Seasonal shift in gut microbiome diversity in wild Sichuan takin (Budorcas tibetanus) and environmental adaptation

Tian-Pei Guan; Jade L L Teng; Jordan Y H Fong; Susanna K P Lau; Patrick C Y Woo

doi:10.1016/j.csbj.2022.12.035

Seasonal shift in gut microbiome diversity in wild Sichuan takin (Budorcas tibetanus) and environmental adaptation

Comput Struct Biotechnol J. 2022 Dec 21:21:1283-1291. doi: 10.1016/j.csbj.2022.12.035. eCollection 2023.

Authors

Tian-Pei Guan¹, Jade L L Teng^{2

3}, Jordan Y H Fong³, Susanna K P Lau³, Patrick C Y Woo^{3

4

5}

Affiliations

¹ Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610225, China.
² Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region of China.
³ Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China.
⁴ PhD Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
⁵ The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung 402, Taiwan.

Abstract

In this study, we investigated the change in microbiome composition of wild Sichuan takin (Budorcas tibetanus) during winter and spring and analyzed the physiological implications for such changes. Diversity analyses of the microbiome (average 15,091 high-quality reads per sample) in 24 fecal samples (15 from winter, 9 from spring) revealed that spring samples had higher species diversity and were compositionally different from winter samples (P < 0.05). Taxonomic composition analysis showed that the relative abundance increased in spring for Patescibacteria (2.7% vs. 0.9% in winter, P < 0.001) and Tenericutes (1.9% vs. 1% in winter, P < 0.05). Substantial increases in relative abundance of Ruminococcaceae and Micrococcaceae were identified in spring and winter, respectively. Mann-Whitney U and ANCOM identified seven differentially abundant genera: Enterococcus, Acetitomaculum, Blautia, Coprococcus 1, Lachnospiraceae UCG 008, Ruminococcus 2 and Ralstonia. All seven genera were significantly more abundant in spring (average 0.016-1.2%) than winter (average 0-0.16%), with the largest difference found in Ruminococcus (1.21% in spring vs. 0.16% in winter). The other six genera were undetectable in winter. Functional prediction and pathway analysis revealed that biosynthesis of cofactors (ko01240) had the highest gene count ratios in the winter, followed by the two-component system (ko02020). Seasonal variation affects the gut microbiomes in wild Sichuan takins, with winter associated with lower species diversity and spring with enrichment of cellulose-degrading genera and phytopathogens. Such changes were crucial in their adaptation to the environment, particularly the difference in food abundance.

Keywords: ANCOM, Analysis of the composition of microbiomes; ASVs, Amplicon sequence variants; Budorcas tibetanus; Composition; Diversity; Gut microbiome; KO, KEGG Orthology; Microbiomes; PCoA, Principal coordinate analysis; PERMANOVA, permutational multivariate analysis of variance; SRA, Sequence Read Archive; Seasonal; Sichuan takin; UCGs, uncultured genus-level groups.