FEMS microbes最新文献

{"title":"Nonpharmaceutical interventions and postpandemic resurgence: the shifting epidemiology of influenza, respiratory syncytial virus, and adenovirus in Hangzhou, Zhejiang Province (2020-2024).","authors":"Shaoni Zhang, Shilei Dong, Yan Qi, Yanjing Shen, Yanhong Sun","doi":"10.1093/femsmc/xtag040","DOIUrl":"10.1093/femsmc/xtag040","url":null,"abstract":"<p><p>Acute respiratory infections caused by influenza A/B (Flu A/Flu B), respiratory syncytial virus (RSV), and adenovirus (ADV) remain a major global health burden. The COVID-19 pandemic profoundly altered respiratory virus transmission through nonpharmaceutical interventions (NPIs). Samples from patients with respiratory tract infections at Hangzhou Hospital of Traditional Chinese Medicine from January 2020 to October 2024 were collected. ADV, Flu A, Flu B, and RSV were detected to evaluate the impact of NPIs on viral epidemiology. Statistical analyses were performed using SPSS software and GraphPad Prism. Multivariable binary logistic regression models, adjusting for age group and sex, were constructed to evaluate the independent effect of NPI relaxation (strict NPI period 2020-2022 vs. post-relaxation period 2023-2024) on virus positivity. Stratified analyses by age group and demographic comparability assessments between periods were also performed. Overall virus positivity declined from 27.4% (2020) to 14.5% (2021) during strict NPIs, then rebounded to 35.1% in 2023 after relaxation. Flu A resurged atypically in summer 2022 and dominated the 2023 winter peak, while Flu B increased annually and peaked in 2024. ADV regained its prepandemic summer seasonality by 2024, whereas RSV showed limited seasonal variation. Higher ADV positivity was observed in males, and higher Flu B positivity in females. By 2024, influenza burden shifted toward adults and geriatric populations, while children under five remained most vulnerable to RSV and ADV. However, after adjusting for demographic shifts-including a significant increase in adult patients (18-60 years: 22.1%-40.0%) and altered sex ratios between periods (both <i>P</i> < 0.001)-the post-relaxation period showed lower adjusted odds of positivity for all four pathogens (Flu A: aOR = 0.64, 95% CI: 0.61-0.67; Flu B: aOR = 0.67, 95% CI: 0.63-0.70; ADV: aOR = 0.72, 95% CI: 0.68-0.76; RSV: aOR = 0.62, 95% CI: 0.59-0.65; all <i>P</i> < 0.001), whereas no significant sex differences were observed after multivariable adjustment (all <i>P</i> > 0.05). Stratified analyses further revealed that the magnitude of period-related risk reduction increased with age for all pathogens. This study demonstrates that the postpandemic resurgence of respiratory viruses in Hangzhou, Zhejiang Province, was not a monolithic recrudescence following NPIs relaxation, but a multifaceted shifting epidemiology driven by three convergent forces: expanded school-based and community screening that broadened the tested denominator, demographic case-mix shifts toward higher-risk adult populations, and pathogen-specific alterations in seasonal and age-specific transmission patterns. The consistently lower adjusted odds of positivity during the post-relaxation period indicate that crude resurgence signals must be interpreted through the lens of surveillance structure. This study demonstrates that the postpandemic resurgence of respiratory v","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag040"},"PeriodicalIF":4.2,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13436969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148674692","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":"Cold atmospheric plasma mediates antibiofilm activity and sensitization to further plasma and antibiotic challenges against <i>Staphylococcus aureus</i>.","authors":"Elena Capuzzo, Guillem Mas Fiol, Nadège Cayet, Hugo Varet, Javier Pizarro-Cerda, Nadira Frescaline, Antoine Rousseau, Olivier Dussurget","doi":"10.1093/femsmc/xtag039","DOIUrl":"10.1093/femsmc/xtag039","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> biofilms pose significant challenges in clinical settings due to their growing resistance to conventional antibiotics. While cold atmospheric plasma (CAP) is known for its bactericidal effects, its impact on biofilm architecture and physiology, and subsequent antimicrobial susceptibility remains poorly understood. This study investigates the effects of CAP treatment on <i>S. aureus</i> biofilms. We demonstrate that CAP not only reduces biofilm but also disrupts biofilm architecture and alters bacterial cell morphology. Transcriptomic analysis reveals distinct gene expression profiles following treatments with CAP and hydrogen peroxide, one of its active components, highlighting unique stress responses. We further show that CAP treatment of <i>S. aureus</i> grown on agar plates sensitizes bacteria to additional CAP exposure and induces genomic alterations involved in cell envelope integrity, defence mechanisms and DNA replication, recombination, and repair. Importantly, CAP treatment enhances bacterial susceptibility to the topical antibiotic for wound care mupirocin. These findings provide novel insights into the mechanisms underlying CAP-mediated biofilm control and offer a promising strategy to potentiate existing antimicrobial therapies.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag039"},"PeriodicalIF":4.2,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13383574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148610776","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":"Chemoproteomic profiling of adaptive ATP-binding protein activity in <i>Enterococcus faecium</i> in response to host-derived cues.","authors":"Jeanette S Grunnvåg, Kristin Hegstad, Stephen Dela Ahator, Christian S Lentz","doi":"10.1093/femsmc/xtag038","DOIUrl":"10.1093/femsmc/xtag038","url":null,"abstract":"<p><p><i>Enterococcus faecium</i> has become a significant nosocomial and opportunistic pathogen, increasingly implicated in severe infections such as urinary tract infections, bacteraemia, and endocarditis. Due to acquired resistance to vancomycin and ampicillin and high intrinsic resistance to other antibiotics, <i>E. faecium</i> infections are often challenging to treat. However, relatively little is known about the molecular factors used by <i>E. faecium</i> during infection. Here, we employed desthiobiotin-ATP as an activity-based probe to investigate the activity profile of ATP-binding proteins in <i>E. faecium</i> upon growth in standard rich laboratory media and in response to host-derived cues. We present a chemoproteomic dataset containing 230 selectively enriched putative ATP-binding proteins. Thirty-one proteins were specifically activated in response to human colonic organoid extract, 19 in response to human serum including the ABC transporter, TcyA, and a sensor histidine kinase, ArlS. Our findings suggest that <i>E. faecium</i> adapts its metabolic and regulatory pathways in response to host-derived signals from human serum and organoid extract, which could be crucial for its survival and pathogenicity in various host tissues. Our study highlights the potential relevance of TcyA and ArlS, that have been implicated in virulence in other pathogens, for further functional characterization in <i>E. faecium</i>.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag038"},"PeriodicalIF":4.2,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13367009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148450920","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":"Comparative genome mining and metabolomics reveal divergent NRPS-derived fengycin biosynthetic gene clusters in <i>Bacillus halotolerans</i>.","authors":"Mokhtar Salah Eddine Belhadj, Omar Messaoudi, Mohamed Yousfi, Amina Bakhrouf","doi":"10.1093/femsmc/xtag037","DOIUrl":"10.1093/femsmc/xtag037","url":null,"abstract":"<p><p>Microbial multidrug resistance is a major public health concern, underscoring the urgent need for new antimicrobial natural products. In this study, strain F11, identified as <i>Bacillus halotolerans</i>, was selected based on its strong antimicrobial activity and taxonomic identification. Whole-genome sequencing revealed a single circular chromosome of 4.15 Mb with a GC content of 43.82%, encoding 4122 predicted proteins. Pangenome analysis identified 17 unique genes. Genome mining predicted 10 biosynthetic gene clusters (BGCs), including a complete fengycin cluster. Comparative analyses using BiG-SCAPE/CORASON and clinker revealed evolutionary divergence within the fengycin BGCs, including those identified in <i>B. halotolerans</i> F11 and <i>B. halotolerans</i> HMB20199. This divergence was further supported by NRPS substrate specificity predictions, which revealed two amino acid variations at positions 6 and 8 in the predicted fengycin decapeptide of strain <i>B. halotolerans</i> F11 compared to the canonical sequence. In contrast, <i>B. halotolerans</i> HMB20199 exhibited a mosaic fengycin-iturin hybrid organization, characterized by an extended NRPS assembly line comprising 19 modules. Furthermore, untargeted metabolomic profiling of <i>B. halotolerans</i> F11 detected 9719 metabolites, of which 3453 were successfully annotated. Integration of genomic and metabolomic datasets enabled the correlation of two compounds-bacillaene and bacillibactin-with their corresponding BGCs. However, the lack of detection of fengycin, surfactin, and subtilosin A was attributable to methodological constraints. Collectively, these findings expand our understanding of <i>B. halotolerans</i> strains as promising genomic reservoirs of novel NRPS-derived lipopeptides and highlight Algerian Sahara soils as a valuable source of antimicrobial natural products.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag037"},"PeriodicalIF":4.2,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13322031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148371330","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":"Reported <i>Cryptococcus neoformans</i> heat-killing protocols show incomplete killing.","authors":"Binyi An, Yingjun Gao, Yingying Wu, Yubing Wu, Xiaoyu Wang, Qingtao Kong, Hong Sang, Haibo Liu","doi":"10.1093/femsmc/xtag031","DOIUrl":"10.1093/femsmc/xtag031","url":null,"abstract":"<p><p>Heat killing is commonly employed to kill microorganisms, including <i>Cryptococcus neoformans</i> (<i>C. neoformans</i>), particularly in immunological studies and vaccine development. To assess the reliability of existing methods, we systematically reviewed 50 publications and identified 23 distinct protocols differing in temperature, duration, suspension concentration, and sample volume. Using two virulent strains, H99 and B3501, we experimentally tested these conditions and found that only 9 protocols achieved complete (100%) killing, whereas 14 resulted in partial killing. Consistent with this, only 17 publications (34%) reported complete killing, and just 20 studies described plating suspensions for validation, raising concerns that incomplete killing may have gone undetected. Further analysis revealed that suspension volume and fungal concentration critically influenced outcomes. These findings highlight substantial variability and insufficient validation across reported protocols, which may undermine reproducibility and biosafety. Our study provides evidence-based guidance for selecting effective heat-killing conditions, thereby supporting safer and more reliable use of heat-killed <i>C. neoformans</i> in experimental research.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag031"},"PeriodicalIF":4.2,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13322030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148371297","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":"Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor.","authors":"Laura G Schaerer, Ryan S Anderson, Joshua Chan, Susan K De Long","doi":"10.1093/femsmc/xtag035","DOIUrl":"10.1093/femsmc/xtag035","url":null,"abstract":"<p><p>Methane-arrested anaerobic digestion (AAD) is a waste management strategy that produces carboxylic acid precursors to industrial products (fuels, bio-based polymers, and pharmaceuticals) from organic wastes. A major challenge preventing application of AAD is highly variable product profiles resulting from an inability to control the microbial communities underlying waste decomposition and product biosynthesis. Over time, lactic acid bacteria (LAB) often dominate AAD bioreactors and overproduce shorter chain acids causing acidosis. Here an AAD bioreactor where caproic acid production increased from an average of 3.9 g/l to an average of 12.3 g/l when the feedstock was switched from manure and paperboard to food waste. Time series shotgun metagenomics is used to investigate how microbial dynamics drive performance shifts. The dominant LAB shifted from <i>Lactobacillus amylovorus</i> spp. to <i>Lactiplantibacillus pentosus</i> spp. following the feedstock switch, corresponding with increased diversity and relative abundance (26.2%) of <i>Caproicibacter</i> spp. (putative chain elongator). Additionally, <i>L. amylovorus</i> MAGs encoded biosynthesis genes to produce the bacteriocin helveticin often produced by LAB to target closely related species. <i>Lactiplantibacillus pentosus</i> MAG.84 encodes bacteriocin-degrading enzymes and helveticin resistance genes, suggesting putitive mechanisms for bacteriocin resistance. These results suggest that bacteriocins may be an underappreciated mechanism for shaping microbial community dynamics in AAD.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag035"},"PeriodicalIF":4.2,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13289733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148320978","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":"Revealing the bacterial diversity and variation of white filamentous microbial mats in marine mangroves of Guadeloupe Island in relation to human activities.","authors":"Mariana Martínez-Noriega, Patrick Jean-Louis, Melody Philippon, Alejandro Sanchez-Flores, Silvina Gonzalez-Rizzo","doi":"10.1093/femsmc/xtag034","DOIUrl":"10.1093/femsmc/xtag034","url":null,"abstract":"<p><p>White filamentous microbial mats are complex benthic communities, typically structured by sulfur-oxidizing bacteria from the Beggiatoaceae family, yet their diversity and ecological responses in mangrove ecosystems remain poorly characterized. Here, we provide a high-resolution analysis of bacterial communities associated with white microbial mats in marine mangrove sediments of Guadeloupe using 16S rRNA metabarcoding. Bacterial community composition was compared across sites with different levels of anthropogenic impact (protected, natural, and urban). While overall diversity remained stable, richness differed significantly between conditions, and beta diversity analyses revealed clear compositional structuring along the disturbance gradient. A conserved core microbiome was identified across all sites, whereas rare taxa were detected exclusively in urban sites, including <i>Ferrimicrobium, Thermonospora, Alcanivorax</i>, and <i>Serratia</i>, which has been previously associated with human-induced environmental changes. In contrast, <i>Prosthecochloris</i> and <i>Chlorobaculum</i> were highly abundant in protected sites, whereas <i>Sulfurovum</i> and <i>Sulfurimonas</i> dominated urban environments. The relative abundance of Beggiatoaceae also varied across sites, suggesting sensitivity to anthropogenic disturbance. Despite these compositional shifts, measured physicochemical parameters did not significantly correlate with the community structure, suggesting that microbial mat organization is influenced by fine-scale or unmeasured environmental gradients. Together, these findings indicate that white microbial mats respond to anthropogenic disturbance primarily through taxonomic restructuring rather than loss of diversity, highlighting their potential as sensitive indicators of environmental change in mangrove ecosystems.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag034"},"PeriodicalIF":4.2,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13296560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148347628","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":"Comparative genomics of space-resilient <i>Chroococcidiopsis</i> cyanobacteria reveals a core genetic repertoire supporting extreme tolerance towards desert and non-Earth conditions.","authors":"Gabriele Rigano, Daniela Billi","doi":"10.1093/femsmc/xtag036","DOIUrl":"10.1093/femsmc/xtag036","url":null,"abstract":"<p><p>Desert cyanobacteria of the <i>Chroococcidiopsis</i> genus, due to their remarkable desiccation and radiation tolerance, are considered model candidates in the field of astrobiology. For this reason, three strains, namely <i>Chroococcidiopsis</i> sp. CCMEE 029, 057, and 064 have been exposed in the dried state to space- and Mars-like conditions throughout laboratory simulations and real space exposure using the EXPOSE facility installed outside the International Space Station. However, how they can recover upon rehydration and repair the damage accumulated under extreme conditions on Earth and in space remains to be fully elucidated through omics-based investigations. Hence, comparative genomics of these three <i>Chroococcidiopsis</i> strains offered a powerful lens to explore the genetic components of their capability to persist under extreme conditions. The analysis of newly obtained gapless genome assemblies of the laboratory-maintained reference strains of CCMEE 029, 057, and 064 allowed the identification of conserved and non-shared genes involved in reactive oxygen species detoxification, desiccation tolerance, DNA protection, and repair. Moreover, a biosynthetic gene cluster for scytonemin production was identified in every strain, while strain CCMEE 057 also harbored the genes for the biosynthesis of a mycosporine-like amino-acid. Such insights are crucial for understanding the adaptation strategies employed by microorganisms to survive in dry, radiation-intense environments, offering clues about the potential for life beyond Earth.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag036"},"PeriodicalIF":4.2,"publicationDate":"2026-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13308351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148347667","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":"Microbial diversity in Pyrenean ice caves: extreme cryogenic environments as analogues for extraterrestrial habitability.","authors":"Víctor Muñoz-Hisado, Fernando Puente-Sánchez, Miguel Bartolomé, Reyes Giménez, Eva Garcia-Lopez, Ana Moreno, Cristina Cid","doi":"10.1093/femsmc/xtag033","DOIUrl":"10.1093/femsmc/xtag033","url":null,"abstract":"<p><p>Pyrenean ice caves are the least studies cryogenic environments that preserve perennial ice. These caves host microbial communities adapted to extreme oligotrophy, low temperatures, and episodic water availability, making them valuable analogues for subsurface habitats on icy planetary bodies. This study investigated four ice caves in the Central Pyrenees (Devaux, Cotiella A294, Sarrios 1 and Somola SO-01) to (i) characterize bacterial and microeukaryotic assemblages, (ii) assess how ice origin, physicochemical gradients, and cave geology structure these communities, and (iii) evaluate their relevance as terrestrial analogs for cold oligotrophic ecosystems. Amplicon sequencing of 16S and 18S rRNA genes, combined with detailed chemical profiling, revealed marked cave-specific differences associated with pH, major ions, short-chain organics, and ice-formation processes. Liquid water samples contained distinct assemblages dominated by ultra-small Patesibacteria, whereas firn-derived and congelation ice hosted stratified or hydrologically entrained communities. Microeukaryotic diversity was highest in light-exposed ice from Cotiella A294 and lowest in Sarrios 1, where fungal taxa prevailed. Redundancy analyses identified acetate, nitrate, sulfate, pH, and trace metals as the environmental variables most strongly aligned with microbial gradients. These findings provide a data-driven characterization of microbial organization in Pyrenean ice caves and offer empirical baseline parameters to inform future studies of microbial persistence and biosignature formation in cold terrestrial and extraterrestrial environments.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag033"},"PeriodicalIF":4.2,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13296558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148347650","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":"Microbial community structure, functional potential, probiotic signatures, and MAG reconstruction of fermented bamboo shoots from Northeast India.","authors":"Rohit Das, Rakshak Kumar, Buddhiman Tamang","doi":"10.1093/femsmc/xtag032","DOIUrl":"10.1093/femsmc/xtag032","url":null,"abstract":"<p><p>Fermented bamboo shoot (FBS) products are widely consumed traditional foods across the Northeast region (NER) of India, yet their microbiome structure, functional capacity, biosynthetic potential, and safety attributes remain insufficiently explored. Here, comparative shotgun metagenomics of ten traditional FBS products from six NER states was used to address these gaps integrating previously generated metagenomic data from Tripura with newly generated datasets from Manipur, Meghalaya, Arunachal Pradesh, Nagaland, and Sikkim thereby bringing the total number of samples to 24. Taxonomic profiling revealed a predominance of lactic acid bacteria, primarily members of <i>Lactiplantibacillus, Levilactobacillus, Lactobacillus, Lactococcus</i>, and <i>Pediococcus</i>, with pronounced product- and region-specific community signatures. Functional annotation demonstrated predominance of genes involved in carbohydrate metabolism, stress response, quorum sensing, ABC transporters, vitamin biosynthesis, and energy metabolism, supporting strong probiotic-associated functional potential across FBS types. AntiSMASH analysis enabled the identification of diverse biosynthetic gene clusters (BGCs) responsible for the production of various secondary metabolites, including bacteriocins, non-ribosomal peptides, terpenes, and siderophores, with higher biosynthetic diversity observed in <i>Mesu</i> (Sikkim), <i>Tuaithar</i> (Manipur), <i>Lung-Seij</i> (Meghalaya), and <i>Bastenga</i> (Nagaland). Antimicrobial resistance (AMR) profiling revealed a generally low resistome burden, dominated by intrinsic resistance determinants, with FBS Sikkim and Tripura exhibiting the lowest AMR prevalence among all products. High-quality metagenome-assembled genomes affiliated with <i>Lactiplantibacillus plantarum, Lactobacillus acetotolerans</i>, and <i>Pediococcus pentosaceus</i> exhibited conserved probiotic traits, carbohydrate-active enzymes, biosynthetic pathways, and a limited presence of mobile genetic elements. Overall, the microbiome-based comparative analysis provides a framework for understanding the microbial community structure and functional potential across the NER, demonstrating broad probiotic potential and biosynthetic richness, with <i>mesu</i> samples from Sikkim showed a comparatively consistent distribution of functional pathways, biosynthetic gene clusters, and AMR-related features relative to the other FBS samples analysed.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"7 ","pages":"xtag032"},"PeriodicalIF":4.2,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13289731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148321022","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}