Temporal variability of the human microbiome, including the gut habitat

Most human microbiome studies to date have taken a sample from a body habitat at a single point in time. But what if the microbial communities vary over time?

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An open access study published in Genome Biology explored how microbial communities varied over time within each individual. Researchers profiled the microorganisms of two skin sites (forehead and palm), as well as the gut and the tongue. They took samples from 85 adults, weekly for a period of three months.

All habitats showed a wide range of variability from week to week. Forehead and palm microbiomes varied most in the number of taxa present, while gut and tongue varied more in how much of each taxa was present at any given time.

Each habitat showed that some individuals consistently harbored more variable communities than others. The best predictor of the differences in variability was the diversity of the microbial community: that is, more diverse communities changed less over time.

In each individual, the variability of the microbial community in one habitat did not predict variability in other body habitats, with the exception of the two skin sites. Subjects who had a more variable forehead microbiome tended to have a more variable palm microbiome.

The largest shifts in community membership coincided with having taken oral antibiotics, but antibiotic use did not always mean there was more temporal variability in that individual through the length of the study.

Authors argue that their data show temporal dynamics should be considered in future human microbiome studies. The concept of the “personal microbiome” should extend to incorporate the rate of change of a person’s microbiome, in addition to its composition.


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 Genome Biology doi:10.1186/s13059-014-0531-y

Kristina Campbell
Kristina Campbell
Science writer Kristina Campbell (M.Sc.), from British Columbia (Canada), specializes in communicating about the gut microbiota, digestive health, and nutrition. Author of the best selling Well-Fed Microbiome Cookbook, her freelance work has appeared in publications around the world. Kristina joined the Gut Microbiota for Health publishing team in 2014.  Find her on: GoogleTwitter