Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data
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, which are often collected from known individuals and sometimes also sampled longitudinally across time. Such collections represent unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome, especially for species of particular conservation concern. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. This uncertainty arises in part because comparisons across storage methods to date generally include only a few (≤5) individuals, or analyze pooled samples. Here, we used n=52 samples from 13 rhesus macaque individuals to compare immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: storage in ethanol, lyophilization following ethanol storage, 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.
Barreiro Luis B.、Wilson Mark E.、Yuan Michael L.、Grieneisen Laura E.、Archie Elizabeth A.、Tung Jenny、Kohn Jordan、Tang Karen、Gesquiere Laurence、Johnson Zachary P.、Blekhman Ran
Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of MontrealYerkes National Primate Research Center, Emory UniversityDepartment of Evolutionary Anthropology, Duke UniversityDepartment of Biological Sciences, University of Notre DameDepartment of Biological Sciences, University of Notre Dame||Institute of Primate Research, National Museums of KenyaInstitute of Primate Research, National Museums of Kenya||Department of Evolutionary Anthropology, Duke University||Department of Biology, Duke University||Duke Population Research Institute, Duke UniversityYerkes National Primate Research Center, Emory UniversityDepartment of Genetics, Cell Biology, and Development, University of Minnesota||Department of Ecology, Evolution, and Behavior, University of MinnesotaDepartment of Biology, Duke UniversityYerkes National Primate Research Center, Emory UniversityDepartment of Genetics, Cell Biology, and Development, University of Minnesota||Department of Ecology, Evolution, and Behavior, University of Minnesota
微生物学动物学生物科学研究方法、生物科学研究技术
Barreiro Luis B.,Wilson Mark E.,Yuan Michael L.,Grieneisen Laura E.,Archie Elizabeth A.,Tung Jenny,Kohn Jordan,Tang Karen,Gesquiere Laurence,Johnson Zachary P.,Blekhman Ran.Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data[EB/OL].(2025-03-28)[2025-04-30].https://www.biorxiv.org/content/10.1101/038844.点此复制
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