Kaela K. Amundson, Mikayla A. Borton, Michael J. Wilkins
{"title":"Anthropogenic impacts on the terrestrial subsurface biosphere","authors":"Kaela K. Amundson, Mikayla A. Borton, Michael J. Wilkins","doi":"10.1038/s41579-024-01110-5","DOIUrl":"https://doi.org/10.1038/s41579-024-01110-5","url":null,"abstract":"<p>The terrestrial subsurface is estimated to be the largest reservoir of microbial life on Earth. However, the subsurface also harbours economic, industrial and environmental resources, on which humans heavily rely, including diverse energy sources and formations for the storage of industrial waste and carbon dioxide for climate change mitigation. As a result of this anthropogenic activity, the subsurface landscape is transformed, including the subsurface biosphere. Through the creation of new environments and the introduction of substrates that fuel microbial life, the structure and function of subsurface microbiomes shift markedly. These microbial changes often have unintended effects on overall ecosystem function and are frequently challenging to manage from the surface of the Earth. In this Review, we highlight emerging research that investigates the impacts of anthropogenic activity on the terrestrial subsurface biosphere. We explore how humans alter the constraints on microbial life in the subsurface through drilling, mining, contamination and resource extraction, along with the resulting impacts of microorganisms on resource recovery and subsurface infrastructure.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":88.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142439449","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}
Athanasia Ioannou, Maryse D. Berkhout, Sharon Y. Geerlings, Clara Belzer
{"title":"Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential","authors":"Athanasia Ioannou, Maryse D. Berkhout, Sharon Y. Geerlings, Clara Belzer","doi":"10.1038/s41579-024-01106-1","DOIUrl":"https://doi.org/10.1038/s41579-024-01106-1","url":null,"abstract":"<p><i>Akkermansia muciniphila</i> is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of <i>A. muciniphila</i> as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host–microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made <i>A. muciniphila</i> a subject of enormous attention from multiple research fields. <i>A. muciniphila</i> is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of <i>A. muciniphila</i> and <i>Akkermansia</i> genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of <i>A. muciniphila</i> for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":88.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142436322","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}
Nathalie M. Delzenne, Laure B. Bindels, Audrey M. Neyrinck, Jens Walter
{"title":"The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer","authors":"Nathalie M. Delzenne, Laure B. Bindels, Audrey M. Neyrinck, Jens Walter","doi":"10.1038/s41579-024-01108-z","DOIUrl":"https://doi.org/10.1038/s41579-024-01108-z","url":null,"abstract":"<p>Dietary fibres constitute a heterogeneous class of nutrients that are key in the prevention of various chronic diseases. Most dietary fibres are fermented by the gut microbiome and may, thereby, modulate the gut microbial ecology and metabolism, impacting human health. Dietary fibres may influence the occurrence of specific bacterial taxa, with this effect varying between individuals. The effect of dietary fibres on microbial diversity is a matter of debate. Most intervention studies with dietary fibres in the context of obesity and related metabolic disorders reveal the need for an accurate assessment of the microbiome to better understand the variable response to dietary fibres. Epidemiological studies confirm that a high dietary fibre intake is strongly associated with a reduced occurrence of many types of cancer. However, there is a need to determine the impact of intervention with specific dietary fibres on cancer risk, therapy efficacy and toxicity, as well as in cancer cachexia. In this Review, we summarize the mechanisms by which the gut microbiome can mediate the physiological benefits of dietary fibres in the contexts of obesity, cardiometabolic diseases and cancer, their incidence being clearly linked to low dietary fibre intake.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":88.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142397749","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}
{"title":"Bacterial small molecule metabolites implicated in gastrointestinal cancer development","authors":"Tayah Turocy, Jason M. Crawford","doi":"10.1038/s41579-024-01103-4","DOIUrl":"https://doi.org/10.1038/s41579-024-01103-4","url":null,"abstract":"<p>Numerous associations have been identified between cancer and the composition and function of the human microbiome. As cancer remains the second leading global cause of mortality, investigating the carcinogenic contributions of microbiome members could advance our understanding of cancer risk and support potential therapeutic interventions. Although fluctuations in bacterial species have been associated with cancer progression, studying their small molecule metabolites offers one avenue to establish support for causal relationships and the molecular mechanisms governing host–microorganism interactions. In this Review, we explore the expanding repertoire of small molecule metabolites and their mechanisms implicated in the risk of developing gastrointestinal cancers.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":88.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142383636","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}
{"title":"Towards next-generation treatment options to combat Plasmodium falciparum malaria","authors":"John Okombo, David A. Fidock","doi":"10.1038/s41579-024-01099-x","DOIUrl":"https://doi.org/10.1038/s41579-024-01099-x","url":null,"abstract":"<p>Malaria, which is caused by infection of red blood cells with <i>Plasmodium</i> parasites, can be fatal in non-immune individuals if left untreated. The recent approval of the pre-erythrocytic vaccines RTS, S/AS01 and R21/Matrix-M has ushered in hope of substantial reductions in mortality rates, especially when combined with other existing interventions. However, the efficacy of these vaccines is partial, and chemotherapy remains central to malaria treatment and control. For many antimalarial drugs, clinical efficacy has been compromised by the emergence of drug-resistant <i>Plasmodium falciparum</i> strains. Therefore, there is an urgent need for new antimalarial medicines to complement the existing first-line artemisinin-based combination therapies. In this Review, we discuss various opportunities to expand the present malaria treatment space, appraise the current antimalarial drug development pipeline and highlight examples of promising targets. We also discuss other approaches to circumvent antimalarial resistance and how potency against drug-resistant parasites could be retained.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":88.1,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374127","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}
Hans-Curt Flemming, Eric D. van Hullebusch, Brenda J. Little, Thomas R. Neu, Per H. Nielsen, Thomas Seviour, Paul Stoodley, Jost Wingender, Stefan Wuertz
{"title":"Microbial extracellular polymeric substances in the environment, technology and medicine","authors":"Hans-Curt Flemming, Eric D. van Hullebusch, Brenda J. Little, Thomas R. Neu, Per H. Nielsen, Thomas Seviour, Paul Stoodley, Jost Wingender, Stefan Wuertz","doi":"10.1038/s41579-024-01098-y","DOIUrl":"https://doi.org/10.1038/s41579-024-01098-y","url":null,"abstract":"<p>Microbial biofilms exhibit a self-produced matrix of extracellular polymeric substances (EPS), including polysaccharides, proteins, extracellular DNA and lipids. EPS promote interactions of the biofilm with other cells and sorption of organics, metals and chemical pollutants, and they facilitate cell adhesion at interfaces and ensure matrix cohesion. EPS have roles in various natural environments, such as soils, sediments and marine habitats. In addition, EPS are relevant in technical environments, such as wastewater and drinking water treatment facilities, and water distribution systems, and they contribute to biofouling and microbially influenced corrosion. In medicine, EPS protect pathogens within the biofilm against the host immune system and antimicrobials, and emerging evidence suggests that EPS can represent potential virulence factors. By contrast, EPS yield a wide range of valuable products that include their role in self-repairing concrete. In this Review, we aim to explore EPS as a functional unit of biofilms in the environment, in technology and in medicine.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":88.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321972","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}
{"title":"The rising mpox crisis","authors":"Agustina Taglialegna","doi":"10.1038/s41579-024-01114-1","DOIUrl":"10.1038/s41579-024-01114-1","url":null,"abstract":"An increasing number of countries in Africa are reporting cases of mpox, prompting the World Health Organization to declare it a public health emergency of international concern.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276036","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}
{"title":"Publisher Correction: Microorganisms, climate change, and the Sustainable Development Goals: progress and challenges","authors":"Janet K. Jansson","doi":"10.1038/s41579-024-01111-4","DOIUrl":"10.1038/s41579-024-01111-4","url":null,"abstract":"","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41579-024-01111-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291523","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}
{"title":"ISME19","authors":"Agustina Taglialegna","doi":"10.1038/s41579-024-01113-2","DOIUrl":"10.1038/s41579-024-01113-2","url":null,"abstract":"Nature Reviews Microbiology attended the 19th biennial meeting of the International Society for Microbial Ecology (ISME) in Cape Town, South Africa.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276037","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}