Pub Date : 2026-01-12DOI: 10.1038/s41579-025-01271-x
J Casper Swarte,Shuyan Zhang,Stephan J L Bakker,Johannes R Björk,Rinse K Weersma
Solid-organ transplantation (for example, kidney or liver) and haematopoietic-stem-cell transplantation have revolutionized treatment of end-stage organ failure and haematological malignancies. However, long-term outcomes are often undermined by complications such as allograft rejection, graft-versus-host disease in haematopoietic-stem-cell recipients, opportunistic infections, adverse effects of drugs and decreased quality of life. Emerging evidence now highlights the gut microbiome and its metabolites (such as short-chain fatty acids) as a potentially modifiable factor influencing transplantation outcomes. Transplantation recipients frequently exhibit gut dysbiosis, which has been linked to graft function, risk of infection (for example, vulnerability to multidrug-resistant bacteria), immune-mediated complications and patient survival. Furthermore, pharmacomicrobiomics studies indicate that microorganisms can metabolize immunosuppressive drugs into less active forms (such as the conversion of the immunosuppressive drug tacrolimus into less active or toxic forms through keto-reduction, glucuronidation or deconjugation) or can activate prodrugs (such as the conversion of mycophenolate mofetil into mycophenolic acid), thereby modulating drug efficacy and safety. Here, we discuss how the intestinal ecosystem is altered and persistently shaped by transplantation-related factors and immunosuppression and how these changes correlate with clinical outcomes. We provide a perspective on leveraging microbiome insights, through biomarkers or microbiome-targeted interventions, to improve outcomes in solid-organ and stem-cell transplantation.
{"title":"The gut microbiome in solid-organ and haematopoietic-stem-cell transplantation.","authors":"J Casper Swarte,Shuyan Zhang,Stephan J L Bakker,Johannes R Björk,Rinse K Weersma","doi":"10.1038/s41579-025-01271-x","DOIUrl":"https://doi.org/10.1038/s41579-025-01271-x","url":null,"abstract":"Solid-organ transplantation (for example, kidney or liver) and haematopoietic-stem-cell transplantation have revolutionized treatment of end-stage organ failure and haematological malignancies. However, long-term outcomes are often undermined by complications such as allograft rejection, graft-versus-host disease in haematopoietic-stem-cell recipients, opportunistic infections, adverse effects of drugs and decreased quality of life. Emerging evidence now highlights the gut microbiome and its metabolites (such as short-chain fatty acids) as a potentially modifiable factor influencing transplantation outcomes. Transplantation recipients frequently exhibit gut dysbiosis, which has been linked to graft function, risk of infection (for example, vulnerability to multidrug-resistant bacteria), immune-mediated complications and patient survival. Furthermore, pharmacomicrobiomics studies indicate that microorganisms can metabolize immunosuppressive drugs into less active forms (such as the conversion of the immunosuppressive drug tacrolimus into less active or toxic forms through keto-reduction, glucuronidation or deconjugation) or can activate prodrugs (such as the conversion of mycophenolate mofetil into mycophenolic acid), thereby modulating drug efficacy and safety. Here, we discuss how the intestinal ecosystem is altered and persistently shaped by transplantation-related factors and immunosuppression and how these changes correlate with clinical outcomes. We provide a perspective on leveraging microbiome insights, through biomarkers or microbiome-targeted interventions, to improve outcomes in solid-organ and stem-cell transplantation.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"4 1","pages":""},"PeriodicalIF":88.1,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145956192","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}
Pub Date : 2026-01-05DOI: 10.1038/s41579-025-01268-6
Roy Hajjar,Ruben A T Mars,Purna C Kashyap
The microbiome is increasingly recognized as a key player in cancer pathogenesis and treatment response, acting through both local and systemic mechanisms. Microbial communities and their metabolites can directly influence drug metabolism, shape the immune landscape, and alter transcriptional and epigenetic programmes in the gut, systemically and in the tumour microenvironment. Emerging data support the potential of microbiome-targeted interventions (such as faecal microbiota transplantation, diet, prebiotics and probiotics) as adjuncts to conventional cancer therapies, with the goal of enhancing efficacy and reducing toxicity. This Review highlights the promise of the microbiome as a prognostic and predictive biomarker, a modifiable factor in cancer care and prevention, and a therapeutic target. We also discuss major knowledge gaps, limitations in current study designs, and the need for mechanism-guided, personalized strategies to advance clinical translation.
{"title":"Harnessing the microbiome for cancer therapy.","authors":"Roy Hajjar,Ruben A T Mars,Purna C Kashyap","doi":"10.1038/s41579-025-01268-6","DOIUrl":"https://doi.org/10.1038/s41579-025-01268-6","url":null,"abstract":"The microbiome is increasingly recognized as a key player in cancer pathogenesis and treatment response, acting through both local and systemic mechanisms. Microbial communities and their metabolites can directly influence drug metabolism, shape the immune landscape, and alter transcriptional and epigenetic programmes in the gut, systemically and in the tumour microenvironment. Emerging data support the potential of microbiome-targeted interventions (such as faecal microbiota transplantation, diet, prebiotics and probiotics) as adjuncts to conventional cancer therapies, with the goal of enhancing efficacy and reducing toxicity. This Review highlights the promise of the microbiome as a prognostic and predictive biomarker, a modifiable factor in cancer care and prevention, and a therapeutic target. We also discuss major knowledge gaps, limitations in current study designs, and the need for mechanism-guided, personalized strategies to advance clinical translation.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"18 1","pages":""},"PeriodicalIF":88.1,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145897565","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}
Pub Date : 2026-01-02DOI: 10.1038/s41579-025-01266-8
Daniel Rios Garza, Didier Gonze, Karoline Faust
Different definitions of keystone taxa and functions agree that they have an outsized role in maintaining community composition, and thus, the keystone concept continues to attract attention even 50 years after its introduction. In this Perspective, we base our definition of microbial keystones on the original one to explore its implications and limitations. We review different mechanisms behind keystoneness, cover the strengths and weaknesses of current keystone prediction methods and present findings on keystones discovered in recent experiments. In addition, we suggest a new prediction method for keystones based on metabolic modelling. Finally, we discuss the role of keystones in community control strategies. Overall, the development of new prediction methods and the insights from recent experiments illustrate the continued relevance of the keystone concept for microbial communities.
{"title":"Keystone concept revisited: insights into microbial community dynamics and control.","authors":"Daniel Rios Garza, Didier Gonze, Karoline Faust","doi":"10.1038/s41579-025-01266-8","DOIUrl":"https://doi.org/10.1038/s41579-025-01266-8","url":null,"abstract":"<p><p>Different definitions of keystone taxa and functions agree that they have an outsized role in maintaining community composition, and thus, the keystone concept continues to attract attention even 50 years after its introduction. In this Perspective, we base our definition of microbial keystones on the original one to explore its implications and limitations. We review different mechanisms behind keystoneness, cover the strengths and weaknesses of current keystone prediction methods and present findings on keystones discovered in recent experiments. In addition, we suggest a new prediction method for keystones based on metabolic modelling. Finally, we discuss the role of keystones in community control strategies. Overall, the development of new prediction methods and the insights from recent experiments illustrate the continued relevance of the keystone concept for microbial communities.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":" ","pages":""},"PeriodicalIF":103.3,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145889607","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}
Pub Date : 2025-12-17DOI: 10.1038/s41579-025-01276-6
Shimona Starling
A study by Medina Ferrer and Nayak identifies an archaeal transcription factor in methanogenic archaea that functions as a one-component system, with a eukaryotic-like DNA-binding motif.
{"title":"A transcription factor that links domains","authors":"Shimona Starling","doi":"10.1038/s41579-025-01276-6","DOIUrl":"10.1038/s41579-025-01276-6","url":null,"abstract":"A study by Medina Ferrer and Nayak identifies an archaeal transcription factor in methanogenic archaea that functions as a one-component system, with a eukaryotic-like DNA-binding motif.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 2","pages":"94-94"},"PeriodicalIF":103.3,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770676","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}
Pub Date : 2025-12-17DOI: 10.1038/s41579-025-01273-9
Shimona Starling
A study by Cazares et al. investigated recent plasmid evolution by sequencing plasmids from the Murray Collection (1917–1954) and comparing with modern genome sequences from public archives.
{"title":"Plasmid evolution in the time of antibiotics","authors":"Shimona Starling","doi":"10.1038/s41579-025-01273-9","DOIUrl":"10.1038/s41579-025-01273-9","url":null,"abstract":"A study by Cazares et al. investigated recent plasmid evolution by sequencing plasmids from the Murray Collection (1917–1954) and comparing with modern genome sequences from public archives.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 2","pages":"95-95"},"PeriodicalIF":103.3,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770677","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}
Pub Date : 2025-12-16DOI: 10.1038/s41579-025-01272-w
Andrea Du Toit
This study reports the structure, specificity and genotoxic activity of colibactin.
本研究报道了大肠杆菌蛋白的结构、特异性和基因毒性活性。
{"title":"Cross-linking gut bacteria to cancer","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01272-w","DOIUrl":"10.1038/s41579-025-01272-w","url":null,"abstract":"This study reports the structure, specificity and genotoxic activity of colibactin.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 2","pages":"94-94"},"PeriodicalIF":103.3,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145768435","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}
Pub Date : 2025-12-15DOI: 10.1038/s41579-025-01274-8
Ashley York
A recent study investigated the effects of chemical pollutants on human gut bacteria in vitro.
最近的一项研究调查了化学污染物对体外人体肠道细菌的影响。
{"title":"Pollutants disrupt gut microbiota","authors":"Ashley York","doi":"10.1038/s41579-025-01274-8","DOIUrl":"10.1038/s41579-025-01274-8","url":null,"abstract":"A recent study investigated the effects of chemical pollutants on human gut bacteria in vitro.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 2","pages":"95-95"},"PeriodicalIF":103.3,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145763226","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}
Pub Date : 2025-12-15DOI: 10.1038/s41579-025-01275-7
Ashley York
A recent study investigated the effect of herpes zoster vaccination at different stages of the dementia disease course.
最近的一项研究调查了带状疱疹疫苗接种在痴呆病程的不同阶段的效果。
{"title":"Immunizing against dementia?","authors":"Ashley York","doi":"10.1038/s41579-025-01275-7","DOIUrl":"10.1038/s41579-025-01275-7","url":null,"abstract":"A recent study investigated the effect of herpes zoster vaccination at different stages of the dementia disease course.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 2","pages":"95-95"},"PeriodicalIF":103.3,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145763300","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}
Pub Date : 2025-12-11DOI: 10.1038/s41579-025-01263-x
Understanding the emergence, evolution and spread of viral pathogens is central to improving global health. This Focus issue highlights advances in our understanding of evolving viral pathogens and the surveillance and preparedness strategies that are needed to control them.
{"title":"Evolving viral threats","authors":"","doi":"10.1038/s41579-025-01263-x","DOIUrl":"10.1038/s41579-025-01263-x","url":null,"abstract":"Understanding the emergence, evolution and spread of viral pathogens is central to improving global health. This Focus issue highlights advances in our understanding of evolving viral pathogens and the surveillance and preparedness strategies that are needed to control them.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 1","pages":"1-2"},"PeriodicalIF":103.3,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41579-025-01263-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145719852","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}
Pub Date : 2025-12-09DOI: 10.1038/s41579-025-01270-y
Peter Osborne, Keir J. Macartney, Matthew G. Miyada
This Genome Watch discusses the great biosynthetic capacity that has been identified in marine environmental and host-associated microbiomes, along with approaches to facilitate research into these diverse and resource-rich microbial communities.
{"title":"Wringing everything out with bioprospecting","authors":"Peter Osborne, Keir J. Macartney, Matthew G. Miyada","doi":"10.1038/s41579-025-01270-y","DOIUrl":"10.1038/s41579-025-01270-y","url":null,"abstract":"This Genome Watch discusses the great biosynthetic capacity that has been identified in marine environmental and host-associated microbiomes, along with approaches to facilitate research into these diverse and resource-rich microbial communities.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 3","pages":"167-167"},"PeriodicalIF":103.3,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145715169","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：