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Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment

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Abstract

Knowledge about the impact of different geographical environments on rhesus macaque gut microbiota is limited. In this study, we compared the characteristics of gut microbiota in six different Chinese rhesus macaque populations, including Hainan, Nanning, Guizhou, Xichang, Jianchuan and Tibet. Through the composition analysis of operational taxonomic units (OTUs), we found that there were significant differences in the abundance of core overlapping OTUs in the six Chinese groups. Specifically, the Tibet population exhibited the highest gut microbial diversity and the most unique OTUs. Statistically significant differences in the composition of gut microbiota among the six groups at phylum and family level were evident. Specifically, Tibet had higher abundances of Firmicutes and lower abundances of Bacteroidetes than the other geographical groups, and the higher abundance of Firmicutes in the Tibetan group was mainly caused by a significant increase in the family Ruminococcaceae and Christensenellaceae. Phylogenetic investigation of communities by reconstruction of unobserved state analysis showed that the enrichment ratio for environmental information processing and organismal systems was the highest in the Tibet population. Additionally, our results suggested that in the adaptation process of rhesus macaques to different geographical environments, the abundance of the core common flora of the intestinal microbes had undergone varying degree of change and produced new and unique flora, both of which helped to reshape the gut microbiota of rhesus macaques. In particular, this change was more obvious for animals in the high-altitude environments.

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Abbreviations

NHPs:

Non-human primates

OTU:

Operational taxonomic units

ACE:

Abundance-based coverage estimator

Chao 1:

The Chao 1 estimator

LEfSe:

Linear discriminant analysis (LDA) effect size

PICRUSt:

Phylogenetic Investigation of Communities by Reconstruction of Unobserved States

KEGG:

Kyoto Encyclopedia of Genes and Genomes

ABC transporters:

ATP-binding cassette transporters

NSTI:

Nearest sequenced taxon index

BMI:

Body mass index

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Funding

This study was supported in part by grants from the National Natural Science Foundation of China (No. 31370407), The experiment was supported by TinyGene Bio-Tech (shanghai) Co. Ltd.

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Author notes

  1. Junsong Zhao and Yongfang Yao contributed equally to this work.

Authors and Affiliations

  1. College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Yucheng District, Ya’an, 625014, Sichuan, People’s Republic of China

    Junsong Zhao, Yongfang Yao, Huaming Xu, Jiayun Wu, Anxiang Wen, Meng Xie & Huailiang Xu

  2. College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China

    Diyan Li, Qingyong Ni & Mingwang Zhang

  3. College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China

    Guangneng Peng

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  1. Junsong Zhao
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  2. Yongfang Yao
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  3. Diyan Li
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  4. Huaming Xu
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  8. Qingyong Ni
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  10. Guangneng Peng
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  11. Huailiang Xu
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Contributions

Conceived and designed the experiments: J.S., Y.F., and H.L. Performed the experiments: J.S., Y.F., D.Y., H.M., J.Y., M., Q.Y., and A.X. Contributed reagents/materials/analysis tools: J.S., Y.F., H.L., G.N., and M.W. All authors reviewed the manuscript. J.S. and Y.F. have the same contribution.

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Correspondence to Huailiang Xu.

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Zhao, J., Yao, Y., Li, D. et al. Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment. Microb Ecol 76, 565–577 (2018). https://doi.org/10.1007/s00248-018-1146-8

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