ISME Journal最新文献

{"title":"Adaptations of gummivorous primate gut-associated bifidobacteria to type-II arabinogalactan utilisation.","authors":"Yuki Sasaki, Tomoya Kozakai, Moe Inoue, Mikiyasu Sakanaka, Toshihiko Katoh, Hiroki Kaneko, Hiroo Imai, Toshitaka Odamaki, Kiyotaka Fujita, Takane Katayama","doi":"10.1093/ismejo/wrag210","DOIUrl":"https://doi.org/10.1093/ismejo/wrag210","url":null,"abstract":"<p><p>Bifidobacteria inhabiting the primate gut exhibit host-dependent genetic diversification, particularly in their gene repertoire related to carbohydrate metabolism, suggesting adaptation to host diets. However, these diverse genetic traits remain poorly associated with specific dietary components. Here, through enzymatic and genetic analyses, we demonstrate that several Bifidobacterium species residing in the gut of gummivorous primates, such as marmosets, possess previously uncharacterised pathways for the efficient utilisation of type-II arabinogalactan (AG), the major polysaccharide component of tree gums. The assimilation pathways comprises two key components: a bifunctional β-1,3-galactanase that cleaves the AG backbone via both endo- and exo-mode actions and an ATP-binding cassette transporter that internalises the released arabinogalactan oligosaccharides (AGOs) into cells. Data mining of deposited metagenomic datasets suggested that the endo/exo-β-1,3-galactanase and the AGO transporter contribute to cross-feeding interactions within Bifidobacterium communities in the gut of gummivorous primates. Our study not only highlights molecular strategies employed by certain Bifidobacterium species to adapt to the dietary habits of a host but may also inform probiotic intervention strategies for the health and welfare of these primates in captive settings.</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":"148800945","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":"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":10.2,"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}

{"title":"Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept.","authors":"Wei Zhang, Ioannis Eleftherianos, Amr Mohamed, Guy Smagghe, George Joseph Chakkalakkal, Rasha Al-Akeel, Umut Toprak, Gianluca Tettamanti, Nemat Keyhani, David Renault","doi":"10.1093/ismejo/wrag137","DOIUrl":"10.1093/ismejo/wrag137","url":null,"abstract":"<p><p>Insect-associated microbiomes, as co-evolved members of the holobiont, play pivotal roles in host physiology, ecological resilience, and evolutionary innovation. This review synthesizes recent advances in understanding microbial symbionts' contributions to metabolic adaptation, insecticide detoxification, and immune modulation. Framed within hologenome theory-which posits host-microbe assemblages as units of natural selection-we explore co-evolutionary dynamics driving mutualistic specialization and adaptive plasticity. Cutting-edge tools like genome editing and metagenomics reveal how gut microbiota mediate cross-kingdom interactions, insecticide resistance, and reproductive fitness. Intriguingly, microbial symbionts can enhance host resistance through detoxification while sensitizing hosts to specific toxins, highlighting context-dependent trade-offs. Targeted manipulation of microbial consortia-via detoxification disruption or symbiont engineering-offers new avenues for sustainable pest control, though ecological risks demand rigorous biosafety protocols. A paradigm shift toward holobiont-centered models promises unified strategies for sustainable agriculture and biodiversity conservation in the Anthropocene.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13310142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148037199","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}

{"title":"Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.","authors":"Xiao-Yu Zhu, Frances E Hopkins, Ruth Airs, Claire E Widdicombe, Bethany Wilkinson, Glen A Tarran, E Malcolm S Woodward, Ornella Carrión, Andrew R J Curson, Qianyao Ma, Libby Hanwell, Gui-Peng Yang, Joseph A Christie-Oleza, David J Lea-Smith, Xiao-Hua Zhang, Jonathan D Todd","doi":"10.1093/ismejo/wrag141","DOIUrl":"10.1093/ismejo/wrag141","url":null,"abstract":"<p><p>Ubiquitous marine microalgae and bacteria produce the abundant organosulfur compound dimethylsulfoniopropionate (DMSP) and/or catabolize it to climate-active gases, such as dimethylsulfide (DMS), with major consequences for global biogeochemistry and climate. However, their relative and dynamic roles in DMSP synthesis and catabolism remain poorly resolved, particularly during natural bloom events. Here, we combined metagenomics and metatranscriptomics, with measurements of intracellular/particulate DMSP (DMSPp), DMS concentrations, and DMSPp production rates, as well as microscopy and flow cytometry, to predict the key microbes and enzymes driving DMSP/DMS dynamics during a spring-summer bloom in the Western English Channel. Microalgae and bacteria expressing the DMSP synthesis genes DSYB/DSYE and dsyB were likely major and significant DMSP producers, respectively, except during the largest observed DMSP spike. This spike coincided with elevated Synechococcus and autotrophic flagellate biomass but minimal DMSP synthesis gene expression. Axenic Synechococcus strains contained no detectable DMSP, implying that flagellates with novel DMSP synthesis genes were likely responsible. Microbial DMSP import potential far exceeded catabolism, suggesting strong selection for DMSP uptake. Bacteria were the major predicted DMSP degraders, with DMSP demethylation potential dwarfing cleavage. However, the highest DMS concentrations were linked to Haptophyta expressing the DMSP lyase gene Alma, implying the significance of algal DMSP cleavage. Methanethiol-dependent DMS production was also likely important, with bacterial mddH transcripts coinciding with another major DMS spike. Overall, these results imply dynamic and contrasting roles of microalgae and bacteria, and their pathways, in coastal DMSP/DMS and sulfur cycling.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13310141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148220453","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}

{"title":"Rapid adaptation accelerates competitive suppression in a parasite community.","authors":"Samuel T E Greenrod, Daniel Cazares, Weronika Ślesak, Tobias E Hector, R Craig MacLean, Kayla C King","doi":"10.1093/ismejo/wrag114","DOIUrl":"10.1093/ismejo/wrag114","url":null,"abstract":"<p><p>Environmental stress leads to changes in community composition by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to environmental sensitivity of infection steps and dependence on host fitness. Parasite populations might avoid extinction through evolutionary rescue-whereby rapid adaptation to stress enables persistence-but the impacts of adaptation to stress on parasite communities remain unclear. Here, we study the evolutionary and ecological impact of thermal stress in a simple parasite community by propagating populations of two viral parasites (bacteriophages φ14-1 and φLUZ19) of Pseudomonas aeruginosa in monoculture and co-culture under two thermal conditions: a control temperature (37°C) and a high temperature that restricts φ14-1 growth (42°C). We show that rapid thermal adaptation of φ14-1 facilitated persistence in monoculture. Rescue of this phage in co-culture made it a superior competitor, and it replaced φLUZ19 as the dominant phage at high temperature. We determine that thermal adaptation occurred through mutations in genes linked to attachment to bacterial hosts and within-host replication. We also show that competitive suppression by φ14-1 constrained φLUZ19 molecular evolution. Our findings suggest that rapid adaptation to environmental stress can prevent the extinction of some parasites but may inadvertently destabilise the community and facilitate further species loss. This work underscores the need to take an eco-evolutionary approach to predict the responses of communities to global climate change.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148240533","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}

{"title":"Bacterial family-VIII esterase displays dual activities: hydrolysis of polyester bioplastics and β-lactam antibiotics.","authors":"Harry Lerner, Diego Casaburi, Nele Charlott Meier, Léa Bernabeu, Marcel Eck, Stefan Mecking, David Schleheck","doi":"10.1093/ismejo/wrag203","DOIUrl":"10.1093/ismejo/wrag203","url":null,"abstract":"<p><p>The plastisphere is a unique ecosystem with microbes colonizing and potentially degrading plastic debris in the environment, provided that the polymers are enzymatically accessible as substrates to drive microbial growth. It also harbors an unusually high occurrence of antibiotic resistance genes, suggesting plastic debris as a potential vector for antibiotic-resistant microorganisms. In this study, we investigated microbial communities in forest soil degrading an emerging type of bioplastics, aliphatic long-chain polyesters (LCAPs). Sequencing analysis revealed a family-VIII esterase strongly associated with LCAP depolymerization that showed high structural similarity to type C β-lactamases. Structural modeling and substrate docking analysis indicated catalytically favorable binding of both LCAP and β-lactam antibiotics. Furthermore, the active site appeared to be located in a large, wide-open groove, rather than in a tunnel, resulting in a protein with a striking \"pac-man\"-like structure. Heterologous expression and in vitro activity testing confirmed its dual functionality as plastic depolymerase and β-lactam hydrolase. Sequence analysis indicated the enzyme as membrane-associated lipoprotein likely to be directed to the outer membrane. The membrane anchoring of the enzyme may offer striking microbial-ecological benefits, by preventing enzyme loss especially in aqueous environments, by increased catalytic efficiency through high enzyme concentration at the cell-plastic interface, and by spatially linking catalysis with membrane transport, thereby limiting monomer loss to non-producing plastisphere-community members (cheaters). Hence, our study highlighted a plastic depolymerizing enzyme with a striking substrate spectrum, bridging plastics and antibiotics degradation, and provides intriguing perspectives for understanding the microbial physiology, ecology, and evolution of (bio)plastic degradation in the environment.</p>","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/PMC13533575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148875744","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}

{"title":"Contrasting salinity regimes reshape microbe-DOM coupling and reduce recalcitrant dissolved organic carbon preservation in a salt lake.","authors":"Xiding Wang, Yang Liu, Xinyue Yang, Ruikai Zhang, Xudong Liu, Fangru Nan, Qi Liu, Junping Lv, Jia Feng, Shulian Xie","doi":"10.1093/ismejo/wrag107","DOIUrl":"10.1093/ismejo/wrag107","url":null,"abstract":"<p><p>Salt lakes account for nearly half of the world's inland water area and play an irreplaceable role as \"carbon conversion and stabilization factories,\" making substantial contributions to the global carbon cycle. Central to this function is the transformation of dissolved organic carbon (DOC) and its accumulation into recalcitrant dissolved organic carbon (RDOC), which together underpin internal carbon processing in these systems. However, the pathways through which DOC is converted to RDOC in salt lakes, and how these pathways are shaped by salinity and microbial communities, remain poorly resolved. Here, using Yuncheng Salt Lake as a within-lake system, we combined field-based in situ characterization with long-term incubation experiments to examine how contrasting salinity regimes were associated with microbial and dissolved organic matter (DOM) variation. Higher salinity was associated with reduced bacterial and dissolved organic matter diversity, stronger deterministic bacterial assembly, and a restructured bacteria-DOM association network. Under the standardized nutrient-replete incubation conditions used here, samples from the higher-salinity regime exhibited higher biodegradable DOC, lower RDOC preservation, and greater overall DOC loss over the 100-day experimental timescale. Salinity-related differences in microbial community composition, metabolomic profiles, and dissolved organic matter characteristics were closely associated with variation in RDOC dynamics, suggesting that these carbon-processing differences were accompanied by coordinated microbial and metabolic reorganization. Together, these results provide process-relevant, condition-specific evidence that contrasting salinity regimes within Yuncheng Salt Lake were associated with differences in microbe-DOM coupling and in DOC/RDOC outcomes.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13200285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845436","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}

{"title":"Deoxycholate induces proline provision from Escherichia coli to enhance Clostridioides difficile virulence.","authors":"Jingpeng Yang, Xilong Deng, Xiaoya Sheng, Yanan Li, Xuna Tang","doi":"10.1093/ismejo/wrag249","DOIUrl":"10.1093/ismejo/wrag249","url":null,"abstract":"<p><p>Clostridioides difficile infection (CDI) is a refractory enteritis. A key indicator of successful treatment and microbial restoration is the elevation of intestinal deoxycholate (DCA) levels. Nevertheless, a small proportion of patients experience disease recurrence despite this apparent metabolic recovery, the underlying mechanisms of which remain poorly understood. We investigated the ecological dynamics of Clostridioides difficile (CD) and Escherichia coli (EC) under DCA exposure, revealing that DCA exacerbates the severity of co-infection. Specifically, DCA promotes the formation of a robust and dense symbiotic biofilm that confers a substantial survival advantage to CD. Through a combination of in vitro co-culture and validation in a murine infection model, we demonstrated that EC produces substantial quantities of L-proline in response to DCA. This amino acid is converted to D-proline by the proline racemase and subsequently catabolized by the D-proline reductase in CD, thereby enhancing its environmental fitness and pathogenicity within the gut. The indispensable nature of this tripartite interaction was further corroborated using additional EC or CD strains, including isogenic mutants deficient in D-proline reductase, in subsequent murine infection models. These experiments collectively confirm that EC, proline, and the D-proline reductase are all essential components mediating the DCA-induced exacerbation of CDI. In summary, our study elucidates a mechanism by which a DCA environment promotes the exacerbation of CDI through a metabolic cross-feeding interaction between CD and EC. Specifically, EC-derived L-proline serves as a critical nutrient that enhances the fitness and pathogenicity of CD. This finding provides a plausible explanation for the paradoxical phenomenon of CDI recurrence in patients exhibiting elevated intestinal DCA levels.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13634199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992274","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}

{"title":"Host and microbial factors influence bacterial colonization of the honey bee gut.","authors":"Silvia Moriano-Gutierrez, Aurélien Pirat, Audam Chhun, Aiswarya Prasad, Alexandra Szigeti, Méline Garcia, Lucie Kesner, Florent Mazel, Philipp Engel","doi":"10.1093/ismejo/wrag127","DOIUrl":"10.1093/ismejo/wrag127","url":null,"abstract":"<p><p>The guts of many animals are colonized by host-specific microbes, yet how host filtering (host-derived constraints) shapes microbial colonization and host specificity remains poorly understood. Here, we used gnotobiotic honey bees (Apis mellifera) as a model system to systematically assess colonization potential of a phylogenetically and ecologically diverse panel of 56 bacterial strains, spanning native symbionts, opportunistic bee-associated taxa, gut microbes from other bee species, and non-bee environmental isolates. Bacterial load and colonization frequency were quantified by strain-specific qPCR seven days post-inoculation, in monocolonization and with a synthetic community of native honeybee core bacteria. Bacterial load was highest for native strains and declined with increasing phylogenetic distance from native symbionts. Co-colonization with the synthetic community reduced bacterial load across all groups, but native strains were least affected. Across strains, KEGG pathway completeness correlated with bacterial load in some ecological groups; however, metabolic capacity did not fully explain colonization patterns, either in monocolonization or under competitive conditions. A key finding was that in vitro sensitivity to antimicrobial peptides (AMPs; apidaecin, abaecin, defensins, and hymenoptaecin) varied widely among strains and was highest in closely related bee-associated bacteria. Even highly successful colonizers such as Gilliamella and Snodgrassella were AMP-sensitive. AMP sensitivity showed a negative correlation with bacterial load, but not with the frequency of host colonization. These findings suggest that AMPs modulate symbiont abundance rather than acting as strict barriers to colonization. Overall, our results reveal that host filtering in the bee gut is multifaceted, integrating immune-mediated barriers, microbial traits, and competitive interactions.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147976876","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}