Current Research in Microbial Sciences最新文献

{"title":"Bacteriophage cocktail in drinking water suppresses systemic avian pathogenic Escherichia coli infection and pathology in laying hens","authors":"Mawra Gohar ,&nbsp;Jae Eun Hyun ,&nbsp;Kat R. Smith ,&nbsp;Waseem Shaukat ,&nbsp;Matthew Waldner ,&nbsp;Nabiha Mehina ,&nbsp;Sidra Moqaddes ,&nbsp;Yiran Ding ,&nbsp;Reham M. Abd-Elsalam ,&nbsp;John Morris Fairbrother ,&nbsp;Trevor Alexander ,&nbsp;Charles Martin Nyachoti ,&nbsp;M. Faizal Abdul Careem ,&nbsp;Yan Dong Niu","doi":"10.1016/j.crmicr.2026.100569","DOIUrl":"10.1016/j.crmicr.2026.100569","url":null,"abstract":"<div><div>Avian colibacillosis, caused by avian pathogenic <em>Escherichia coli</em> (APEC), results in high morbidity and mortality and reduces egg production in domestic poultry. Increasing antimicrobial resistance (AMR) and restriction on antibiotic use necessitate alternative disease control strategies. We evaluated the efficacy of a phage cocktail (<em>Tequatrovirus, Sashavirus</em>, and an unclassified Caudoviricetes) at a multiplicity of infection &gt; 100, administered for 4 days in drinking water (DW) or as a single intramuscular (IM) treatment, in preventing experimental APEC infection (10⁸ CFU given intravenously) in specific–pathogen–free laying hens (25–27 weeks old, n=10 per experimental group). Phage treatment reduced mortality from 20% to 0 and morbidity by 30%. Birds receiving phages in DW showed a marginal trend toward reduced weight loss (<em>p</em> = 0.063) than those in IM or APEC–only groups at 4 days post–infection. Macroscopic lesions were present in 6.7–11.7% of organs in APEC–only and IM groups but were absent in DW–treated hens. In the DW group, median histopathological scores were lower, with the most notable reduction (<em>p</em> = 0.006) in the spleen. Across organs, concentrations of recovered phages were similar between DW and IM groups (<em>p</em> = 0.227); however, in the DW group, 1.3−2.1 log₁₀ PFU/g of phages were detected in all tissues except blood. Based on 16S rRNA gene sequencing, neither IM nor DW phage treatments altered the overall general bacterial structure or population in the cecum. We conclude that this phage cocktail, administered via DW, lysed APEC without disrupting gut microbiota, improved overall bird health and welfare, and protected internal organs from APEC invasion.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100569"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147448637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing endometrial microbiota in endometriosis: culturomics and sequencing analysis of receptive-phase tissue","authors":"A. Canha-Gouveia ,&nbsp;C.M. Tenorio ,&nbsp;T. Rööp ,&nbsp;S. Kõljalg ,&nbsp;I. Smidt ,&nbsp;E. Sepp ,&nbsp;J. Štšepetova ,&nbsp;M. Saare ,&nbsp;S. Vela ,&nbsp;I. Pérez-Prieto ,&nbsp;E. Vargas ,&nbsp;J. Mozas ,&nbsp;A. Clavero ,&nbsp;A. Sola-Leyva ,&nbsp;A. Salumets ,&nbsp;R. Mändar ,&nbsp;S. Altmäe","doi":"10.1016/j.crmicr.2026.100593","DOIUrl":"10.1016/j.crmicr.2026.100593","url":null,"abstract":"<div><div>Endometriosis has been associated with alterations in the reproductive tract microbiota, yet studies focusing on the endometrial microbiome remain inconsistent, partly due to the low-biomass nature of this niche and methodological heterogeneity. In this prospective pilot study, we investigated whether the receptive-phase endometrial microbiota differs between women with and without endometriosis using a combined culturomics and 16S rRNA gene sequencing approach. Endometrial samples were collected from 20 women undergoing fertility assessment, including 10 women with a previous diagnosis of endometriosis and 10 controls with male factor infertility. Biopsies were used for culturomics and Tao brush samples for sequencing, both obtained during the mid-secretory phase. Viable bacterial growth was recovered from 19 of 20 biopsies, yielding approximately 2500 colonies corresponding to 40 non-redundant species. Direct plating and aerobic pre-incubation shared around 45% of detected species, with pre-incubation enhancing species recovery but limiting quantitative comparisons. Bacterial load estimated from direct cultures showed wide inter-individual variability and no significant differences between groups, consistent with 16S rRNA gene sequencing results, which also revealed no clear differences in microbial diversity or overall community composition within this cohort. Only a limited overlap was observed between taxa detected by culture and sequencing, highlighting the complementarity and methodological biases of each approach. Overall, this study demonstrates the feasibility of recovering viable bacteria from receptive-phase endometrial samples and supports the combined use of culturomics and sequencing as complementary tools for studying microbiota in low-biomass uterine environments. These findings should, however, be interpreted considering the exploratory design and limited sample size.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100593"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147656313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bifidobacterium stercoris KC84 attenuates IBS-D-like symptoms via modulation of serotonin-related pathways and dendritic cell-mediated IFN-β induction","authors":"Seokcheon Song ,&nbsp;Myeonghwan Han ,&nbsp;Kwanwoo Moon ,&nbsp;Haeseong Lee ,&nbsp;Sungchan Ha ,&nbsp;Juseok Seo ,&nbsp;Seungki Lee ,&nbsp;Soyong Jang ,&nbsp;Sang Kyun Lim ,&nbsp;Nayoung Kim ,&nbsp;GwangPyo Ko","doi":"10.1016/j.crmicr.2026.100603","DOIUrl":"10.1016/j.crmicr.2026.100603","url":null,"abstract":"<div><div>Irritable bowel syndrome with diarrhea (IBS-D) is a prevalent disorder that significantly impairs quality of life, yet therapeutic advances remain limited. Serotonin dysregulation, primarily driven by enterochromaffin cells in the intestinal epithelium, is central to IBS-D pathogenesis. We hypothesized that targeted modulation of enterochromaffin cell activity through microbiome-based interventions could provide a novel treatment approach. Here, we screened 128 <em>Bifidobacterium</em> isolates and identified <em>B. stercoris</em> KC84 as a promising candidate. KC84 alleviated IBS-D-like symptoms in both chemically and stress-induced models, accompanied by changes in serotonin-related markers. Transcriptomic analysis revealed activation of type I interferon (IFN)-associated pathways, consistent with <em>ex vivo</em> evidence of KC84-induced IFN-β secretion, predominantly from CD11b^- dendritic cells. Furthermore, IFN-β treatment attenuated contractile activity in colonic smooth muscle cells. Collectively, these findings suggest that KC84 mitigates IBS-D-like symptoms, potentially through modulation of serotonin-related pathways and activation of a KC84-IFN-β-smooth muscle regulatory axis, supporting KC84 as a mechanism-guided probiotic candidate for IBS-D therapy.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100603"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147951462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Manganese homeostasis supports Stenotrophomonas maltophilia oxidative stress defense and replication in Acanthamoeba castellanii phagosomes","authors":"Fulvia-Stefany Argueta-Zepeda ,&nbsp;Javier Rivera ,&nbsp;Julio César Valerdi-Negreros ,&nbsp;Christopher Rensing ,&nbsp;Pablo Vinuesa","doi":"10.1016/j.crmicr.2026.100604","DOIUrl":"10.1016/j.crmicr.2026.100604","url":null,"abstract":"<div><div>Manganese homeostasis is essential for the environmental adaptability and pathogenic potential of <em>Stenotrophomonas maltophilia</em>, a bacterium that thrives across diverse and fluctuating environments. Here, we characterize the manganese homeostasis network of <em>S. maltophilia</em> strain Sm18, identifying a coordinated system that integrates conserved transporters with previously unrecognized candidate components. Central to this system is an MntR-controlled gene module that includes the canonical Mn²⁺ importer MntH and exporter MntP, together with a TonB-dependent receptor (TBDR) and a periplasmic thioredoxin-fold protein (pTFP), both representing novel protein families with restricted phylogenetic distribution. Transcriptomic analyses under varying Mn²⁺ and Fe²⁺ conditions revealed a tight interplay between these metals, highlighting the ferrophilic nature of <em>S. maltophilia</em> and the differential regulation of module components. Notably, the TBDR-pTFP locus is strongly induced under combined Mn²⁺ and Fe²⁺ limitation, suggesting a specialized role in metal acquisition under nutrient-restricted conditions. Functional analyses showed that MntP contributes to protection from Mn toxicity even at sub-inhibitory concentrations, whereas MntH supports growth under oxidative stress and promotes intracellular replication within <em>Acanthamoeba castellanii</em> phagosomes. Together, these findings identify a Mn-responsive module candidate associated with manganese homeostasis and provides new insight into mechanisms that support <em>S. maltophilia</em> adaptation to metal-limited and host-associated environments.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100604"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147995696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional insights into nucleoside diphosphate kinases encoded by two ndk paralogs in Waddlia chondrophila","authors":"Giti Ghazi-Soltani,&nbsp;Carole Kebbi-Beghdadi,&nbsp;Simone E. Adams,&nbsp;Gilbert Greub","doi":"10.1016/j.crmicr.2026.100635","DOIUrl":"10.1016/j.crmicr.2026.100635","url":null,"abstract":"<div><div>The <em>Chlamydiota</em> phylum consists of obligate intracellular bacteria, including well-known pathogens and emerging environmental species, with diverse host ranges and metabolic capabilities. Among these bacteria, the gene which encodes nucleoside diphosphate kinase, <em>ndk</em> is present in variable numbers. While most chlamydial species carry a single paralog of <em>ndk</em>, some species have two paralogs. In Waddlia chondrophila, the two Ndk proteins encoded by <em>ndk</em> paralogs retain conserved kinase motifs but differ in subcellular localization, suggesting divergent functional roles. According to localization studies performed in heterologous expression systems, WcNdk1 is confined to the bacteria-containing vacuole and probably supports nucleotide metabolism, while WcNdk2 localizes to the host nucleus, perinuclear space, and Golgi apparatus, suggesting involvement in host interaction. Azidothymidine (AZT), a known Ndk inhibitor, impaired W. chondrophila growth, potentially through inhibition of WcNdk2. However, the lack of genetic tools currently limits definitive functional conclusions. Our data suggests potential functions for Ndks in <em>W. chondrophila,</em> providing a foundation for future studies on Ndk-mediated interactions between this pathogen and its host, which might possibly be translated into a new therapeutic approach.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"11 ","pages":"Article 100635"},"PeriodicalIF":5.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148342836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting cyclic di-AMP signaling through diadenylate cyclase inhibition reduces methicillin resistance in clinical MRSA isolates","authors":"Niti Kumari ,&nbsp;Itishree Jali ,&nbsp;Priyanka Garg ,&nbsp;Repally Ayanna ,&nbsp;Vinay Bhaskar ,&nbsp;Vasundhra Bhandari ,&nbsp;Shailesh Sharma ,&nbsp;Bappaditya Dey","doi":"10.1016/j.crmicr.2026.100615","DOIUrl":"10.1016/j.crmicr.2026.100615","url":null,"abstract":"<div><h3>Background</h3><div>Methicillin-resistant Staphylococcus aureus (MRSA) remains a major clinical challenge due to persistent β-lactam resistance and biofilm-associated tolerance. While canonical resistance mechanisms are well defined, non-canonical pathways such as cyclic di-adenosine monophosphate (c-di-AMP) signaling remain poorly understood, and no effective inhibitors have yet been shown to reduce MRSA resistance.</div></div><div><h3>Methods</h3><div>Clinical MRSA isolates were analyzed for c-di-AMP levels, gene expression, biofilm formation, and host immune responses under sub-inhibitory methicillin exposure. Structure-based virtual screening of FDA-approved compounds was performed to identify inhibitors of diadenylate cyclase (DacA), followed by biochemical validation, antimicrobial susceptibility testing, macrophage infection assays, and cytotoxicity evaluation.</div></div><div><h3>Results</h3><div>Methicillin exposure and biofilm growth significantly increased intracellular c-di-AMP levels via upregulation of DacA and associated signaling genes. Elevated c-di-AMP promoted bacterial persistence and induced STING-dependent immune modulation, characterized by increased IFN-β and reduced IL-1β in infected macrophages. Tropinone and eucalyptol were identified as DacA inhibitors that reduced c-di-AMP production, disrupted biofilms, and restored methicillin susceptibility, achieving up to 4–8 fold reduction in MICs. Both compounds demonstrated low cytotoxicity and favorable predicted ADME profiles.</div></div><div><h3>Conclusion</h3><div>c-di-AMP signaling represents a key non-canonical regulator of methicillin resistance and pharmacological inhibition of DacA restores β-lactam susceptibility and represents a promising adjunctive strategy against MRSA.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"11 ","pages":"Article 100615"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148171352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nutrient-driven small-colony variants as an adaptive outcome in Carbapenem-resistant Acinetobacter baumannii","authors":"Samyar Moheb ,&nbsp;Shayra D. Sanchez ,&nbsp;Irene Luu ,&nbsp;Azadeh Varnado ,&nbsp;German M. Traglia ,&nbsp;Karina Lopez ,&nbsp;Jenny Escalante ,&nbsp;Cecilia Rodriguez ,&nbsp;Marisel R. Tuttobene ,&nbsp;Marcelo E. Tolmasky ,&nbsp;Robert A. Bonomo ,&nbsp;Luis A. Actis ,&nbsp;Gauri G. Rao ,&nbsp;Fernando Pasteran ,&nbsp;Maria S. Ramirez","doi":"10.1016/j.crmicr.2026.100614","DOIUrl":"10.1016/j.crmicr.2026.100614","url":null,"abstract":"<div><div>Carbapenem-resistant <em>Acinetobacter baumannii</em> (CRAB) is a serious threat, and resistance is emerging to cefiderocol, one of the few remaining treatment options. However, how host micronutrients drive bacterial adaptation under antibiotic pressure is poorly defined. Using the AB5075 and CDC AR Bank #0033 (M27835) CRAB isolates, we combined time-kill assays, whole-genome sequencing, gene expression analysis, and phenotyping to test how vitamin B12 promotes small-colony variants (SCVs) -like adaptive derivatives and alters cefiderocol response. Vitamin B12 reproducibly selected slow-growing SCV-like adaptive derivatives that showed incomplete cefiderocol killing and frequent regrowth across drug concentrations in both genetic backgrounds. These derivatives carried genetic alterations affecting cell-surface structures, nutrient transport and TonB-dependent iron uptake, and energy balance, with capsule/biofilm remodeling and altered aminoglycoside killing. Co-exposure to vitamin B12 and cefiderocol further enriched SCV-like adaptive derivatives with changes in siderophore receptors and the BfmRS sensor BfmS. These findings identify vitamin B12 as an environmental cue that promotes the emergency of SCV-like adaptive derivatives and modulates cefiderocol response in CRAB, highlight nutrient availability as an underrecognized factor influencing antibiotic efficacy.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100614"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148178226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-based taxonomy and provirus identification in Halococcus from hypersaline environments","authors":"Ruby Setiawan,&nbsp;Jeroen G. Nijland,&nbsp;Sabine Schwarzer,&nbsp;Thomas Hackl,&nbsp;Dian Alfian Nurcahyanto,&nbsp;Ekowati Chasanah,&nbsp;Tessa E.F. Quax","doi":"10.1016/j.crmicr.2026.100637","DOIUrl":"10.1016/j.crmicr.2026.100637","url":null,"abstract":"<div><div><em>Halococcus</em> species are widely distributed in hypersaline environments and possess unusual cell wall structures. However, their genomic diversity, antiviral defenses, and interactions with viruses remain poorly understood. Here, we sequenced and analyzed the genomes of seven <em>Halococcus</em> strains isolated from hypersaline habitats. Comparative analyses showed substantial variation in growth dynamics, genome size, and defense repertoires, revealing considerable differences among species within the genus. Growth analyses showed distinct behavior among closely related strains, with slow-growing isolates strongly associated with the presence of proviruses, suggesting a fitness cost of lysogeny. Genome-based metrics, including ANI and dDDH, indicated that five of the seven isolates represent four novel species candidates. Two divergent Caudoviricetes-like proviruses were identified. A CRISPR spacer-protospacer match in one strain suggests virus-host interactions and may indicate maintenance of lysogeny. The low sequence similarity of these proviruses to known archaeal viruses supports the existence of previously unrecognized viral lineages infecting <em>Halococcus</em>, providing new insights into the ecology and evolution of this genus in extreme saline environments.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"11 ","pages":"Article 100637"},"PeriodicalIF":5.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13321033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148370153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to ‘Current trends in plant growth-promoting microorganisms research for sustainable food security’ [Current Research in Microbial Sciences Volume 2, December 2021, 100016]","authors":"Sergio de los Santos-Villalobos,&nbsp;Fannie Isela Parra-Cota","doi":"10.1016/j.crmicr.2026.100629","DOIUrl":"10.1016/j.crmicr.2026.100629","url":null,"abstract":"","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"11 ","pages":"Article 100629"},"PeriodicalIF":5.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148730241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Melioidosis in South Asia: The hidden endemicity we can no longer ignore","authors":"Chiranjay Mukhopadhyay ,&nbsp;Md Shariful Alam Jilani ,&nbsp;Enoka Corea ,&nbsp;Ivo Steinmetz","doi":"10.1016/j.crmicr.2025.100515","DOIUrl":"10.1016/j.crmicr.2025.100515","url":null,"abstract":"","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100515"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146187827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}