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Gut Microbiota

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. About this content.

Core collection

Complex microbial communities shape the dynamics of various environments. In this Review, Knight and colleagues discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets.

Review Article | | Nature Reviews Microbiology

Metagenomic sequencing analysis of stool samples from 903 children as part of the TEDDY study shows that breastfeeding was the most important factor associated with microbiome structure, and the cessation of breast milk resulted in faster maturation of the gut microbiome.

Letter | open | | Nature

An analysis of more than 10,000 metagenomes from the TEDDY study provides a detailed functional profile of the gut microbiome in relation to islet autoimmunity, and supports the protective effects of short-chain fatty acids in early-onset type 1 diabetes.

Letter | open | | Nature

The authors compare human fecal viromes from three isolated villages of the Amazon rain forest with those from city dwellers. They report that the diversity of human viruses is not reduced in isolated villages, suggesting frequent viral introductions or increased susceptibility to enteric infections.

Article | open | | Nature Communications

Gut microbial dysbiosis in infancy is associated with childhood atopy and the development of asthma. Here, the authors show that gut microbiota perturbation is evident in the very earliest stages of postnatal life, continues throughout infancy, and can be partially rescued by Lactobacillus supplementation in high-risk for asthma infants.

Article | open | | Nature Communications

Recent microbiome genome-wide association studies have identified numerous associations between human genetic variants and the gut microbiome. Here, the authors review how genetic variation in the host can alter the composition of the gut microbiome towards a disease state, with a focus on disorders of immunity and metabolism.

Review Article | | Nature Reviews Genetics

Lipopeptides secreted by Bacillus bacteria block quorum sensing by Staphylococcus aureus and thereby inhibit the growth of this opportunistic pathogen in the gut, suggesting why people in rural Thailand who are colonized by Bacillus are not also colonized by S. aureus.

Article | | Nature

Current nutritional approaches to prevent and treat various diseases have limited effectiveness. Here, Zmora et al. review the major principles underlying effects of dietary constituents on the gut microbiota, resolving aspects of the diet–microbiota–host crosstalk, and present the promises and challenges of incorporating microbiome data into dietary planning.

Review Article | | Nature Reviews Gastroenterology & Hepatology

Further Reading

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.

Article | | Nature

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.

Letter | | Nature

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.

Letter | | Nature

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.

Review Article | | Nature Reviews Gastroenterology & Hepatology

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.

Review Article | | Nature Reviews Microbiology

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.

Review Article | | Nature Reviews Genetics