The ISME Journal最新文献_第7页

Inositol phosphates as an overlooked phosphorous source in marine ecosystems. 肌醇磷酸盐是海洋生态系统中一个被忽视的磷源。

The ISME Journal Pub Date : 2025-08-11 DOI: 10.1093/ismejo/wraf161

Zhao-Jie Teng,Xiao-Jie Yuan,Rui Liu,Shao-Chun Xu,Xiu-Lan Chen,Yin Chen,Yu-Zhong Zhang

{"title":"Inositol phosphates as an overlooked phosphorous source in marine ecosystems.","authors":"Zhao-Jie Teng,Xiao-Jie Yuan,Rui Liu,Shao-Chun Xu,Xiu-Lan Chen,Yin Chen,Yu-Zhong Zhang","doi":"10.1093/ismejo/wraf161","DOIUrl":"https://doi.org/10.1093/ismejo/wraf161","url":null,"abstract":"Inositol phosphates, common phosphorus storage compounds that are also crucial for eukaryotic cell signaling, constitute a significant portion of dissolved organic phosphorus in coastal waters. The hydrolysis of inositol phosphates could be an important contributor to phosphorus cycling in phosphorus-limited marine ecosystems, yet this process remains poorly understood in marine contexts. In this study, we reveal substantial concentrations of Inositol phosphates in marine macrophytes, including green, brown, and red algae as well as common seagrasses, suggesting that these organisms are likely major biological sources of inositol phosphates in the oceans. A comprehensive analysis of genes involved in inositol phosphates hydrolysis in global marine metagenomes and metatranscriptomes identified key roles for γ-, α-, and δ-proteobacteria, with additional contributions from Flavobacteriia. The degradation of marine inositol phosphates was predominantly mediated by alkaline β-propeller phytases, though genes associated with acidic cysteine phytases and purple acid phytases were also widely present. Community structure and functional traits linked to inositol phosphates degradation were shaped largely by stochastic processes. Further examination of enzyme activity at the protein and community levels indicated that phytate metabolism by marine microbes is likely a widespread phenomenon in the ocean. Overall, this study highlights inositol phosphates hydrolysis as an essential yet overlooked adaptation by marine microorganisms to address phosphorus limitations in ocean ecosystems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Global dominance of Haloquadratum walsbyi by a single highly clonal genomovar with distinct gene content and viral cohorts from close relatives. 一个具有不同基因含量的高克隆基因组变体和来自近亲的病毒群在全球占据优势地位。

The ISME Journal Pub Date : 2025-08-04 DOI: 10.1093/ismejo/wraf165

Esteban Bustos-Caparros,Tomeu Viver,Juan F Gago,Juanita R Avontuur,Souad Amiour,Bonnie K Baxter,María E Llames,Mehmet B Mutlu,Aharon Oren,Ana S Ramírez,Matthew B Stott,Stephanus N Venter,Fernando Santos,Josefa Antón,Luis M Rodriguez-R,Rafael Bosch,Brian P Hedlund,Konstantinos T Konstantinidis,Ramon Rossello-Mora

{"title":"Global dominance of Haloquadratum walsbyi by a single highly clonal genomovar with distinct gene content and viral cohorts from close relatives.","authors":"Esteban Bustos-Caparros,Tomeu Viver,Juan F Gago,Juanita R Avontuur,Souad Amiour,Bonnie K Baxter,María E Llames,Mehmet B Mutlu,Aharon Oren,Ana S Ramírez,Matthew B Stott,Stephanus N Venter,Fernando Santos,Josefa Antón,Luis M Rodriguez-R,Rafael Bosch,Brian P Hedlund,Konstantinos T Konstantinidis,Ramon Rossello-Mora","doi":"10.1093/ismejo/wraf165","DOIUrl":"https://doi.org/10.1093/ismejo/wraf165","url":null,"abstract":"Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > ANI > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"112 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rapid water flow triggers long-distance positive rheotaxis for thermophilic bacteria 快速水流触发嗜热细菌的长距离正流变性

The ISME Journal Pub Date : 2025-08-01 DOI: 10.1093/ismejo/wraf164

Naoki A Uemura, Naoya Chiba, Ryota Morikawa, Masatada Tamakoshi, Daisuke Nakane

{"title":"Rapid water flow triggers long-distance positive rheotaxis for thermophilic bacteria","authors":"Naoki A Uemura, Naoya Chiba, Ryota Morikawa, Masatada Tamakoshi, Daisuke Nakane","doi":"10.1093/ismejo/wraf164","DOIUrl":"https://doi.org/10.1093/ismejo/wraf164","url":null,"abstract":"Bacteria thrive in nearly all environments on Earth, demonstrating remarkable adaptability to physical stimuli, as well as chemicals and light. However, the mechanisms by which bacteria locate and settle in ecological niches optimal for their growth remains poorly understood. Here, we show that Thermus thermophilus, a highly thermophilic non-flagellated species of bacteria, exhibits positive rheotaxis, navigating upstream in unidirectional rapid water flow. Mimicking their natural habitat at 70°C with a water current under optical microscopy, cells traveled distances up to 1 mm in 30 min, with infrequent directional changes. This long-distance surface migration is driven by type IV pili, facilitating vertical attachment at the cell pole, and shear-induced tilting of the cell body, resulting in alignment of the leading pole toward the direction of water flow. Direct visualization of T4P filaments and their dynamics revealed that rheotaxis is triggered by weakened attachment at the cell pole, regulated by ATPase activity, which was further validated by mathematical modeling. Flow experiments on 15 bacterial strains and species in the Deinococcota (synonym Deinococcus-Thermus) phylum revealed that positive rheotaxis is highly conserved among rod-shaped Thermaceae, but absent in spherical-shaped Deinococcus. Our findings suggest that thermophilic bacteria reach their ecological niches by responding to the physical stimulus of rapid water flow, a ubiquitous feature in hot spring environments. This study highlights unforeseen survival strategies, showcasing an evolutionary adaptation to a surface-associated lifestyle where swimming bacteria would otherwise be swept away.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Engineering Plant Holobionts for Climate-Resilient Agriculture 气候适应型农业的植物全息生物工程

The ISME Journal Pub Date : 2025-08-01 DOI: 10.1093/ismejo/wraf158

Nayanci Portal-Gonzalez, Wenbo Wang, Wenxing He, Ramon Santos-Bermudez

{"title":"Engineering Plant Holobionts for Climate-Resilient Agriculture","authors":"Nayanci Portal-Gonzalez, Wenbo Wang, Wenxing He, Ramon Santos-Bermudez","doi":"10.1093/ismejo/wraf158","DOIUrl":"https://doi.org/10.1093/ismejo/wraf158","url":null,"abstract":"The plant holobiont—an integrated unit of the host and its microbiome—has co-evolved through ecological and genetic interactions. Microbiome engineering offers a promising route to enhance resilience in response to climate stress, soil degradation, and yield stagnation. This review presents an integrated framework combining microbial ecology, synthetic biology, and computational modeling to rationally design synthetic microbial communities (SynComs) for agriculture. We outline ecological principles—priority effects, keystone taxa, and functional redundancy—that shape microbiome assembly and guide SynCom design. Strategies like CRISPR interference, biosensor circuits, and quorum-sensing modules enable programmable microbial functions. We also highlight the predictive potential of in silico modeling—including genome-scale metabolic models, dynamic flux balance analysis, and machine learning—to simulate interactions, optimize SynCom composition, and enhance design accuracy. To bridge lab and field, we discuss native microbial chassis, encapsulation, and precision delivery as tools for scalable, ecosystem-integrated deployment. We introduce the concept of the programmable holobiont: an engineered plant-microbe partnership capable of dynamic feedback, interkingdom signaling, and ecological memory. This systems-level perspective reframes plants as designable ecosystems. By synthesizing cross-disciplinary advances, we offer a roadmap for climate-resilient agriculture, where engineered microbiomes improve sustainability, yield stability, and environmental adaptation.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Habitat filtering more than microbiota origin controls microbiome transplant outcomes in soil 生境过滤比微生物群来源更能控制微生物群在土壤中的移植结果

The ISME Journal Pub Date : 2025-08-01 DOI: 10.1093/ismejo/wraf162

Senka Causevic, Janko Tackmann, Vladimir Sentchilo, Lukas Malfertheiner, Christian von Mering, Jan Roelof van der Meer

{"title":"Habitat filtering more than microbiota origin controls microbiome transplant outcomes in soil","authors":"Senka Causevic, Janko Tackmann, Vladimir Sentchilo, Lukas Malfertheiner, Christian von Mering, Jan Roelof van der Meer","doi":"10.1093/ismejo/wraf162","DOIUrl":"https://doi.org/10.1093/ismejo/wraf162","url":null,"abstract":"Human activities cause a global loss of soil microbiome diversity and functionality. One way to reverse this trend is through microbiota transplants, but the processes determining merger outcomes are not well understood. Here, we investigated the roles of habitat filtering and microbiota origin on microbiome development upon mergers, with the hypothesis that native strains are better adapted to their own habitat and will outcompete non-native ones in niche colonization. To test this, we contrasted community development in soil microcosms between two taxa-diverse microbiota originating from either topsoil (SoilCom) or freshwater lake (LakeCom), and a defined mixture of 21 soil bacteria (SynCom). When inoculated separately, SoilCom and LakeCom showed similar taxa and colonization patterns contributing to community growth and decline within the soil microcosms. SynCom transplants to either SoilCom or LakeCom under renewed growth conditions permanently altered their community trajectories, and slightly further converged their taxa compositions. Levels of SynCom members in both resident backgrounds decreased from initial 50-80% to below 1% within two months. Merged as well as non-merged communities resembled natural soils in comparison to over 81,000 publicly available soil, sediment, and lake microbiomes. Our results show that habitat filtering is dominant over microbiota taxa origin in determining transplant outcomes. Even though the proliferation of SynCom transplants remained limited, their capacity to influence community merger trajectories long term opens new paths for soil microbiome engineering.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Presence of a biofilm beneficiary alters the evolutionary trajectory of a biofilm former 受益生物膜的存在改变了原生物膜的进化轨迹

The ISME Journal Pub Date : 2025-07-31 DOI: 10.1093/ismejo/wraf160

Xinli Sun, Zhihui Xu, Guohai Hu, Jiyu Xie, Yun Li, Lili Tao, Nan Zhang, Weibing Xun, Youzhi Miao, Ruifu Zhang, Qirong Shen, Christian Kost, Ákos T Kovács

{"title":"Presence of a biofilm beneficiary alters the evolutionary trajectory of a biofilm former","authors":"Xinli Sun, Zhihui Xu, Guohai Hu, Jiyu Xie, Yun Li, Lili Tao, Nan Zhang, Weibing Xun, Youzhi Miao, Ruifu Zhang, Qirong Shen, Christian Kost, Ákos T Kovács","doi":"10.1093/ismejo/wraf160","DOIUrl":"https://doi.org/10.1093/ismejo/wraf160","url":null,"abstract":"Biofilm evolution is typically studied in monocultures or in communities displaying mutualistic or exploitative interactions. However, in communities with fluctuating interactions, the influence of biofilm-beneficiary bacteria on the evolution of biofilm-founder bacteria remains less understood. Biofilm-beneficiary bacteria cannot form robust biofilms independently but can incorporate into the biofilm of biofilm-formers, thereby gaining the ability to colonize given niche. In this study, we demonstrate that the biofilm-former Bacillus velezensis SQR9 reproducibly diversified into biofilm-enhanced slimy and biofilm-weakened rough types, both in the presence and absence of a biofilm-beneficiary Stutzerimonas degradans XL272 (formerly Pseudomonas stutzeri), but with variable frequencies under the two conditions. The exopolysaccharide producer slimy types dominated B. velezensis populations in monoevolution, whereas the exploiter rough types, which exploit the exopolysaccharides produced by the slimy types, dominate in coculture evolution. Phenotypic changes in B. velezensis were linked to mutations in specific genes that regulate biofilm formation and sporulation, including ywcC, comA, comP, degS, degQ, and spo0F. A frameshift mutation in the cpsA gene of Saccharophagus degradans increased its exopolysaccharide production in the dual-species biofilm, which served as shared resources and allow the B. velezensis exploiter (i.e., rough type) to outcompete the producer (i.e., slimy type) during coculture evolution. Additionally, longitudinal population sequencing and “replay” evolution experiments with the S. degradans mutant revealed that the cpsA mutation accelerated the fixation of the rough type within B. velezensis populations. In conclusion, this research demonstrates that interspecific interactions can adaptively favor exploiters within biofilm populations.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144747521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Horizontal transmission of heat-evolved microalgal symbionts in adult corals. 热进化微藻共生体在成年珊瑚中的水平传播。

The ISME Journal Pub Date : 2025-07-30 DOI: 10.1093/ismejo/wraf157

Bede G Johnston,Matthew R Nitschke,Wing Yan Chan,Madeleine J H van Oppen

{"title":"Horizontal transmission of heat-evolved microalgal symbionts in adult corals.","authors":"Bede G Johnston,Matthew R Nitschke,Wing Yan Chan,Madeleine J H van Oppen","doi":"10.1093/ismejo/wraf157","DOIUrl":"https://doi.org/10.1093/ismejo/wraf157","url":null,"abstract":"Traditional coral reef restoration methods often fail to consider rising sea-surface temperatures driven by climate change. The introduction of experimentally heat-evolved algal symbionts into corals offers a promising solution by enhancing coral holobiont thermotolerance in a relatively short timeframe. However, the scalability of this approach remains a key challenge. Coral expulsion of viable symbiont cells may provide a passive pathway for upscaling this intervention by facilitating the widespread transmission of heat-evolved symbionts and their physiological benefits across coral reefs. Here, we investigated the expulsion and horizontal transmission dynamics of heat-evolved Cladocopium proliferum (strain SS8) in the scleractinian coral Galaxea fascicularis. First, we assessed the 24-hour symbiont expulsion dynamics of three colonies of G. fascicularis hosting SS8 in addition to homologous symbionts. SS8 was detected in the expelled symbiont community of all colonies, with diel peaks in mitotic index and photochemical efficiency observed at night and the majority of expelled cells appearing morphologically intact. Second, we tested whether expelled SS8 could be acquired by chemically bleached adult G. fascicularis fragments in a custom-designed multi-lane raceway experiment. After 55 days of exposure to an SS8-expelling G. fascicularis donor, SS8 was detected at background levels (≤0.06%) in 11.1% of recipient fragments (5/45). These findings provide the first empirical evidence that viable, heat-evolved symbionts can be expelled and acquired by bleached adult corals, highlighting a potential natural pathway for the scaling up of this intervention to enhance coral thermal resilience.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"111 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Decoding the SCFA-CpxAR-OMP Axis as a Dietary Checkpoint against Antimicrobial Resistance Transmission across Gut-Environment Interfaces. 解码SCFA-CpxAR-OMP轴作为抗微生物耐药性在肠道-环境界面传播的膳食检查点

The ISME Journal Pub Date : 2025-07-30 DOI: 10.1093/ismejo/wraf156

Rong Tan,Yuanyuan Song,Jing Yin,Danyang Shi,Haibei Li,Tianjiao Chen,Yating Wang,Min Jin,Junwen Li,Dong Yang

{"title":"Decoding the SCFA-CpxAR-OMP Axis as a Dietary Checkpoint against Antimicrobial Resistance Transmission across Gut-Environment Interfaces.","authors":"Rong Tan,Yuanyuan Song,Jing Yin,Danyang Shi,Haibei Li,Tianjiao Chen,Yating Wang,Min Jin,Junwen Li,Dong Yang","doi":"10.1093/ismejo/wraf156","DOIUrl":"https://doi.org/10.1093/ismejo/wraf156","url":null,"abstract":"The transmission of environmental-originated antibiotic resistance genes (ARGs) into the human gut via the food chain or water has transformed the intestinal tract into a critical reservoir and dissemination hub for ARGs. Moreover, human to human oral-fecal transmission is likely to intensify this dissemination cycle. Gut microbiota harboring ARGs not only drive clinical infections but also exacerbate diverse pathologies, including inflammatory bowel disease and metabolic disorders. Furthermore, amplified ARGs can re-enter environmental compartments through fecal discharge, establishing a persistent bidirectional \"gut-environment\" resistance transmission cycle. In this study, we demonstrate that short-chain fatty acids (SCFAs), key metabolites derived from gut microbiota, potently suppress the horizontal transfer of ARGs. A high-fiber diet reshaped gut microbial composition, elevating SCFA production by 2.3-fold and reducing ARGs dissemination rates by up to 5.8-fold in vivo. The anti-conjugation activity of SCFAs was further validated through in vitro observations and in vivo models. Mechanistically, we propose the CpxAR-OMP pathway as a previously uncharacterized regulatory axis, wherein SCFAs inhibit ARGs transfer by downregulating conjugation-associated promoters (trfAp and trbBp) and disrupting membrane function via CpxAR-mediated suppression of OMPs expression. To our knowledge, this work provides comprehensive evidence of SCFAs in curbing exogenous ARGs dissemination within the gut ecosystem, deciphers the CpxAR-OMP-driven molecular mechanism, and proposes dietary fiber intervention as a feasible strategy to mitigate antimicrobial resistance across the \"One-Health\" continuum.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"715 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolic interactions underlying phyllosphere microbiota assembly. 层球微生物群聚集背后的代谢相互作用。

The ISME Journal Pub Date : 2025-07-28 DOI: 10.1093/ismejo/wraf155

Wenzhuo Feng,Fengquan Liu

引用次数: 0

Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri. 社会群体内的细菌传播塑造了狐猴Indri Indri未被探索的肠道微生物群。

The ISME Journal Pub Date : 2025-07-25 DOI: 10.1093/ismejo/wraf136

Francisca Labisa-Morais,Daria Valente,Aitor Blanco-Míguez,Paolo Manghi,Albert Garcia-Valiente,Harilala Andriamaniraka,Federica Armanini,Francesco Asnicar,Chiara De Gregorio,Davide Golzato,Serena Manara,Monica Modesto,Elisa Piperni,Michal Punčochář,Donatella Scarafile,Valeria Torti,Luigimaria Borruso,Paola Mattarelli,Cristina Giacoma,Camillo Sandri,Caterina Spiezio,Nicola Segata,Mireia Valles-Colomer

{"title":"Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri.","authors":"Francisca Labisa-Morais,Daria Valente,Aitor Blanco-Míguez,Paolo Manghi,Albert Garcia-Valiente,Harilala Andriamaniraka,Federica Armanini,Francesco Asnicar,Chiara De Gregorio,Davide Golzato,Serena Manara,Monica Modesto,Elisa Piperni,Michal Punčochář,Donatella Scarafile,Valeria Torti,Luigimaria Borruso,Paola Mattarelli,Cristina Giacoma,Camillo Sandri,Caterina Spiezio,Nicola Segata,Mireia Valles-Colomer","doi":"10.1093/ismejo/wraf136","DOIUrl":"https://doi.org/10.1093/ismejo/wraf136","url":null,"abstract":"The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this lemur's virtually unexplored gut microbiome will deepen our understanding of the species' health determinants and inform conservation efforts. Through metagenomic assembly and integration into an updated reference database, we found the I. indri faecal microbiome remains largely uncultivated (cultivated species representing <0.1% relative abundance) and is largely specific to this primate species. After reconstructing 342 metagenome-assembled genomes encompassing 48 candidate species from a total of 22 samples (18 of which newly sequenced), we substantially improved microbiome mappability to 85% on average and found evidence for a proportionally large core microbiome. Social group membership emerged as the main determinant of both their taxonomic and functional gut microbiome composition. Using strain-level profiling, we detected extensive microbiome transmission within social groups, suggesting physical interaction is key in promoting microbiome acquisition. Strain sharing rates were highest between mothers and their offspring. Intergroup strain sharing was minimal and inversely correlated with geographical distance, aligning with the rare intergroup interactions and stable territory occupancy coupled with ongoing habitat fragmentation. No evidence of microbiome acquisition through geophagy was detected. These findings underscore the profound influence of social structure on microbiome transmission and composition in I. indri, and highlight the importance of considering social dynamics into research and conservation strategies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0