Microbiome最新文献

{"title":"Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira synthesizing osmoprotectants in a wastewater microbiome treating high-ammonia brackish landfill leachate.","authors":"Shohei Yasuda, Alejandro Palomo, Barth F Smets, Akihiko Terada","doi":"10.1186/s40168-026-02351-7","DOIUrl":"10.1186/s40168-026-02351-7","url":null,"abstract":"<p><strong>Background: </strong>In the late stages of landfill operation, leachate becomes brackish and contains high concentrations of ammonia with limited organic carbon. At leachate treatment facilities, it is typically subjected to nitrification followed by denitrification, with methanol supplied as an external electron donor. This unique environment may harbor novel microorganisms, including nitrifiers. Although a variety of microorganisms are involved in nitrification, their substrate specificity and salinity tolerance remain insufficiently understood. In this study, a genome-centric metagenome analysis was conducted on the microbiome from a leachate treatment facility at a closed landfill.</p><p><strong>Results: </strong>A total of 68 metagenome-assembled genomes (MAGs) were reconstructed, including 64 putative novel species. Among these, two Nitrospira MAGs were recovered: a novel complete ammonia-oxidizing bacterium (comammox), Nitrospira LAS72 (88.72% completeness, 2.10% contamination), and canonical nitrite-oxidizing Nitrospira LAS18 (99.98% completeness, 2.29% contamination). Comparative genomic analysis with 260 publicly available Nitrospira genomes revealed that LAS18 represents a new sub-lineage within lineage VII of the Nitrospira genus. Two ammonia-oxidizing archaea (AOA), Candidatus Nitrosocosmicus LAS21 and Nitrosarchaeum LAS73, were also identified, while canonical ammonia-oxidizing bacteria were not detected. Given the brackish conditions (1.23% salinity) and the methanol-fed operation of the treatment facility, the genomic potential for osmotic stress adaptation and methanol metabolism was investigated. Comammox Nitrospira LAS72 harbors biosynthetic pathways for several compatible solutes (osmoprotectants), including glycine betaine, proline, trehalose, and L-glutamate. Moreover, comammox Nitrospira LAS72 possesses genetic potential for oxidizing formaldehyde, suggesting that it may exploit these methanol-derived intermediates as energy sources. These features indicate that LAS72 may withstand osmotic fluctuations through the production of various osmoprotectants and thrive under the unique conditions of a methanol-fed environment.</p><p><strong>Conclusions: </strong>The discovery of novel comammox Nitrospira and canonical Nitrospira forming a new sub-lineage within lineage VII of the Nitrospira genus in an ammonia-rich brackish environment provides the first genomic evidence for evolutionary adaptation among nitrifiers to saline, methanol-fed environments. These findings enhance our understanding of the ecological and evolutionary dynamics shaping nitrifier communities in complex treatment ecosystems. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":12.7,"publicationDate":"2026-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13032477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147276594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiota-derived propionate suppresses Salmonella virulence gene expression via LuxS quorum sensing.","authors":"Qianyun Zhang, Qidong Zhu, Yunqi Xiao, Shiyong Liao, Shangzhou Liu, Shourong Shi","doi":"10.1186/s40168-026-02366-0","DOIUrl":"10.1186/s40168-026-02366-0","url":null,"abstract":"<p><strong>Background: </strong>Despite mounting evidence that commensal microbes enhance host defenses, whether and how they directly suppress pathogen virulence remains elusive. Here, we investigate metabolites from the gut microbiota of infection‑resistant Tibetan chickens for their ability to reduce Salmonella virulence gene expression and elucidate the molecular mechanism by which these compounds inhibit the LuxS/AI‑2 quorum‑sensing system.</p><p><strong>Results: </strong>Initially, we compared the expression of the quorum‑sensing gene luxS and biofilm-associated virulence genes in Tibetan chickens and broiler chickens post-Salmonella infection. Notably, Tibetan chickens exhibited significantly lower virulence gene expression than broiler chickens. Subsequently, fecal microbiota transplantation (FMT) from Tibetan chickens to broiler chickens reduced virulence gene expression in infected recipients. Further, 16S rRNA gene sequencing of cecal contents revealed that FMT enhanced microbial diversity and altered composition in infected broiler chickens, specifically enriching short-chain fatty acids (SCFA)-producing beneficial bacteria (e.g., Bacteroides, Rikenellaceae_RC9_gut_group, Phascolarctobacterium, Desulfovibrio). Critically, using Transwell chambers to separate microbes and metabolites, we identified metabolites as mediators of this effect. Subsequent liquid chromatography-mass spectrometry (LC-MS) quantification demonstrated significantly elevated propionate concentrations in both uninfected and infected Tibetan chickens, and FMT-recipient broiler chickens. Propionate levels correlated negatively with key virulence factor expression. Moreover, in vitro experiments showed that propionate inhibited Salmonella biofilm formation, reduced autoinducer-2 (AI-2) activity, and downregulated the expression of virulence genes. In vivo, we further confirmed that propionate decreased the expression of Salmonella virulence genes. Taken together, these results support that propionate suppresses Salmonella virulence gene expression by targeting the LuxS/AI-2 quorum-sensing pathway. To validate this mechanism, we generated a luxS knockout strain by homologous recombination; strikingly, propionate failed to attenuate virulence gene expression in this mutant, thereby establishing the essential role of LuxS/AI-2. Finally, molecular docking identified propionate-LuxS binding sites (Ile53), and site-directed mutagenesis validated critical functional residues, highlighting structural determinants for virulence gene expression regulation.</p><p><strong>Conclusion: </strong>These findings underscore the role of the gut-derived metabolite propionate in directly modulating pathogen virulence gene expression by targeting the LuxS/AI-2 quorum‑sensing system, offering novel insights into microbiota-based strategies for infectious disease management.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":"70"},"PeriodicalIF":12.7,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12918161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146220484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.","authors":"Luoyang Ding, Shuai Yang, Feifan Wu, Dale Pilling, Jinying Zhang, Kelsey Pool, Mira Nishvanthi, Sarah Babington, Shane K Maloney, Lianmin Chen, Jing Shi, Yifeng Wang, Dominique Blache, Mengzhi Wang","doi":"10.1186/s40168-025-02332-2","DOIUrl":"10.1186/s40168-025-02332-2","url":null,"abstract":"<p><strong>Background: </strong>Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep.</p><p><strong>Methods: </strong>The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured.</p><p><strong>Results: </strong>Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the γ-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation.</p><p><strong>Conclusions: </strong>Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":12.7,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12937511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146227346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.","authors":"Jiayu Zhang, Le Xu, Xuehai Ge, Xiannian Zi, Shiyu Chen, Chen Liu, Kun Wang, Jinping Zhou, Tengfei Dou, Jonathan W C Wong, Qiuye Lin, Xiangtao Kang, Zhenhui Cao","doi":"10.1186/s40168-026-02347-3","DOIUrl":"10.1186/s40168-026-02347-3","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiome possesses substantial genetic diversity that supports microbial adaptation, but the genomic variation patterns across its prokaryotic and viral populations remain incompletely characterized.</p><p><strong>Results: </strong>Through integrated metagenomic and metatranscriptomic analysis of ten indigenous chicken breeds from China, we recovered 1527 representative prokaryotic MAGs, 37,555 representative DNA viral contigs, and 1867 representative RNA viral contigs (primarily comprising Bacillota/Bacteroidota, Uroviricota, and Lenarviricota/Pisuviricota, respectively). By integrating complementary short-read and long-read metagenomics with metatranscriptomics, we identified structural variants (SVs) and single-nucleotide variants (SNVs) in these cross-kingdom genomes. Positive SV-SNV density correlations occurred consistently across all microbial groups, indicating coordinated mutational processes. DNA viruses exhibited the highest variant prevalence (86.9% SNVs, 47.7% SVs), with temperate phages accumulating significantly more variants than virulent phages. Functionally, prokaryotic variants accumulated in carbohydrate metabolism and amino acid metabolism, while viral variants demonstrated broad metabolic hijacking. Horizontal gene transfer (HGT) was characterized by a strong virus-associated signature (69.40% of 536 events) and marked by an asymmetric pattern, with phage-to-bacteria (P-to-B) flow alone constituting 37.50% of all events. Random forest analysis revealed a strong bidirectional predictive relationship between SV and SNV densities across prokaryotic, DNA viral, and RNA viral populations, suggesting coupled genomic instability. Niche breadth emerged as a major driver of SNVs across kingdoms and was positively correlated with variant density. In prokaryotes, HGT events significantly shaped variant patterns. For viruses, genomic GC content was an important factor and consistently showed a negative correlation with SNV density in both DNA and RNA viruses.</p><p><strong>Conclusions: </strong>These findings demonstrate that coordinated mutational processes and kingdom-specific intrinsic factors drive genomic variation, with viruses serving as key genetic exchange vectors in chicken gut ecosystems. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":12.7,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13019907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146227323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.","authors":"Youyoung Choi, Mi Zhou, Masahito Oba, Atmir Romero-Pérez, Karen A Beauchemin, Stephane Duval, Maik Kindermann, Le Luo Guan","doi":"10.1186/s40168-025-02201-y","DOIUrl":"10.1186/s40168-025-02201-y","url":null,"abstract":"<p><strong>Background: </strong>The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics.</p><p><strong>Results: </strong>Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H₂) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H₂ producing hydrogenase were decreased, while those encoding H₂ sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H₂ sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":"72"},"PeriodicalIF":12.7,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12918512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146227349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenolic acid biosynthesis is associated with deleterious microbiome changes during Plasmodiophora brassicae-induced clubroot in pakchoi.","authors":"Haibo Hao, Zhenghong Wang, Zitong Meng, Xiaofeng Li, Hui Chen, Pengfei Meng, Liming Miao, Lu Gao, Xinman Wang, Benke Kuai, Yi Song, Hongfang Zhu, Dingyu Zhang","doi":"10.1186/s40168-026-02349-1","DOIUrl":"10.1186/s40168-026-02349-1","url":null,"abstract":"<p><strong>Background: </strong>Diverse diseases are typically associated with perturbed microbiome homeostasis, across ecosystems such as the gut and root habitats. Clubroot, which is caused by the devastating soil-borne pathogen Plasmodiophora brassicae, is a broad-spectrum disease that infects almost all cruciferous vegetables. However, the microbial ecological and metabolic cues underlying pathogen-driven deleterious disruptions of the microbiome remain enigmatic.</p><p><strong>Results: </strong>In this study, changes in the microbiome and metabolome of the rhizosphere and roots in susceptible (diseased and nondiseased) and resistant pakchoi plants infected with P. brassicae were investigated. Diverse potential beneficial and disease-suppressive microbial families, including Rhizobiaceae and Sphingomonadaceae, were enriched in the healthy group compared with the diseased group. Rhizobiaceae was further characterized as a core driver family between the healthy and diseased groups. Reductionist-based strain validation studies further confirmed that Rhizobium sp. 25F3 showed drastic disease-suppressing activity in soil. The integrated metabolome‒microbiome correlation analysis revealed that phenolic acids were negatively correlated with the relative abundance of Rhizobiaceae. We further confirmed that genes related to phenolic acids were upregulated in diseased roots and that two phenolic acids suppressed beneficial Rhizobiaceae growth and accelerated P. brassicae infection in pakchoi.</p><p><strong>Conclusions: </strong>Upon P. brassicae infection, significant differences in the microbiome and metabolome were observed between diseased and healthy plants, as well as between resistant and susceptible varieties. Rhizobiaceae is dominant in the root microbiome and acts as a keystone family affected by P. brassicae infection. P. brassicae-induced phenolic acid metabolites selectively inhibit the growth of beneficial Rhizobium sp. 25F3 while promoting P. brassicae bursts in pakchoi. Our work provides ecological and metabolic explanations for how pathogenesis ultimately triggers a decrease in the relative abundance of beneficial microbes, which can guide future genetic and microbiome-based approaches to control clubroot disease. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":12.7,"publicationDate":"2026-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13011381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146194853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"L-kynurenine reshapes immune microenvironment to alleviate methamphetamine-induced chronic lung injury through gut-lung axis.","authors":"Pei-Jun Ma, Ming Li, Wei-Ting Hu, Ding Yang, Ye-Kui Liang, Lei Chen, Xin Wang, Ying Pan, Yun Wang","doi":"10.1186/s40168-026-02348-2","DOIUrl":"10.1186/s40168-026-02348-2","url":null,"abstract":"<p><strong>Background: </strong>Long-term abuse of methamphetamine (MA) is strongly associated with severe lung injury. Microbiome metabolites are one way to understand the interactions between microbes and disease. Although gut microbes and their metabolites play a crucial role in the gut-lung axis, the microbial mechanism by which MA induces lung injury is unclear. The purpose of this work was to identify the omics characteristic factor associated with MA abuse and explore its immune regulatory mechanism by 16 s rDNA sequencing, LC-MS/MS non-targeted metabolomics analysis, hemodynamics, flow cytometry, and some methods of cellular and molecular biology and morphology.</p><p><strong>Results: </strong>Based on the joint analysis of the gut microbiome and metabolomics, it was found that MA abuse disrupted the structure of the gut microbiome and drove the reprogramming of metabolites, leading to a reduction in Lactobacillus rhamnosus and its metabolite L-kynurenine (L-KYN). Activated Lactobacillus increased L-KYN level in MA-administrated mice. L-KYN, as a product of Lactobacillus, is a key omics signature factor for MA abuse, which has been further confirmed in vivo. L-KYN induced Treg cells differentiated from CD4⁺ T cells and reshaped the immune microenvironment. L-KYN induced the secretion of IL-10 by Treg cells, mediated the communication between Treg cells and alveolar epithelial cells (AEC) through IL-10, and alleviated MA-induced lung inflammation and alveolar barrier damage through the IL-10/JAK1/STAT3 pathway.</p><p><strong>Conclusions: </strong>From the perspective of intestinal microbiome-metabolite-immune network regulation, the omics characteristic factor L-KYN reshaped the immune microenvironment and alleviated methamphetamine-induced chronic lung injury through the gut-lung axis, providing a new theoretical and experimental basis for the prevention and treatment of MA-induced chronic lung injury. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":"71"},"PeriodicalIF":12.7,"publicationDate":"2026-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12918256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146180955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.","authors":"David Touchette, Grégoire Michoud, Martin Boutroux, Martina Gonzalez Mateu, Florian Baier, Ianina Altshuler, Hannes Peter, Tom J Battin","doi":"10.1186/s40168-026-02336-6","DOIUrl":"10.1186/s40168-026-02336-6","url":null,"abstract":"<p><strong>Background: </strong>Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.</p><p><strong>Results: </strong>Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103 days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6 h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24 h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24 h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.</p><p><strong>Conclusions: </strong>These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":"65"},"PeriodicalIF":12.7,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12896324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146165885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RamEx: an R package for high-throughput microbial ramanome analyses with accurate quality assessment.","authors":"Yanmei Zhang, Gongchao Jing, Rongze Chen, Yanhai Gong, Yuandong Li, Yongshun Wang, Xixian Wang, Jia Zhang, Yuli Mao, Yuehui He, Xiaoshan Zheng, Mingchao Wang, Hao Yuan, Jian Xu, Luyang Sun","doi":"10.1186/s40168-026-02339-3","DOIUrl":"10.1186/s40168-026-02339-3","url":null,"abstract":"<p><strong>Background: </strong>Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped.</p><p><strong>Results: </strong>Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets-including pathogenic bacteria, probiotic strains, and yeast fermentation populations-demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic-associated fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++ acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour.</p><p><strong>Conclusions: </strong>By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx . Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":12.7,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12990539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146157606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial membrane transporters reveal trace metal niche adaptation in distinct water masses of the Southern Ocean.","authors":"Rui Zhang, Pavla Debeljak, Sharvari Sunil Gadegaonkar, Corentin Baudet, Antoine Ringard, Stéphane Blain, Ingrid Obernosterer","doi":"10.1186/s40168-025-02293-6","DOIUrl":"10.1186/s40168-025-02293-6","url":null,"abstract":"<p><strong>Background: </strong>Trace metals are co-factors for enzymes that are essential for microbial metabolism and the cycling of major elements. Membrane transporters allow microbes to sense and react to trace elements in the environment and to balance their uptake and export for the regulation of intracellular metal homeostasis. The acquisition and efflux of trace metals could lead to reciprocal feedbacks between microbes and the surrounding environment. Whether these processes vary among trace metals and across habitats is presently not known. We used membrane transporters into and out of the cell as indicators for the uptake and efflux of trace metals and provide a detailed picture of the distribution of the respective genes in distinct provinces in surface waters and in subsurface water masses across a transect in the Southern Indian Ocean.</p><p><strong>Results: </strong>We observed marked spatial and vertical patterns in normalized gene abundances of transporters of iron (Fe), manganese (Mn), nickel (Ni) and copper (Cu). Changes in gene abundances were specific to the type of transporter and trace metal, and pronounced differences between surface and specific water masses emerged. We found an enrichment in genes related to efflux and homeostasis of Fe, Ni and Cu in two water masses of the deep ocean that are North Atlantic Deep Water (NADW) and Lower Circumpolar Deep Water (LCDW). This pattern was observed on the community level and for metagenome-assembled genomes (MAGs) affiliated with Alteromonadaceae and Burkholderiaceae that were abundant in these two water masses.</p><p><strong>Conclusions: </strong>The enrichment in trace metal efflux and resistance genes points to microbially mediated processes, exerted by homeostasis, with potential influence on the trace metal speciation and distribution in specific water masses in the deep ocean. The gene repertoire and distinct distribution pattern of the taxa identified as potential key players could reflect an adaptation to these old water masses with trace metals acting as selective driver. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":12.7,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12990642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146157611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}