title: Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data.
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.
authors.affiliation: Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55108, USA.|Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55108, USA.
authors.forename: Ran
authors.initials: R
authors.lastname: Blekhman
authors.affiliation: Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55108, USA.|Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55108, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Tang
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 45665, USA.|Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Archie
authors.affiliation: Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Quebec, H3T 1C5 Canada.
authors.forename: Luis B
authors.initials: LB
authors.lastname: Barreiro
authors.affiliation: Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA.
authors.forename: Zachary P
authors.initials: ZP
authors.lastname: Johnson
authors.affiliation: Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA.
authors.forename: Mark E
authors.initials: ME
authors.lastname: Wilson
authors.affiliation: Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA.
authors.forename: Jordan
authors.initials: J
authors.lastname: Kohn
authors.affiliation: Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Yuan
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Laurence
authors.initials: L
authors.lastname: Gesquiere
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 45665, USA.
authors.forename: Laura E
authors.initials: LE
authors.lastname: Grieneisen
authors.affiliation: Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya.|Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.|Department of Biology, Duke University, Durham, NC 27708, USA.|Duke Population Research Institute, Duke University, Durham NC 27708, USA.
authors.forename: Jenny
authors.initials: J
authors.lastname: Tung
mesh_terms: D000818:Animals; D000835:Animals, Wild; D044822:Biodiversity; D005243:Feces / Q000382:microbiology; D005612:Freeze Drying; D000069196:Gastrointestinal Microbiome; D013048:Specimen Handling