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The microbial communities that inhabit our gastrointestinal tract, termed the gut microbiota, are well known to play a fundamental role in many host processes, and our understanding of these complex communities continues to advance at a rapid pace. Research has characterized the gut microbiota in health and disease at increasing resolution, aided by the continuous development of tools and approaches. Greater mechanistic understanding of how our microbial partners, including the non-bacterial members, contribute to or protect against disease is a major focus of recent initiatives with the ultimate goal of translating these findings into clinical applications.
This collection brings together Research, Reviews and Comment published in several Nature journals covering key topics on the gut microbiota. The selected content has been published over the past year in Nature, Nature Microbiology, Nature Medicine, Nature Genetics, Nature Communications, Nature Reviews Microbiology, Nature Reviews Genetics and Nature Reviews Gastroenterology and Hepatology, some of which have been made freely available for 6 months, thanks to support from Yakult Honsha Co., Ltd.
This Collection is editorially independent, produced with financial support from a third party.
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Integration of longitudinal gut metagenomic datasets from children in Finland, Estonia and Russian Karelia reveals high strain-level diversity, which consequently impacts the functional capabilities of the early life microbiome.
Statistical analyses of a metagenomics-sequenced human cohort identify a relatively minor role for genetics in determining microbiome composition and show that several human phenotypes are as strongly associated with the gut microbiome as with host genetics.
Stool microbiota composition correlates with the ethnic backgrounds of people living in the same city, suggesting that geographical location and ethnicity have distinct effects on microbiota.
Here the authors show that the human gut microbiome can recover after a clinically relevant, broad-spectrum antibiotic treatment and characterization of the resistome indicates that antibiotic resistance genes can impact the recovery process.
Finely tuned control of strain engraftment and abundance in the mouse gut microbiota was achieved using the marine polysaccharide porphyran, which could exclusively be used by an introduced subset of wild-type or genetically modified Bacteroides strains.
Here the authors have characterized the growth of 96 human gut bacteria on a range of defined media, providing valuable insights into their metabolic capabilities and unique media for future studies.
Roseburia intestinalis is a butyrate-producing member of the gut microbiome that can use dietary plant polysaccharides to alter host metabolism, transcription and epigenetics, and lower inflammation and endotoxaemia, resulting in reduced atherosclerosis.
Preliminary evidence from two cases suggests that fecal microbiota transplantation may provide a viable treatment option for a severe adverse effect of immune checkpoint blockade therapy in patients with cancer.
Tungstate inhibits molybdenum-cofactor-dependent microbial respiratory pathways and shows potential as a selective treatment for microbial imbalances that occur during inflammation of the gastrointestinal tract.
Quantitative metagenomics reveals an altered bacteriophage community in a mouse model of colitis, which overlaps with that observed in humans with inflammatory bowel disease (IBD), providing a tool for interrogating phage dynamics in IBD.
Attention has turned to the gut microbiota in liver disease, including alcoholic and nonalcoholic fatty liver disease and hepatocellular carcinoma. This Review describes gut–liver communications, including evidence from animal and human studies, compares conditions within the liver disease spectrum and highlights key points for designing microbiome-based studies for liver disease research.
Faecal microbiota richness is considered a hallmark of gut health and stability. However, in healthy hosts, richness would primarily reflect the stage of ecosystem development through the gut, rather than community resilience. This Comment discusses the need to rethink microbiome biomarkers in the context of gut ecology.
Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut. In this Review, Raoult and colleagues discuss the development of culturomics and how it has extended our understanding of bacterial diversity, and highlight the potential implications for human health.
Comparing the microbiomes of great apes enables an evolutionary perspective on microbial communities. This approach is revealing not only new insights about humans and what differentiates us from our closest relatives but also the factors that influence microbiome composition and the ways in which microbiomes diverge.