Enterotypes in the landscape of gut microbial community composition

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Abstract

<p class="first" id="P1">Population stratification is a useful approach towards a better understanding of complex biological problems in human health and well-being. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types, termed “enterotypes”, was met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the enterotype concept, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into a functional, ecological and medical context. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept. </p>

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Most cited references 38

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Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella.

Petia Kovatcheva-Datchary, Anne Nilsson, Rozita Akrami … (2015)

The gut microbiota plays an important role in human health by interacting with host diet, but there is substantial inter-individual variation in the response to diet. Here we compared the gut microbiota composition of healthy subjects who exhibited improved glucose metabolism following 3-day consumption of barley kernel-based bread (BKB) with those who responded least to this dietary intervention. The Prevotella/Bacteroides ratio was higher in responders than non-responders after BKB. Metagenomic analysis showed that the gut microbiota of responders was enriched in Prevotella copri and had increased potential to ferment complex polysaccharides after BKB. Finally, germ-free mice transplanted with microbiota from responder human donors exhibited improved glucose metabolism and increased abundance of Prevotella and liver glycogen content compared with germ-free mice that received non-responder microbiota. Our findings indicate that Prevotella plays a role in the BKB-induced improvement in glucose metabolism observed in certain individuals, potentially by promoting increased glycogen storage.

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Towards standards for human fecal sample processing in metagenomic studies

Michael Blaut, Hidetoshi Morita, Paul W. O'Toole … (2017)

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Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans.

Junhai Ou, Franck Carbonero, Erwin G Zoetendal … (2013)

Epidemiologic studies have suggested that most cases of sporadic colon cancer can be attributed to diet. The recognition that colonic microbiota have a major influence on colonic health suggests that they might mediate colonic carcinogenesis. To examine the hypothesis that the influence of diet on colon cancer risk is mediated by the microbiota through their metabolites, we measured differences in colonic microbes and their metabolites in African Americans with a high risk and in rural native Africans with a low risk of colon cancer. Fresh fecal samples were collected from 12 healthy African Americans aged 50-65 y and from 12 age- and sex-matched native Africans. Microbiomes were analyzed with 16S ribosomal RNA gene pyrosequencing together with quantitative polymerase chain reaction of the major fermentative, butyrate-producing, and bile acid-deconjugating bacteria. Fecal short-chain fatty acids were measured by gas chromatography and bile acids by liquid chromatography-mass spectrometry. Microbial composition was fundamentally different, with a predominance of Prevotella in native Africans (enterotype 2) and of Bacteroides in African Americans (enterotype 1). Total bacteria and major butyrate-producing groups were significantly more abundant in fecal samples from native Africans. Microbial genes encoding for secondary bile acid production were more abundant in African Americans, whereas those encoding for methanogenesis and hydrogen sulfide production were higher in native Africans. Fecal secondary bile acid concentrations were higher in African Americans, whereas short-chain fatty acids were higher in native Africans. Our results support the hypothesis that colon cancer risk is influenced by the balance between microbial production of health-promoting metabolites such as butyrate and potentially carcinogenic metabolites such as secondary bile acids.

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Author and article information

Journal

Title: Nature Microbiology

Abbreviated Title: Nat Microbiol

Publisher: Springer Nature

ISSN (Electronic): 2058-5276

Publication date Created: January 2018

Publication date (Print): December 2017

Volume: 3

Issue: 1

Pages: 8-16

Article

DOI: 10.1038/s41564-017-0072-8

PMC ID: 5832044

PubMed ID: 29255284

SO-VID: 3045642d-ee88-4da5-8d9c-d1dcf37319cc

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