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An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut 基于图像的转录组图谱揭示了小鼠肠道的区域和微生物依赖的分子，细胞和空间结构
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-19 DOI: 10.1016/j.chom.2026.01.018
Rosalind J. Xu, Hao Zhang, Paolo Cadinu, Phillip B. Nicol, Uli S. Herrmann, Tyrone Lee, Ludwig Geistlinger, Rafael A. Irizarry, Jeffrey R. Moffitt
{"title":"An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut","authors":"Rosalind J. Xu, Hao Zhang, Paolo Cadinu, Phillip B. Nicol, Uli S. Herrmann, Tyrone Lee, Ludwig Geistlinger, Rafael A. Irizarry, Jeffrey R. Moffitt","doi":"10.1016/j.chom.2026.01.018","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.018","url":null,"abstract":"The gastrointestinal environment is home to a massive diversity of diet-, host-, and microbiota-derived small molecules, collectively sensed by a remarkable variety of cells. To explore the cellular and spatial organization of sensation, we use MERFISH to profile receptor expression across 2.1 million cells in multiple regions of the murine gut under specific-pathogen-free (SPF) and germ-free (GF) conditions. This atlas reveals expected and previously unidentified cell types—including a candidate murine homolog of human BEST4⁺ enterocytes—demonstrates cell-type regional specialization, discovers extensive location-dependent spatial fine-tuning in mucosal cell expression, and suggests cell-type-specific mediators of the effects of microbiota-derived small molecules. Additionally, this atlas reveals that, aside from immune cell abundance, many aspects of the murine gut are host-intrinsic and modified only modestly in the absence of a microbiota. Collectively, this atlas provides a valuable resource for understanding the cellular and spatial organization underlying small-molecule sensation in the gut.","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"37 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146223317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A modular alliance: Probiotics and macrophages converge on glioblastoma 一个模块化的联盟：益生菌和巨噬细胞聚集在胶质母细胞瘤
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-11 DOI: 10.1016/j.chom.2026.01.005
Jiarui Zhao, Jian Chen
{"title":"A modular alliance: Probiotics and macrophages converge on glioblastoma","authors":"Jiarui Zhao, Jian Chen","doi":"10.1016/j.chom.2026.01.005","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.005","url":null,"abstract":"","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"42 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
How a coral holobiont stays in sync in nature 珊瑚全息生物是如何在自然界中保持同步的
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-11 DOI: 10.1016/j.chom.2026.01.010
Cheong Xin Chan
{"title":"How a coral holobiont stays in sync in nature","authors":"Cheong Xin Chan","doi":"10.1016/j.chom.2026.01.010","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.010","url":null,"abstract":"","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"47 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Microbial communities in semi-mature oak trees are resilient to drought, nutrient limitation, and pathogen challenge 半成熟橡树的微生物群落对干旱、营养限制和病原体的挑战具有弹性
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-11 DOI: 10.1016/j.chom.2026.01.009
Usman Hussain, Marine C. Cambon, Bridget Crampton, Sunitha Subramaniam, Anparasy Kajamuhan, Alejandra Ordoñez, Jim Downie, Jasen Finch, Manfred Beckmann, Nathan Brown, Amy Elison, Carrie Brady, Elena Vanguelova, Sandra Denman, James E. McDonald
{"title":"Microbial communities in semi-mature oak trees are resilient to drought, nutrient limitation, and pathogen challenge","authors":"Usman Hussain, Marine C. Cambon, Bridget Crampton, Sunitha Subramaniam, Anparasy Kajamuhan, Alejandra Ordoñez, Jim Downie, Jasen Finch, Manfred Beckmann, Nathan Brown, Amy Elison, Carrie Brady, Elena Vanguelova, Sandra Denman, James E. McDonald","doi":"10.1016/j.chom.2026.01.009","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.009","url":null,"abstract":"","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"60 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Outsmarting the wicked smart: Using chemistry to overcome bacterial anti-viral systems 智胜邪恶的聪明人：利用化学物质来克服细菌的抗病毒系统
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-11 DOI: 10.1016/j.chom.2026.01.015
Antonio Tinoco
{"title":"Outsmarting the wicked smart: Using chemistry to overcome bacterial anti-viral systems","authors":"Antonio Tinoco","doi":"10.1016/j.chom.2026.01.015","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.015","url":null,"abstract":"","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"43 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Seeing the forest: Microbiome resilience in mature trees 观赏森林：成熟树木的微生物群弹性
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-11 DOI: 10.1016/j.chom.2026.01.014
Zahavah Rojer, Tory A. Hendry
{"title":"Seeing the forest: Microbiome resilience in mature trees","authors":"Zahavah Rojer, Tory A. Hendry","doi":"10.1016/j.chom.2026.01.014","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.014","url":null,"abstract":"","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"4 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146161113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protist predators engineer bacterial metabolic cooperation 原生捕食者设计细菌的代谢合作
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-11 DOI: 10.1016/j.chom.2026.01.011
Lu Ma, Longfei Shu
{"title":"Protist predators engineer bacterial metabolic cooperation","authors":"Lu Ma, Longfei Shu","doi":"10.1016/j.chom.2026.01.011","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.011","url":null,"abstract":"","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"10 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146160734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gut DNA virome enterotype dictates inflammation heterogeneity through tuning the phage-bacteria-sphingosine-intestine axis in Crohn's disease 肠道DNA病毒组肠型通过调节克罗恩病中噬菌体-细菌-鞘氨醇-肠轴来指示炎症异质性
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-09 DOI: 10.1016/j.chom.2026.01.016
Weijie Wen, Runping Su, Yunyun Liu, Zhiyang Feng, Yancai Li, Jieli Li, Ziyu Huang, Fen Zhang, Shanshan Gao, Yingfei Ma, Qinghua Zhou, Emad M. El-Omar, Jeremy J. Barr, Tao Zuo
{"title":"Gut DNA virome enterotype dictates inflammation heterogeneity through tuning the phage-bacteria-sphingosine-intestine axis in Crohn's disease","authors":"Weijie Wen, Runping Su, Yunyun Liu, Zhiyang Feng, Yancai Li, Jieli Li, Ziyu Huang, Fen Zhang, Shanshan Gao, Yingfei Ma, Qinghua Zhou, Emad M. El-Omar, Jeremy J. Barr, Tao Zuo","doi":"10.1016/j.chom.2026.01.016","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.016","url":null,"abstract":"The human gut harbors a diverse virome, believed to play a crucial role in maintaining intestinal homeostasis. However, the magnitude of heterogeneity of the gut mucosal virome, and how it differentially regulates host inflammation phenotypes, such as those observed in Crohn’s disease (CD), remains unclear. Here, we identify two mucosal DNA virome enterotypes (E1 and E2) in humans, with E2 subjects exhibiting higher virome diversity and nuanced bacteriophage-bacteria correlations. Moreover, E2-enterotyped CD patients exhibited higher <ce:italic>Wulfhauvirus</ce:italic> abundance than healthy controls. The E2 virome is causally more proinflammatory in inducing intestinal inflammation in mice. Mechanistically, the novel E2-virome-enriched phage øBTZT001P (belonging to <ce:italic>Wulfhauvirus</ce:italic>) lysogenically infects <ce:italic>Bacteroides thetaiotaomicron</ce:italic>, increasing sphingosine production. Downstream, sphingosine suppresses the commensal bacterium <ce:italic>Blautia obeum</ce:italic> in the gut, leading to worsened intestinal inflammation. Our findings reveal that configurational differences in the gut virome may dictate disease outcome through a phage-bacteria-metabolite-intestine axis, highlighting the importance of gut phage-bacteria crosstalk in health.","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"16 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146146660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health 对全球11,115个宏基因组中未培养的肠道微生物组的荟萃分析揭示了健康的候选特征
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-09 DOI: 10.1016/j.chom.2026.01.013
Ana C. da Silva, Jacob Lapkin, Qi Yin, Efrat Muller, Alexandre Almeida
{"title":"Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health","authors":"Ana C. da Silva, Jacob Lapkin, Qi Yin, Efrat Muller, Alexandre Almeida","doi":"10.1016/j.chom.2026.01.013","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.013","url":null,"abstract":"","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"9 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146152834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
HMGB1 functions as a critical mediator of host defense at the gut mucosal barrier HMGB1在肠道粘膜屏障中作为宿主防御的关键介质起作用
IF 30.3 1区 医学
Cell host & microbe Pub Date : 2026-02-03 DOI: 10.1016/j.chom.2026.01.008
Anne-Marie C. Overstreet, McKenzie Burge, Brady Anderson, Xiaorong Zhu, Yun Tao, Candace M. Cham, Brenna Michaud, Soyar Horam, Naseer Sangwan, Mohammed Dwidar, Xuefeng Liu, Akeem Santos, Vartika Srivastava, Chelsea Finney, Christopher M. Goins, Zhanghan Dai, B. Ben Koff, Shaun R. Stauffer, Vanessa A. Leone, Jeannette S. Messer
{"title":"HMGB1 functions as a critical mediator of host defense at the gut mucosal barrier","authors":"Anne-Marie C. Overstreet, McKenzie Burge, Brady Anderson, Xiaorong Zhu, Yun Tao, Candace M. Cham, Brenna Michaud, Soyar Horam, Naseer Sangwan, Mohammed Dwidar, Xuefeng Liu, Akeem Santos, Vartika Srivastava, Chelsea Finney, Christopher M. Goins, Zhanghan Dai, B. Ben Koff, Shaun R. Stauffer, Vanessa A. Leone, Jeannette S. Messer","doi":"10.1016/j.chom.2026.01.008","DOIUrl":"https://doi.org/10.1016/j.chom.2026.01.008","url":null,"abstract":"","PeriodicalId":9693,"journal":{"name":"Cell host & microbe","volume":"43 1","pages":""},"PeriodicalIF":30.3,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146110542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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