, Deli Nazmín Tirado González, Roberto Reynoso Santos, Ismael Fernando Chávez Díaz, Lily Xochilt Zelaya-Molina, Gustavo Tirado Estrada and Luis Yobani Gayosso Rosales
Microorganisms 2026, 14(9), 2006; https://doi.org/10.3390/microorganisms14092006 - 10 Sep 2026
Abstract
Excessive nitrogen (N) fertilization in maize (Zea mays L.) production causes environmental degradation, particularly in semi-arid regions where high chemical inputs are necessary to maintain crop production. Plant growth-promoting rhizobacteria (PGPR) could reduce the optimal N fertilization doses. This investigation aimed to
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Excessive nitrogen (N) fertilization in maize (Zea mays L.) production causes environmental degradation, particularly in semi-arid regions where high chemical inputs are necessary to maintain crop production. Plant growth-promoting rhizobacteria (PGPR) could reduce the optimal N fertilization doses. This investigation aimed to isolate bacteria, screen them for plant growth-promoting traits, and evaluate their potential effects on maize grain under different chemical N fertilization doses. Isolates Stenotrophomonas maltophilia LIMN and Enterobacter roggenkampii LCMG demonstrated multifunctional growth-promoting traits in vitro, including N2 fixation, indole-3-acetic acid and siderophore production, potassium solubilization, and desiccation tolerance, with E. roggenkampii LCMG also solubilizing inorganic phosphate. A field trial across four chemical N fertilization rates (0, 40, 80, and 120 kg N ha−1) revealed that single bacterial inoculation without N fertilizer matched or exceeded uninoculated controls receiving up to 80 kg of N ha−1 (the standard recommendation). Specifically, S. maltophilia LIMN combined with the recommended rate of 80 kg N ha−1 achieved the maximum grain yield (4601.2 kg DM ha−1), outperforming uninoculated controls (without PGPR) receiving excessive fertilization at 120 kg N ha−1 (3760.4 DM ha−1). Although maize plants benefited from inoculation with S. maltophilia LIMN or E. roggenkampii LCMG, achieving similar or better yields than crops fertilized with high chemical N inputs under stress factors such as deficiency of moisture, low-nutrient soils, and high temperatures, the present study did not test the pathogenicity and biosecurity of S. maltophilia or E. roggenkampii in crops; therefore, the results are not a direct recommendation of their use as biofertilizers before novel studies to assess all the limitations and the potential to reduce N dependency in order to design novel sustainable strategies for crop production.
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(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)
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Open AccessEditorial
Editorial for the Special Issue “Advances in Microbial and Plant Biotechnology”
by
Svetlana Veselova and Igor Maksimov
Microorganisms 2026, 14(9), 2005; https://doi.org/10.3390/microorganisms14092005 - 10 Sep 2026
Abstract
Introduction [...]
Full article
(This article belongs to the Special Issue Advances in Microbial and Plant Biotechnology)
Open AccessArticle
Antimicrobial Resistance Profiles, Resistance Genes, and Their Association with Bacteriophage Susceptibility Among Vibrio parahaemolyticus Isolates from Zhanjiang Shrimp Aquaculture Farms
by
Lukman Iddrisu, Baochen Chai, Evodia Moses Mkulo, Salifu Ibrahim, Felix Danso, Muqadas Altaf, Muhammad Fahad Khan, Bingyu Zhang, Shumei Zhang, Jiesen Su, Yinyan Chen, Zhijia Fang and Jianzhi Ye
Microorganisms 2026, 14(9), 2004; https://doi.org/10.3390/microorganisms14092004 - 9 Sep 2026
Abstract
Vibrio parahaemolyticus is an important foodborne and aquaculture-associated pathogen, and its increasing antimicrobial resistance threatens shrimp production, seafood safety, and public health. Although bacteriophages have emerged as a potential solution to the growing challenge of antimicrobial resistance, whether antibiotic resistance is associated with
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Vibrio parahaemolyticus is an important foodborne and aquaculture-associated pathogen, and its increasing antimicrobial resistance threatens shrimp production, seafood safety, and public health. Although bacteriophages have emerged as a potential solution to the growing challenge of antimicrobial resistance, whether antibiotic resistance is associated with phage tolerance remains unclear. This study characterized antimicrobial resistance profiles and resistance genes in Vibrio parahaemolyticus isolates from Zhanjiang shrimp aquaculture farms and evaluated their association with bacteriophage susceptibility. A total of 132 isolates were tested against 18 antibiotics, while molecular and phage-related analyses were performed on 132 isolates. High resistance was observed against kanamycin (95.5%), sulfamethoxazole (94.7%), cefazolin (78.8%), imipenem (78.8%), amoxicillin (70.5%), and ampicillin (65.2%). Multidrug resistance was detected in 131/132 isolates (99.24%), indicating an extensive resistance burden. PCR analysis showed high detection rates of aphA (100.00%), sul1 (99.24%), blaTEM (98.48%), blaOXA (73.48%), blaCTX-M (53.03%), qnrA (45.45%), tetA (37.88%), and tetB (21.21%). Phage response analysis showed that 70.45% and 68.18% of isolates were phage-resistant at 4 h and 5 h, respectively. Genes potentially associated with phage–host interactions were also detected, with luxS showing the highest frequency (85.61%). Association analysis revealed significant links between tetA, tetB, blaOXA, and bacteriophage responses. These findings suggest that antimicrobial resistance and reduced phage susceptibility can co-occur among V. parahaemolyticus isolates recovered from shrimp farms in Zhanjiang, highlighting the need for regional resistance surveillance and careful phage selection.
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(This article belongs to the Special Issue Foodborne Pathogens: Detection, Resistance, Risk Assessment and Control)
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