ISME Journal最新文献

{"title":"Streptococcus pneumoniae adaptation to nutrient deprivation and immune modulation drives upper respiratory tract colonization.","authors":"Daan W Arends, Kristin Surmann, Lucille F van Beek, Robert S Jansen, Rob J Mesman, Jeroen D Langereis, Monique van Scherpenzeel, Manuela Gesell Salazar, Uwe Völker, Gerco den Hartog, Marien I de Jonge","doi":"10.1093/ismejo/wrag213","DOIUrl":"https://doi.org/10.1093/ismejo/wrag213","url":null,"abstract":"<p><p>Streptococcus pneumoniae is a successful colonizer of the human upper respiratory tract, however the mechanisms that enable its persistence in this nutrient-limited environment, with numerous immune mechanisms in place, remain enigmatic. Here, we examined how pneumococci adapt to upper respiratory tract conditions and how this affects host interactions. We measured intranasal metal ion and monosaccharide concentrations to create an in vivo-mimicking medium for studying pneumococcal adaptation. Growth in this medium was reduced compared to glucose-rich chemically defined media (CDM). Proteome analysis revealed a shift to galactose as the major carbohydrate source, and decreased levels of fatty acid biosynthesis proteins and pneumolysin, compared to other CDMs. Glycerophosphocholine accumulated extracellularly leading to decreased CRP and IgM binding to pneumococci. Pneumococci grown in in vivo-mimicking medium, compared to glucose-rich media, were more capable colonizers of primary epithelium and induced less epithelial cytokine release. Together this shows how pneumococci adapt to the nutrient-limited respiratory environment, modulate epithelial cells and evade humoral responses to facilitate persistent colonization.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148801033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High molecular weight dissolved organic matter drives soil resistome proliferation by enhancing microbial competition and viral carbon metabolism.","authors":"Zi-Teng Liu, Xin-Di Zhao, Jia-Qi Li, Shu-Xin Li, Xianjin Tang, Si-Yu Zhang","doi":"10.1093/ismejo/wrag212","DOIUrl":"https://doi.org/10.1093/ismejo/wrag212","url":null,"abstract":"<p><p>Soil organic carbon is a key determinant of microbial community structure and function, yet the role of dissolved organic matter (DOM) bioavailability in shaping the soil antibiotic resistome remains poorly understood. Here, we combined previous continental-scale field sampling across 18 provinces in China (n = 141) with additional microcosm experiments to investigate how DOM molecular weight influences soil antibiotic resistance genes (ARGs) proliferation. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic analyses, we found that soils enriched in high molecular weight (HMW) DOM harbored significantly greater ARG abundance and diversity compared to low molecular weight (LMW) DOM soils. HMW DOM intensified microbial competition, as evidenced by a higher proportion of negative correlations in the co-occurrence network and lower niche breadth, favoring the enrichment of co-hosts that simultaneously carried ARGs, carbon metabolism genes, and biosynthetic gene clusters for antimicrobial compounds. Microcosm experiments confirmed that HMW DOM (lignin) addition significantly increased ARG transcript abundance (2.4-fold) and co-host relative abundance (2.3-fold), accompanied by a concurrent increase in transcribed viral auxiliary metabolic genes (2.5-fold) involved in complex carbon degradation. Structural equation modeling revealed that HMW DOM abundance and chemodiversity exerted the strongest positive effects on ARG abundance, primarily by shaping microbial community competition and metabolic potential. Collectively, our findings establish DOM bioavailability, particularly its molecular weight, as a critical yet previously overlooked driver of soil resistome development, challenging the conventional focus on total carbon content and highlighting the potential for molecular-level organic matter management to mitigate the spread of ARGs.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148800964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phage Triggers Spatial Sporulation Defense Trade-offs.","authors":"Mengjie Wu, Zhonghua Cai, Jin Zhou","doi":"10.1093/ismejo/wrag209","DOIUrl":"https://doi.org/10.1093/ismejo/wrag209","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148762794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Natural transformation drives large-scale genome mosaicism in human gut bifidobacteria.","authors":"Yohei Watanabe, Kento Orihara, Naoki Tsukuda, Taeko Hara, Takahiro Matsuki","doi":"10.1093/ismejo/wrag208","DOIUrl":"https://doi.org/10.1093/ismejo/wrag208","url":null,"abstract":"<p><p>Although horizontal gene transfer drives bacterial diversification, its contribution to chromosome-scale variation in human gut commensals remains unclear. This study demonstrated that human-associated bifidobacteria undergo extensive chromosomal transfer through natural transformation. Comparative genomics of coexisting Bifidobacterium pseudocatenulatum isolates from a single individual revealed extensive recombination signatures between the lineages. We experimentally reproduced this recombination by co-culturing strains, resulting in the transfer of multiple chromosomal regions and generation of mosaic genomes. Individual recombination tracts reached up to 247 kb per site, with cumulative replacements accounting for up to 28.9% of the recipient chromosome. These transfers occurred with heat-killed donors or purified DNA and were abolished by DNase, thereby identifying natural transformation as the underlying mechanism. Furthermore, we observed that environmental factors strongly influenced transformation frequency, suggesting that gut environmental conditions play a role regulating this process. Using natural transformation, we established a simple markerless genome-editing method that enables efficient gene deletions. Deletions of the Tad pili, ComEA-ComEC, or DprA-ComM-YraN gene clusters abolished transformation, defining the core machinery. The conservation of these genes across the genus Bifidobacterium and experimental demonstration of natural transformation in Bifidobacterium longum and Bifidobacterium breve indicate that natural transformation capacity is widespread within the genus. Our findings establish natural transformation as a key mechanism that promotes genome plasticity and contributes to adaptive evolution in bifidobacteria, thereby expanding our current understanding of horizontal gene transfer in the human gut microbiota.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration and regulation of stolen organelles in a marine protist.","authors":"Julian M Jacobs, Zachary L Reitz, Erica Lasek-Nesselquist, Amelie L'Etoile-Goga, Brittany N Sprecher, Matthew D Johnson, Holly V Moeller","doi":"10.1093/ismejo/wrag204","DOIUrl":"https://doi.org/10.1093/ismejo/wrag204","url":null,"abstract":"<p><p>Chloroplast-stealing (a.k.a., \"kleptoplastidic\") plankton transiently obtain and integrate prey metabolic machinery into their own cells. To do so, they must address a series of challenges, including physical localization of acquired machinery, metabolic integration of organelles and their products, and maintenance of machinery. Here, we study this transient integration in the marine ciliate Mesodinium chamaeleon by pulse feeding the ciliate with cryptophyte algal prey (Storeatula major) and then tracking changes in ciliate cellular ultrastructure, physiology (growth and photosynthesis), and gene expression over time. We demonstrate a predictable series of changes, from the reconfiguration of metabolic activity fueled by recent ingestion, to a period of rapid growth, to a reduction in physiological performance as prey organelle number and functionality become limiting. Because M. chamaeleon also steals transcriptionally active prey nuclei, gene expression is a complex milieu of host and cryptophyte expression, with much of prey metabolism apparently intact in the new host, albeit at low levels. Collectively, our results highlight the holistic orchestration of stolen organelles to produce rapid-yet transient-growth in a new host.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148671129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association analysis reveals specialization to hosts and niches in multiple species of the Lactobacillaceae.","authors":"Dalimil Bujdoš, Jens Walter, Paul W O'Toole","doi":"10.1093/ismejo/wrag198","DOIUrl":"https://doi.org/10.1093/ismejo/wrag198","url":null,"abstract":"<p><p>The Lactobacillaceae inhabit diverse environments, but the extent of their habitat adaptation remains unclear and the colonization factors unknown. First, we applied multiple machine learning models to determine if we can distinguish strains of the same species isolated from two different habitats based on their gene content. Surprisingly, we show that no species is differentially adapted to the oral cavity versus the human gut, or food versus the human gut, while only Lactobacillus crispatus showed specialization to the human urogenital system versus human gut. We then asked which species of Lactobacillaceae are habitat-specialized and how they could be identified. Using multiple lifestyle predictors incorporated in logistic regression models, we found that Limosilactobacillus reuteri, Ligilactobacillus ruminis, Ligilactobacillus salivarius, L. crispatus, and Limosilactobacillus mucosae displayed the highest degrees of host specialization. Applying our microbial genome-wide association study tool, aurora, to these species identified genes encoding adhesins and bacteriocins as the strongest and most common adaptation factors. This work establishes a generalizable framework for identifying novel species-habitat pairs with strong evidence of specialization and for uncovering the genomic features underlying within-species host and habitat adaptation.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes.","authors":"Jordan R Walker, Natascha S Varona, Bailey A Wallace, Abelardo Aguilar, Molly D O'Beirne, Josef P Werne, Antoni Luque, William P Gilhooly, Alice Bosco-Santos, Cynthia B Silveira","doi":"10.1093/ismejo/wrag197","DOIUrl":"https://doi.org/10.1093/ismejo/wrag197","url":null,"abstract":"<p><p>Meromictic lakes serve as analogs of redox-stratified ancient oceans with well-mixed surface waters and anoxic bottoms. In sulfide-rich lakes, purple and green sulfur bacteria (PSB, GSB) dominate the anoxic zones where light penetrates, and their biosignatures can guide interpretations of geologic records. Although PSB and GSB biosignatures indicate presence, they do not directly reflect the community composition of modern analog lakes, posing a challenge for interpretation. Here, we investigate this decoupling by integrating metagenomics, metatranscriptomics, and metaHi-C virus-host linkages with the geochemical profiles of three meromictic lakes. In the phototrophic microbial plates, PSB transcriptional activity far exceeded their abundance (73% of total microbial community activity versus 30% of abundance), whereas GSBs displayed the opposite pattern. Concurrently, PSBs were exclusively associated with temperate viruses, however, GSBs were targeted by lytic infections. Sulfate-reducing bacteria and viruses encoding genes for sulfate reduction were most active where sulfide concentration was lowest. These results reveal that viral replication strategies are associated with the decoupling between abundance and activity in anoxygenic phototrophs and sulfate reducers. These relationships could accelerate sulfur regeneration, contribute to sustaining phototrophy, and ultimately reflect in the lake's bulk biosignatures.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ruminosignatures associated with methane emissions and feed efficiency across geographies and cattle breeds.","authors":"Ioanna-Theoni Vourlaki, Ori Furman, Ilma Tapio, Le Luo Guan, Sinéad M Waters, David Kenny, Paul Smith, Stuart F Kirwan, David Kelly, Ross Evans, Raquel Quintanilla, Miriam Piles, Antonio Reverter, Pâmela A Alexandre, Fuyong Li, Philip C Garnsworthy, Paolo Bani, Phillip B Pope, Diego P Morgavi, Itzhak Mizrahi, Yuliaxis Ramayo-Caldas","doi":"10.1093/ismejo/wrag185","DOIUrl":"https://doi.org/10.1093/ismejo/wrag185","url":null,"abstract":"<p><p>The cattle rumen microbiota represents a complex and dynamic ecosystem whose organization and relationship to host phenotypes are important for food security and environmental sustainability. We analyzed rumen microbiota profiles from 2,496 cattle representing five breeds and production systems across five countries, identifying microbial co-abundance groups termed Ruminosignatures. We detected fourteen distinct Ruminosignatures, including two consistently observed across all populations dominated by Prevotella and UBA2810. Additional Ruminosignatures showed breed- and diet-specific patterns and collectively explained 96-99% of variance in rumen microbial composition. Integrative cross-country analysis confirmed 10 out of 14 Ruminosignatures identified in cohort-specific analyses. Several Ruminosignatures were associated with methane emissions and feed efficiency traits and were partially under host genetic control, with heritability estimates ranging from 0.09 to 0.58. Structural equation modelling revealed consistent negative genetic and phenotypic correlations between the UBA2810-dominated Ruminosignature (RS_UBA2) and methane emissions across cohorts (rg = -0.40 to -0.65), with structural coefficients concordant in sign across all populations, supporting the expected direction of phenotypic response to selection on RS_UBA2. Meta-analysis confirmed positive associations of RS_UBA2 with average daily gain and negative associations with methane-related traits and feed conversion ratio. Functional genome-based predictions suggested RS_UBA2 may reduce methanogenesis through alternative hydrogen utilization pathways competing with methanogenic archaea. Production system type influenced both Ruminosignature occurrence and relationships with host phenotypes, emphasizing the relevance of context-specific strategies for microbiome modulation. Our findings highlight the potential of the Ruminosignatures framework for microbiome-informed breeding programs aimed at improving feed efficiency while reducing the environmental impact of cattle production.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148425956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota control host lipid deposition through HDAC9-driven PPARγ acetylation.","authors":"Yunxia Li, Qi Yuan, Yapeng Yang, Leli Wang, Qi Han, Yan Yang, Jingjing Zhang, Hong Wei, Yulong Yin, Shiyu Tao, Jie Yin","doi":"10.1093/ismejo/wrag109","DOIUrl":"https://doi.org/10.1093/ismejo/wrag109","url":null,"abstract":"<p><p>The healthy gut microbiota communities play a complex and significant role in lipid absorption and deposition, leading to multiple health benefits. Here, we confirmed an impaired absorption and deposition function in germ-free pigs and mice, which was partially reversed after human fecal microbiota transplantation. By integrating single-cell data from adipose tissue, we identified HDAC9 as a key regulator, marked by the presence of a population of small mature adipocytes exhibiting high HDAC9 and low PPARγ expression in germ-free pigs. HDAC9 deficiency of preadipocytes drove FABP4/5-mediated lipid deposition by directly targeting PPARγ expression and acetylation modification. Finally, we verified the interaction between gut microbiota and host HDAC9/PPARγ/FABP4/5 signaling cascade might be microbial receptors (ie, Dectin1 or TLRs)-dependent rather than microbial metabolites. Altogether, our study uncovers the gut microbiota-HDAC9-PPARγ axis as a key regulator of adipocyte function and lipid deposition, offering a potential therapeutic target for lipid-related metabolic diseases.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147935098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis.","authors":"","doi":"10.1093/ismejo/wraf123","DOIUrl":"10.1093/ismejo/wraf123","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13247519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148206789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}