Pub Date : 2025-01-10DOI: 10.1038/s41564-024-01916-2
Global food insecurity is a growing crisis, but microbes could offer an effective tool for sustainable agriculture.
全球粮食不安全是一场日益严重的危机，但微生物可以为可持续农业提供有效的工具。
{"title":"Use microbes to tackle food insecurity","authors":"","doi":"10.1038/s41564-024-01916-2","DOIUrl":"10.1038/s41564-024-01916-2","url":null,"abstract":"Global food insecurity is a growing crisis, but microbes could offer an effective tool for sustainable agriculture.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"1-1"},"PeriodicalIF":20.5,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01916-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939571","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 : 2025-01-08DOI: 10.1038/s41564-024-01910-8
Zhiyu Zang, Chengqian Zhang, Kyoung Jin Park, Daniel A. Schwartz, Ram Podicheti, Jay T. Lennon, Joseph P. Gerdt
To overtake competitors, microbes produce and secrete secondary metabolites that kill neighbouring cells and sequester nutrients. This metabolite-mediated competition probably evolved in complex microbial communities in the presence of viral pathogens. We therefore hypothesized that microbes secrete natural products that make competitors sensitive to phage infection. We used a binary-interaction screen and chemical characterization to identify a secondary metabolite (coelichelin) produced by Streptomyces sp. that sensitizes its soil competitor Bacillus subtilis to phage infection in vitro. The siderophore coelichelin sensitized B. subtilis to a panel of lytic phages (SPO1, SP10, SP50, Goe2) via iron sequestration, which prevented the activation of B. subtilis Spo0A, the master regulator of the stationary phase and sporulation. Metabolomics analysis revealed that other bacterial natural products may also provide phage-mediated competitive advantages to their producers. Overall, this work reveals that synergy between natural products and phages can shape the outcomes of competition between microbes. A secondary metabolite sensitizes competitor Bacillus subtilis to a wide panel of lytic phages by sequestering iron and preventing the activation of Spo0A.
{"title":"Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection","authors":"Zhiyu Zang, Chengqian Zhang, Kyoung Jin Park, Daniel A. Schwartz, Ram Podicheti, Jay T. Lennon, Joseph P. Gerdt","doi":"10.1038/s41564-024-01910-8","DOIUrl":"10.1038/s41564-024-01910-8","url":null,"abstract":"To overtake competitors, microbes produce and secrete secondary metabolites that kill neighbouring cells and sequester nutrients. This metabolite-mediated competition probably evolved in complex microbial communities in the presence of viral pathogens. We therefore hypothesized that microbes secrete natural products that make competitors sensitive to phage infection. We used a binary-interaction screen and chemical characterization to identify a secondary metabolite (coelichelin) produced by Streptomyces sp. that sensitizes its soil competitor Bacillus subtilis to phage infection in vitro. The siderophore coelichelin sensitized B. subtilis to a panel of lytic phages (SPO1, SP10, SP50, Goe2) via iron sequestration, which prevented the activation of B. subtilis Spo0A, the master regulator of the stationary phase and sporulation. Metabolomics analysis revealed that other bacterial natural products may also provide phage-mediated competitive advantages to their producers. Overall, this work reveals that synergy between natural products and phages can shape the outcomes of competition between microbes. A secondary metabolite sensitizes competitor Bacillus subtilis to a wide panel of lytic phages by sequestering iron and preventing the activation of Spo0A.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"362-373"},"PeriodicalIF":20.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142935883","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 : 2025-01-08DOI: 10.1038/s41564-024-01896-3
Alena. L. Pribyl, Philip Hugenholtz, Matthew A. Cooper
Microbiome science has evolved rapidly in the past decade, with high-profile publications suggesting that the gut microbiome is a causal determinant of human health. This has led to the emergence of microbiome-focused biotechnology companies and pharmaceutical company investment in the research and development of gut-derived therapeutics. Despite the early promise of this field, the first generation of microbiome-derived therapeutics (faecal microbiota products) have only recently been approved for clinical use. Next-generation therapies based on readily culturable and as-yet-unculturable colonic bacterial species (with the latter estimated to comprise 63% of all detected species) have not yet progressed to pivotal phase 3 trials. This reflects the many challenges involved in developing a new class of drugs in an evolving field. Here we discuss the evolution of the live biotherapeutics field over the past decade, from the development of first-generation products to the emergence of rationally designed second- and third-generation live biotherapeutics. Finally, we present our outlook for the future of this field. This Perspective reflects on advances made in the field of human gut microbiome-derived biotherapeutics, from faecal microbiota products to rationally designed second- and third-generation live biotherapeutics, and discusses the future of this developing field.
{"title":"A decade of advances in human gut microbiome-derived biotherapeutics","authors":"Alena. L. Pribyl, Philip Hugenholtz, Matthew A. Cooper","doi":"10.1038/s41564-024-01896-3","DOIUrl":"10.1038/s41564-024-01896-3","url":null,"abstract":"Microbiome science has evolved rapidly in the past decade, with high-profile publications suggesting that the gut microbiome is a causal determinant of human health. This has led to the emergence of microbiome-focused biotechnology companies and pharmaceutical company investment in the research and development of gut-derived therapeutics. Despite the early promise of this field, the first generation of microbiome-derived therapeutics (faecal microbiota products) have only recently been approved for clinical use. Next-generation therapies based on readily culturable and as-yet-unculturable colonic bacterial species (with the latter estimated to comprise 63% of all detected species) have not yet progressed to pivotal phase 3 trials. This reflects the many challenges involved in developing a new class of drugs in an evolving field. Here we discuss the evolution of the live biotherapeutics field over the past decade, from the development of first-generation products to the emergence of rationally designed second- and third-generation live biotherapeutics. Finally, we present our outlook for the future of this field. This Perspective reflects on advances made in the field of human gut microbiome-derived biotherapeutics, from faecal microbiota products to rationally designed second- and third-generation live biotherapeutics, and discusses the future of this developing field.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"301-312"},"PeriodicalIF":20.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142935885","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 : 2025-01-08DOI: 10.1038/s41564-024-01882-9
Robert C. Keskey, Jason Xiao, Sanjiv Hyoju, Adam Lam, Daniel Kim, Ashley M. Sidebottom, Alexander Zaborin, Anne Dijkstra, Rebecca Meltzer, Abhimanyu Thakur, Kui Zhang, Huanhuan Joyce Chen, Natalia V. Beloborodova, Alisa K. Pautova, Krysta Wolfe, Bhakti Patel, Renee Thewissen, Olga Zaborina, John C. Alverdy
Sepsis is a major cause of morbidity and mortality, but our understanding of the mechanisms underlying survival or susceptibility is limited. Here, as pathogens often subvert host defence mechanisms, we hypothesized that this might influence the outcome of sepsis. We used microbiota analysis, faecal microbiota transplantation, antibiotic treatment and caecal metabolite analysis to show that gut-microbiota-derived tryptophan metabolites including indoles increased host survival in a mouse model of Serratia marcescens sepsis. Infection in macrophage-specific aryl hydrocarbon receptor (AhR) knockout mice revealed that AhR activation induced transcriptional reprogramming in macrophages and increased bacterial clearance and host survival. However, culture supernatants from multiple bacterial pathogens inhibited AhR activation in vitro. We showed that the secreted siderophore, enterobactin, inhibited AhR activation in vitro and increased sepsis mortality in vivo. By contrast, oral or systemic tryptophan supplementation increased survival. These findings show that sepsis survival depends upon the interplay between pathogen inhibition and the activation of AhR by a microbiota-derived metabolite. Bacterial pathogens produce enterobactin, which suppresses microbiota-derived indole activation of Ahr in macrophages to inhibit bacterial clearance and increase the severity of bacterial sepsis.
{"title":"Enterobactin inhibits microbiota-dependent activation of AhR to promote bacterial sepsis in mice","authors":"Robert C. Keskey, Jason Xiao, Sanjiv Hyoju, Adam Lam, Daniel Kim, Ashley M. Sidebottom, Alexander Zaborin, Anne Dijkstra, Rebecca Meltzer, Abhimanyu Thakur, Kui Zhang, Huanhuan Joyce Chen, Natalia V. Beloborodova, Alisa K. Pautova, Krysta Wolfe, Bhakti Patel, Renee Thewissen, Olga Zaborina, John C. Alverdy","doi":"10.1038/s41564-024-01882-9","DOIUrl":"10.1038/s41564-024-01882-9","url":null,"abstract":"Sepsis is a major cause of morbidity and mortality, but our understanding of the mechanisms underlying survival or susceptibility is limited. Here, as pathogens often subvert host defence mechanisms, we hypothesized that this might influence the outcome of sepsis. We used microbiota analysis, faecal microbiota transplantation, antibiotic treatment and caecal metabolite analysis to show that gut-microbiota-derived tryptophan metabolites including indoles increased host survival in a mouse model of Serratia marcescens sepsis. Infection in macrophage-specific aryl hydrocarbon receptor (AhR) knockout mice revealed that AhR activation induced transcriptional reprogramming in macrophages and increased bacterial clearance and host survival. However, culture supernatants from multiple bacterial pathogens inhibited AhR activation in vitro. We showed that the secreted siderophore, enterobactin, inhibited AhR activation in vitro and increased sepsis mortality in vivo. By contrast, oral or systemic tryptophan supplementation increased survival. These findings show that sepsis survival depends upon the interplay between pathogen inhibition and the activation of AhR by a microbiota-derived metabolite. Bacterial pathogens produce enterobactin, which suppresses microbiota-derived indole activation of Ahr in macrophages to inhibit bacterial clearance and increase the severity of bacterial sepsis.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"388-404"},"PeriodicalIF":20.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142935884","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 : 2025-01-07DOI: 10.1038/s41564-024-01875-8
Characterization of gut metagenomes from 21,561 volunteers on omnivore, vegetarian or vegan diets shows how major food groups may shape the gut microbiome not only through the selection of microbes that aid in digestion, but also through the acquisition of microbes from foods themselves.
{"title":"Dietary exclusion of major food groups shapes the gut microbiome and may influence health","authors":"","doi":"10.1038/s41564-024-01875-8","DOIUrl":"10.1038/s41564-024-01875-8","url":null,"abstract":"Characterization of gut metagenomes from 21,561 volunteers on omnivore, vegetarian or vegan diets shows how major food groups may shape the gut microbiome not only through the selection of microbes that aid in digestion, but also through the acquisition of microbes from foods themselves.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"10-11"},"PeriodicalIF":20.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142934884","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 : 2025-01-06DOI: 10.1038/s41564-024-01870-z
Gloria Fackelmann, Paolo Manghi, Niccolò Carlino, Vitor Heidrich, Gianmarco Piccinno, Liviana Ricci, Elisa Piperni, Alberto Arrè, Elco Bakker, Alice C. Creedon, Lucy Francis, Joan Capdevila Pujol, Richard Davies, Jonathan Wolf, Kate M. Bermingham, Sarah E. Berry, Tim D. Spector, Francesco Asnicar, Nicola Segata
As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology. Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes.
{"title":"Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals","authors":"Gloria Fackelmann, Paolo Manghi, Niccolò Carlino, Vitor Heidrich, Gianmarco Piccinno, Liviana Ricci, Elisa Piperni, Alberto Arrè, Elco Bakker, Alice C. Creedon, Lucy Francis, Joan Capdevila Pujol, Richard Davies, Jonathan Wolf, Kate M. Bermingham, Sarah E. Berry, Tim D. Spector, Francesco Asnicar, Nicola Segata","doi":"10.1038/s41564-024-01870-z","DOIUrl":"10.1038/s41564-024-01870-z","url":null,"abstract":"As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology. Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"41-52"},"PeriodicalIF":20.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01870-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142934992","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 : 2025-01-06DOI: 10.1038/s41564-024-01898-1
David A. Pearce, James E. Lawrence, Maria Luisa Avila Jimenez
Three different studies in this issue use metagenomics to study the bacterial and viral dynamics of freshwater microbiomes, highlighting the ecological and environmental drivers of these ecosystems.
{"title":"Crucial stepping stones in freshwater microbiology","authors":"David A. Pearce, James E. Lawrence, Maria Luisa Avila Jimenez","doi":"10.1038/s41564-024-01898-1","DOIUrl":"10.1038/s41564-024-01898-1","url":null,"abstract":"Three different studies in this issue use metagenomics to study the bacterial and viral dynamics of freshwater microbiomes, highlighting the ecological and environmental drivers of these ecosystems.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"6-7"},"PeriodicalIF":20.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929423","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 : 2025-01-06DOI: 10.1038/s41564-024-01892-7
Jacob E. Choby, David S. Weiss
Chemical genomics reveals the fitness cost of bacterial metallo-β-lactamase in zinc-deplete environments, with implications for treatment options.
化学基因组学揭示了细菌金属-β-内酰胺酶在缺锌环境中的适应性成本，并对治疗方案产生影响。
{"title":"Zinc-dependent β-lactam resistance at a cost","authors":"Jacob E. Choby, David S. Weiss","doi":"10.1038/s41564-024-01892-7","DOIUrl":"10.1038/s41564-024-01892-7","url":null,"abstract":"Chemical genomics reveals the fitness cost of bacterial metallo-β-lactamase in zinc-deplete environments, with implications for treatment options.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"4-5"},"PeriodicalIF":20.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929586","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 : 2025-01-06DOI: 10.1038/s41564-024-01897-2
Marta Giovanetti
The Oropouche virus has long been overlooked, but following a recent global expansion the virologist Marta Giovanetti argues for a One Health strategy to address this emergent public health threat.
{"title":"Oropouche virus and the urgent need for global surveillance","authors":"Marta Giovanetti","doi":"10.1038/s41564-024-01897-2","DOIUrl":"10.1038/s41564-024-01897-2","url":null,"abstract":"The Oropouche virus has long been overlooked, but following a recent global expansion the virologist Marta Giovanetti argues for a One Health strategy to address this emergent public health threat.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"2-3"},"PeriodicalIF":20.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929585","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 : 2025-01-03DOI: 10.1038/s41564-024-01876-7
Zhichao Zhou, Patricia Q. Tran, Cody Martin, Robin R. Rohwer, Brett J. Baker, Katherine D. McMahon, Karthik Anantharaman
As freshwater lakes undergo rapid anthropogenic change, long-term studies reveal key microbial dynamics, evolutionary shifts and biogeochemical interactions, yet the vital role of viruses remains overlooked. Here, leveraging a 20 year time series from Lake Mendota, WI, USA, we characterized 1.3 million viral genomes across time, seasonality and environmental factors. Double-stranded DNA phages from the class Caudoviricetes dominated the community. We identified 574 auxiliary metabolic gene families representing over 140,000 auxiliary metabolic genes, including important genes such as psbA (photosynthesis), pmoC (methane oxidation) and katG (hydrogen peroxide decomposition), which were consistently present and active across decades and seasons. Positive associations and niche differentiation between virus–host pairs, including keystone Cyanobacteria, methanotrophs and Nanopelagicales, emerged during seasonal changes. Inorganic carbon and ammonium influenced viral abundances, underscoring viral roles in both ‘top-down’ and ‘bottom-up’ interactions. Evolutionary processes favoured fitness genes, reduced genomic heterogeneity and dominant sub-populations. This study transforms understanding of viral ecology and evolution in Earth’s microbiomes. A long-term metagenomic time series reveals how viruses impact diversity, ecological dynamics and evolution of freshwater microbiomes.
{"title":"Unravelling viral ecology and evolution over 20 years in a freshwater lake","authors":"Zhichao Zhou, Patricia Q. Tran, Cody Martin, Robin R. Rohwer, Brett J. Baker, Katherine D. McMahon, Karthik Anantharaman","doi":"10.1038/s41564-024-01876-7","DOIUrl":"10.1038/s41564-024-01876-7","url":null,"abstract":"As freshwater lakes undergo rapid anthropogenic change, long-term studies reveal key microbial dynamics, evolutionary shifts and biogeochemical interactions, yet the vital role of viruses remains overlooked. Here, leveraging a 20 year time series from Lake Mendota, WI, USA, we characterized 1.3 million viral genomes across time, seasonality and environmental factors. Double-stranded DNA phages from the class Caudoviricetes dominated the community. We identified 574 auxiliary metabolic gene families representing over 140,000 auxiliary metabolic genes, including important genes such as psbA (photosynthesis), pmoC (methane oxidation) and katG (hydrogen peroxide decomposition), which were consistently present and active across decades and seasons. Positive associations and niche differentiation between virus–host pairs, including keystone Cyanobacteria, methanotrophs and Nanopelagicales, emerged during seasonal changes. Inorganic carbon and ammonium influenced viral abundances, underscoring viral roles in both ‘top-down’ and ‘bottom-up’ interactions. Evolutionary processes favoured fitness genes, reduced genomic heterogeneity and dominant sub-populations. This study transforms understanding of viral ecology and evolution in Earth’s microbiomes. A long-term metagenomic time series reveals how viruses impact diversity, ecological dynamics and evolution of freshwater microbiomes.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"231-245"},"PeriodicalIF":20.5,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917052","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}
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