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DeCandia AL, Cassidy KA, Stahler DR, Stahler EA, vonHoldt BM. Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves ( Canis lupus). Ecol Evol 2021; 11:9472-9488. [PMID: 34306636 PMCID: PMC8293786 DOI: 10.1002/ece3.7767] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/20/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
The host-associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site-specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site-specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long-term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.
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Affiliation(s)
- Alexandra L. DeCandia
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
- Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Kira A. Cassidy
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Daniel R. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Erin A. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
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102
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Affiliation(s)
- Abigail L Lind
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA, USA
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103
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Levin D, Raab N, Pinto Y, Rothschild D, Zanir G, Godneva A, Mellul N, Futorian D, Gal D, Leviatan S, Zeevi D, Bachelet I, Segal E. Diversity and functional landscapes in the microbiota of animals in the wild. Science 2021; 372:science.abb5352. [PMID: 33766942 DOI: 10.1126/science.abb5352] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/17/2020] [Accepted: 03/09/2021] [Indexed: 12/11/2022]
Abstract
Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.
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Affiliation(s)
| | | | | | - Daphna Rothschild
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | | | | | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Center for Studies in Physics and Biology, Rockefeller University, New York, NY 10065, USA
| | - Ido Bachelet
- Wild Biotech, Rehovot, Israel.,Augmanity, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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