Temporal and technical variability of human gut metagenomes

• Verfasst von: Voigt, Anita Yvonne [VerfasserIn]
• Verfasst von: Bork, Peer [VerfasserIn]
• Titel: Temporal and technical variability of human gut metagenomes
• Verf.angabe: Anita Y Voigt, Paul I Costea, Jens Roat Kultima, Simone S Li, Georg Zeller, Shinichi Sunagawa and Peer Bork
• E-Jahr: 2015
• Jahr: 8 April 2015
• Fussnoten: Gesehen am 12.07.2017
• Titel Quelle: Enthalten in: Genome biology
• Ort Quelle: London : BioMed Central, 2000
• Jahr Quelle: 2015
• Band/Heft Quelle: 16(2015) Artikel-Nummer 73, 12 Seiten
• ISSN Quelle: 1474-760X
• DOI: doi:10.1186/s13059-015-0639-8
• Datenträger: Online-Ressource
• Sprache: eng
• K10plus-PPN: 1560750715

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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0639-8) contains supplementary material, which is available to authorized users.