Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data

• Type of Material: Article
• Authors: Ran Blekhman, University of Minnesota; Karen Tang, University of Minnesota; Elizabeth A. Archie, University of Notre Dame; Luis B. Barreiro, University of Montreal; Zachary Johnson, Emory University; Mark E. Wilson, Emory University; Jordan Kohn, Emory University; Michael L. Yuan, Duke University; Laurence Gesquiere, Duke University; Laura E. Grieneisen, University of Notre Dame; Jenny Tung, Duke University
• Language: English
• Date: 2016-08-16
• Publisher: Nature Publishing Group: Open Access Journals - Option C
• Publication Version: Final Published Version
• Copyright Statement: © 2016, The Author(s)
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1038/srep31519
• Title of Journal or Parent Work: Scientific Reports
• ISSN: 2045-2322
• Volume: 6
• Start Page: 31519
• End Page: 31519
• Grant/Funding Information: We gratefully acknowledge support from the National Science Foundation (IOS 1053461 to E.A.A.), National Institutes of Health (R01-GM102562 to J.T., L.B.B., and M.E.W. and 2-P2CHD065563-06 to Seth Sanders), and the Clare Boothe Luce Foundation (E.A.A.).
• Research Categories: Biology, Cell; Biology, Genetics; Biology, General

Abstract

Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples—unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.