Editors' ChoiceMicrobiome

The Sum of One’s Parts? What Our Microbiomes Say About Us

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Science Translational Medicine  30 Apr 2014:
Vol. 6, Issue 234, pp. 234ec78
DOI: 10.1126/scitranslmed.3009260

We have long known that our bodies are populated by a massive number of diverse microorganisms. As advanced DNA sequencing technologies emerged, so did the ability to comprehensively define these commensals. To that end, the National Institutes of Health oversees the international Human Microbiome Project (HMP), which characterizes the microbiome in health and disease. Advancing this effort, Ding and Schloss offer an analysis of the microbiome over time, at different body sites, and in relation to our lives—past and present.

Before making these associations, the authors first asked a more fundamental question: How to profile hundreds of bacterial genera so as to compare across sites, over time, and between individuals? Two models have been proposed, each associated with a different biological interpretation: partitioning around the medoid and the Dirichlet multinomial mixture. Applying both revealed the latter to be superior, suggesting that the types of bacterial communities represent clusters of relative abundance profiles, as opposed to partitioning of an abundance gradient.

Armed with this analytical strategy, the authors defined multiple community types in 300 healthy adults. Serial samples were obtained from 18 body sites (15 in men) in conjunction with clinical, demographic, geographic, and socioeconomic data. The first and perhaps most intriguing finding was the association between community type and history of breastfeeding (seen in stool community types), gender (stool and skin), and education level (vaginal sites). Sampling multiple body sites revealed high correlations at similar locations such as the hard palate and saliva. Last, the authors compared communities over time and found variable stability. Stool and vaginal communities were the most stable, whereas oral communities were the least.

There is a growing literature highlighting the importance of the microbiome in illness. By defining the spectrum of community types across the bodies of so many healthy individuals, Ding and Schloss provide a context for future comparisons and highlight the importance of incorporating personal history in future microbiome research.

T. Ding, P. D. Schloss, Dynamics and associations of microbial community types across the human body. Nature, published online 16 April 2014 (10.1038/nature13178). [Full Text]

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