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Temporal and technical variability of human gut metagenomes

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Item Type:Article
Title:Temporal and technical variability of human gut metagenomes
Creators Name:Voigt, A.Y. and Costea, P.I. and Kultima, J.R. and Li, S.S. and Zeller, G. and Sunagawa, S. and Bork, P.
Abstract:BACKGROUND: Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health. However, the temporal variability of the healthy gut microbiome has not yet been studied in depth using metagenomics and little is known about the effects of different sampling and preservation approaches. We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced variation, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject. RESULTS: We find that the human gut microbiome is temporally stable and highly personalized at both taxonomic and functional levels. Over multiple time points, samples from the same subject clustered together, even in the context of a large dataset of 888 European and American fecal metagenomes. One exception was observed in an antibiotic intervention case where, more than one year after the treatment, samples did not resemble the pre-treatment state. Clustering was not affected by the preservation method. No species differed significantly in abundance, and only 0.36% of gene families were differentially abundant between preservation methods. CONCLUSIONS: Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability. Thus, short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of fecal samples for metagenomic studies.
Keywords:Bacterial DNA, Cluster Analysis, Feces, Gastrointestinal Microbiome, Gastrointestinal Tract, Human Genome, Metagenome, Metagenomics, Time Factors
Source:Genome Biology
ISSN:1465-6906
Publisher:BioMed Central (U.K.)
Volume:16
Number:1
Page Range:73
Date:8 April 2015
Official Publication:https://doi.org/10.1186/s13059-015-0639-8
PubMed:View item in PubMed

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