Temporal variability is a personalized feature of the human microbiome

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1 Department of Biology, California State University, Northridge, Northridge, CA, USA
2 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States
3 Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
4 Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
5 Cooperative Institute for Research in Environmental Scienes, University of Colorado at Boulder, Boulder, CO, USA
6 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
7 Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, USA
8 Department of Computer Science, University of Colorado at Boulder, Boulder, CO, USA
9 Biofrontiers Institute, University of Colorado at Boulder, Boulder, CO, USA
10 Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO, USA
11 Department of Chemistry and Biochemistry, University of Colorado of Boulder, Boulder, CO, USA
12 Department of Biology and Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA
DOI
10.7287/peerj.preprints.509v1
Published
Accepted
Subject Areas
Bioinformatics, Ecology, Genomics, Microbiology
Keywords
human microbiome, personalized medicine, qiime, temporal dynamics
Copyright
© 2014 Flores et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vázquez-Baeza Y, Gonzalez A, Knight R, Dunn RR, Fierer N. 2014. Temporal variability is a personalized feature of the human microbiome. PeerJ PrePrints 2:e509v1

Abstract

Background: It is now apparent that the complex microbial communities found on and in the human body (the human microbiome) vary across individuals. What has largely been missing from previous studies is an understanding of how these communities vary over time within individuals. To the extent to which it has been considered, it is often assumed that temporal variability is negligible for healthy adults. Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over three months.

Results: We found that skin (forehead and palm) varied most in the number of taxa present, whereas gut and tongue communities varied more in the relative abundances of taxa. Within each body habitat, there was a wide range of temporal variability across the study population, with some individuals consistently harboring more variable communities than others. The best predictor of these differences in variability across individuals was microbial diversity; individuals with more diverse gut or tongue communities were less variable than individuals with less diverse communities.

Conclusions: This expanded sampling allowed us to observe consistently high levels of temporal variability in both diversity and community structure in all body habitats studied. These findings suggest that temporal dynamics may need to be considered when attempting to link changes in microbiome structure to changes in health status.Furthermore, our findings show that, not only is the composition of an individual’s microbiome highly personalized, but their degree of temporal variability is also a personalized feature.

Author Comment

This manuscript is currently under review at Genome Biology.