Nature Microbiology最新文献

How microbial growth adapts to temperature shifts

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-12-23 DOI: 10.1038/s41564-024-01847-y

引用次数: 0

Bacterial and host fucosylation maintain IgA homeostasis to limit intestinal inflammation in mice 细菌和宿主岩藻糖基化维持 IgA 平衡，限制小鼠肠道炎症

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-12-17 DOI: 10.1038/s41564-024-01873-w

Chao Lei, Chao Luo, Zhishan Xu, Shu Ding, Mukesh K. Sriwastva, Gerald Dryden, Ting Wang, Manman Xu, Yi Tan, Qilong Wang, Xiaozhong Yang, Craig J. McClain, Zhongbin Deng

{"title":"Bacterial and host fucosylation maintain IgA homeostasis to limit intestinal inflammation in mice","authors":"Chao Lei, Chao Luo, Zhishan Xu, Shu Ding, Mukesh K. Sriwastva, Gerald Dryden, Ting Wang, Manman Xu, Yi Tan, Qilong Wang, Xiaozhong Yang, Craig J. McClain, Zhongbin Deng","doi":"10.1038/s41564-024-01873-w","DOIUrl":"https://doi.org/10.1038/s41564-024-01873-w","url":null,"abstract":"Inflammatory bowel disease is associated with several genetic risk loci. Loss-of-function mutation in the α1,2-fucosyltransferase (fut2) gene, which alters fucosylation on the surface of intestinal epithelial cells, is one example. However, whether bacterial fucosylation can contribute to gut inflammation is unclear. Here we show that host fucosylation status influences fucosylation biosynthesis by gut commensal bacteria. Mice colonized with faecal microbiota of Fut2 knockout mice or Bacteroides fragilis with lower surface fucosylation are predisposed to colitis. This was supported by human cohort data showing that bacterial fucosylation levels decrease in patients with inflammatory bowel disease and correlate with intestinal inflammation. Using a mouse model for Bacteroides fragilis to explore the role of fucosylation in gut immunity, we show that the fucosylation status of epithelial cells and bacteria is critical for maintaining B cell responses in the gut. Host-derived and dietary fucose mediate immunoglobulin A (IgA) recognition of gut microbiota, and this interaction facilitates the translocation of commensals to Peyer’s patches and alters the immune landscape of Peyer’s patches with increased germinal centre B cells and IgA-secreting antigen-specific B cells. Finally, dietary fucose enhances the IgA response against Salmonella and protects against systemic bacterial dissemination. This highlights the role of host and bacterial fucosylation in maintaining IgA homeostasis and immune escape mechanisms.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"22 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142832156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolic rearrangement enables adaptation of microbial growth rate to temperature shifts

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-12-13 DOI: 10.1038/s41564-024-01841-4

Benjamin D. Knapp, Lisa Willis, Carlos Gonzalez, Harsh Vashistha, Joanna Jammal-Touma, Mikhail Tikhonov, Jeffrey Ram, Hanna Salman, Josh E. Elias, Kerwyn Casey Huang

{"title":"Metabolic rearrangement enables adaptation of microbial growth rate to temperature shifts","authors":"Benjamin D. Knapp, Lisa Willis, Carlos Gonzalez, Harsh Vashistha, Joanna Jammal-Touma, Mikhail Tikhonov, Jeffrey Ram, Hanna Salman, Josh E. Elias, Kerwyn Casey Huang","doi":"10.1038/s41564-024-01841-4","DOIUrl":"https://doi.org/10.1038/s41564-024-01841-4","url":null,"abstract":"Temperature is a key determinant of microbial behaviour and survival in the environment and within hosts. At intermediate temperatures, growth rate varies according to the Arrhenius law of thermodynamics, which describes the effect of temperature on the rate of a chemical reaction. However, the mechanistic basis for this behaviour remains unclear. Here we use single-cell microscopy to show that Escherichia coli exhibits a gradual response to temperature upshifts with a timescale of ~1.5 doublings at the higher temperature. The response was largely independent of initial or final temperature and nutrient source. Proteomic and genomic approaches demonstrated that adaptation to temperature is independent of transcriptional, translational or membrane fluidity changes. Instead, an autocatalytic enzyme network model incorporating temperature-sensitive Michaelis–Menten kinetics recapitulates all temperature-shift dynamics through metabolome rearrangement, resulting in a transient temperature memory. The model successfully predicts alterations in the temperature response across nutrient conditions, diverse E. coli strains from hosts with different body temperatures, soil-dwelling Bacillus subtilis and fission yeast. In sum, our model provides a mechanistic framework for Arrhenius-dependent growth.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"146 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Multikingdom and functional gut microbiota markers for autism spectrum disorder

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-12-04 DOI: 10.1038/s41564-024-01900-w

Qi Su, Oscar W. H. Wong, Wenqi Lu, Yating Wan, Lin Zhang, Wenye Xu, Moses K. T. Li, Chengyu Liu, Chun Pan Cheung, Jessica Y. L. Ching, Pui Kuan Cheong, Ting Fan Leung, Sandra Chan, Patrick Leung, Francis K. L. Chan, Siew C. Ng

引用次数: 0

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-12-02 DOI: 10.1038/s41564-024-01857-w

Nazgul Sakenova, Elisabetta Cacace, Askarbek Orakov, Florian Huber, Vallo Varik, George Kritikos, Jan Michiels, Peer Bork, Pascale Cossart, Camille V. Goemans, Athanasios Typas

{"title":"Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics","authors":"Nazgul Sakenova, Elisabetta Cacace, Askarbek Orakov, Florian Huber, Vallo Varik, George Kritikos, Jan Michiels, Peer Bork, Pascale Cossart, Camille V. Goemans, Athanasios Typas","doi":"10.1038/s41564-024-01857-w","DOIUrl":"https://doi.org/10.1038/s41564-024-01857-w","url":null,"abstract":"By acquiring or evolving resistance to one antibiotic, bacteria can become cross-resistant to a second antibiotic, which further limits therapeutic choices. In the opposite scenario, initial resistance leads to collateral sensitivity to a second antibiotic, which can inform cycling or combinatorial treatments. Despite their clinical relevance, our knowledge of both interactions is limited. We used published chemical genetics data of the Escherichia coli single-gene deletion library in 40 antibiotics and devised a metric that discriminates between known cross-resistance and collateral-sensitivity antibiotic interactions. Thereby we inferred 404 cases of cross-resistance and 267 of collateral-sensitivity, expanding the number of known interactions by over threefold. We further validated 64/70 inferred interactions using experimental evolution. By identifying mutants driving these interactions in chemical genetics, we demonstrated that a drug pair can exhibit both interactions depending on the resistance mechanism. Finally, we applied collateral-sensitive drug pairs in combination to reduce antibiotic-resistance development in vitro.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"204 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Environmentally dependent interactions shape patterns in gene content across natural microbiomes

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-12-02 DOI: 10.1038/s41564-024-01899-0

Kyle Crocker, Kiseok Keith Lee, Milena Chakraverti-Wuerthwein, Zeqian Li, Mikhail Tikhonov, Madhav Mani, Karna Gowda, Seppe Kuehn

引用次数: 0

Influenza A(H5N1) shedding in air corresponds to transmissibility in mammals

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-12-02 DOI: 10.1038/s41564-024-01885-6

Ilona I. Tosheva, Fabien Filaire, Willemijn F. Rijnink, Dennis de Meulder, Bianca van Kekem, Theo M. Bestebroer, Mathis Funk, Monique I. Spronken, C. Joaquin Cáceres, Daniel R. Perez, Mathilde Richard, Marion P. G. Koopmans, Pieter L. A. Fraaij, Ron A. M. Fouchier, Sander Herfst

{"title":"Influenza A(H5N1) shedding in air corresponds to transmissibility in mammals","authors":"Ilona I. Tosheva, Fabien Filaire, Willemijn F. Rijnink, Dennis de Meulder, Bianca van Kekem, Theo M. Bestebroer, Mathis Funk, Monique I. Spronken, C. Joaquin Cáceres, Daniel R. Perez, Mathilde Richard, Marion P. G. Koopmans, Pieter L. A. Fraaij, Ron A. M. Fouchier, Sander Herfst","doi":"10.1038/s41564-024-01885-6","DOIUrl":"https://doi.org/10.1038/s41564-024-01885-6","url":null,"abstract":"An increase in spillover events of highly pathogenic avian influenza A(H5N1) viruses to mammals suggests selection of viruses that transmit well in mammals. Here we use air-sampling devices to continuously sample infectious influenza viruses expelled by experimentally infected ferrets. The resulting quantitative virus shedding kinetics data resembled ferret-to-ferret transmission studies and indicated that the absence of transmission observed for earlier A(H5N1) viruses was due to a lack of infectious virus shedding in the air, rather than the absence of necessary mammalian adaptation mutations. Whereas infectious human A(H1N1pdm) virus was efficiently shed in the air, infectious 2005 zoonotic and 2024 bovine A(H5N1) viruses were not detected in the air. By contrast, shedding of infectious virus was observed for 1 out of 4 ferrets infected with a 2022 European polecat A(H5N1) virus and a 2024 A(H5N1) virus isolated from a dairy farm worker.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"20 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deep mutation, insertion and deletion scanning across the Enterovirus A proteome reveals constraints shaping viral evolution 对 A 型肠病毒蛋白质组进行深度突变、插入和缺失扫描，揭示影响病毒进化的制约因素

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-28 DOI: 10.1038/s41564-024-01871-y

William Bakhache, Walker Symonds-Orr, Lauren McCormick, Patrick T. Dolan

引用次数: 0

A year of microbiology 微生物学年

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-11-27 DOI: 10.1038/s41564-024-01880-x

引用次数: 0

Gut physiology and environment explain variations in human gut microbiome composition and metabolism 肠道生理学和环境可解释人类肠道微生物群组成和代谢的变化

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-11-27 DOI: 10.1038/s41564-024-01856-x

Nicola Procházková, Martin F. Laursen, Giorgia La Barbera, Eirini Tsekitsidi, Malte S. Jørgensen, Morten A. Rasmussen, Jeroen Raes, Tine R. Licht, Lars O. Dragsted, Henrik M. Roager

{"title":"Gut physiology and environment explain variations in human gut microbiome composition and metabolism","authors":"Nicola Procházková, Martin F. Laursen, Giorgia La Barbera, Eirini Tsekitsidi, Malte S. Jørgensen, Morten A. Rasmussen, Jeroen Raes, Tine R. Licht, Lars O. Dragsted, Henrik M. Roager","doi":"10.1038/s41564-024-01856-x","DOIUrl":"10.1038/s41564-024-01856-x","url":null,"abstract":"The human gut microbiome is highly personal. However, the contribution of gut physiology and environment to variations in the gut microbiome remains understudied. Here we performed an observational trial using multi-omics to profile microbiome composition and metabolism in 61 healthy adults for 9 consecutive days. We assessed day-to-day changes in gut environmental factors and measured whole-gut and segmental intestinal transit time and pH using a wireless motility capsule in a subset of 50 individuals. We observed substantial daily fluctuations, with intra-individual variations in gut microbiome and metabolism associated with changes in stool moisture and faecal pH, and inter-individual variations accounted for by whole-gut and segmental transit times and pH. Metabolites derived from microbial carbohydrate fermentation correlated negatively with the gut passage time and pH, while proteolytic metabolites and breath methane showed a positive correlation. Finally, we identified associations between segmental transit time/pH and coffee-, diet-, host- and microbial-derived metabolites. Our work suggests that gut physiology and environment are key to understanding the individuality of the human gut microbial composition and metabolism. An observational longitudinal clinical trial, incorporating a SmartPill and metabolomics, reveals the role of host factors in shaping the gut microbiome in healthy human adults.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3210-3225"},"PeriodicalIF":20.5,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01856-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142718340","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}

引用次数: 0