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Open Access Highly Accessed Research

Host lifestyle affects human microbiota on daily timescales

Lawrence A David1112, Arne C Materna3, Jonathan Friedman4, Maria I Campos-Baptista5, Matthew C Blackburn6, Allison Perrotta7, Susan E Erdman8 and Eric J Alm10479*

Author Affiliations

1 Society of Fellows, Harvard University, Cambridge, MA 02138, USA

2 FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA

3 QIAGEN Aarhus A/S, Silkeborgvej 2, 8000 Aarhus C, Denmark

4 Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

5 Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

6 Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland

7 Department of Civil & Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

8 Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

9 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

10 The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA

11 Present address: Molecular Genetics & Microbiology and Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA

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Genome Biology 2014, 15:R89  doi:10.1186/gb-2014-15-7-r89

Published: 25 July 2014

Abstract

Background

Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics of human-associated microbial communities.

Results

Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. Travel from the developed to the developing world in one subject led to a nearly two-fold increase in the Bacteroidetes to Firmicutes ratio, which reversed upon return. Enteric infection in the other subject resulted in the permanent decline of most gut bacterial taxa, which were replaced by genetically similar species. Still, even during periods of overall community stability, the dynamics of select microbial taxa could be associated with specific host behaviors. Most prominently, changes in host fiber intake positively correlated with next-day abundance changes among 15% of gut microbiota members.

Conclusions

Our findings suggest that although human-associated microbial communities are generally stable, they can be quickly and profoundly altered by common human actions and experiences.