Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal

Karmacharya, Dibesh; Manandhar, Prajwol; Manandhar, Sulochana; Sherchan, Adarsh M.; Sharma, Ajay N.; Joshi, Jyoti; Bista, Manisha; Bajracharya, Shailendra; Awasthi, Nagendra P.; Sharma, Netra; Llewellyn, Bronwyn; Waits, Lisette P.; Thapa, Kanchan; Kelly, Marcella J.; Vuyisich, Momchilo; Starkenburg, Shawn R.; Hero, Jean-Marc; Hughes, Jane; Wultsch, Claudia; Bertola, Laura; Fountain-Jones, Nicholas M.; Sinha, Amit K.

doi:10.1371/journal.pone.0221868

Title: Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal

Journal Article · 28 August 2019 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0221868 · OSTI ID:1627887

^[1]; Manandhar, Prajwol ^[2]; Manandhar, Sulochana ^[2]; Sherchan, Adarsh M. ^[2]; Sharma, Ajay N. ^[2]; Joshi, Jyoti ^[2]; Bista, Manisha ^[2]; Bajracharya, Shailendra ^[2]; Awasthi, Nagendra P. ^[2]; Sharma, Netra ^[3]; Llewellyn, Bronwyn ^[3]; Waits, Lisette P. ^[4]; Thapa, Kanchan ^[5]; Kelly, Marcella J. ^[5]; Vuyisich, Momchilo ^[6]; Starkenburg, Shawn R. ^[6]; Hero, Jean-Marc ^[7]; Hughes, Jane ^[8]; Wultsch, Claudia ^[9]; Bertola, Laura ^[10] more »

Center for Molecular Dynamics Nepal, Kathmandu, (Nepal); Griffith Univ., Queensland (Australia). School of Environment; DOE/OSTI
Center for Molecular Dynamics Nepal, Kathmandu, (Nepal)
US Agency for International Development, Kathmandu, (Nepal). Environment Team
Univ. of Idaho, Moscow, ID (United States). Dept. of Fish and Wildlife Sciences
Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States). Dept. of Fish and Wildlife Conservation
Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Applied Genomics
Univ. of the Sunshine Coast, Queensland (Australia). School of Science and Education
Griffith Univ., Queensland (Australia). School of Environment
American Museum of Natural History (AMNH), New York, NY (United States). Slacker Inst. for Comparative Genomics; City Univ. of New York (CUNY), NY (United States). Hunter College. Bioinformatics and Computational Genomics Lab.
City Univ. of New York (CUNY), NY (United States). Dept. of Biology; Leiden Univ. (Netherlands). Inst. of Environmental Sciences
Univ. of Minnesota, Minneapolis, MN (United States). Dept. of Veterinary Population Medicine

Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1627887

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 8 Vol. 14; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape Karmacharya, Dibesh figshare https://doi.org/10.6084/m9.figshare.5896063	dataset	January 2018
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