Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens)

Vet World Vol.19 February-2026 Article - 29

Research Article

Veterinary World, 19(2): 864-876

https://doi.org/10.14202/vetworld.2026.864-876

Bingbing Ye^1,2, Ruilan Liu¹, Rongqing Li¹, Mohd Rohaizad Md Roduan³, Wan Syaidatul Aqma Wan Mohd Noor³, and Fareed Sairi^3,4

1. Key Laboratory of Ecological Protection and Characteristic Industry Cultivation in Hengduan Mountain Area, Sichuan Minzu College of Sichuan Provincial Department of Education, Ganzi Prefecture, Kangding, 626001, Sichuan, China.

2. Department of Biological Sciences & Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi43600, Selangor, Malaysia.

3. Department of Biological Sciences & Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi43600, Selangor, Malaysia.

4. UKM Culture Collection (UKMCC), Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia. .

Background and Aim: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.

Materials and Methods: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), α- and β-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch’s t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.

Results: α-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, β-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.

Conclusion: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.

Keywords: Yak (Bos grunniens), Free-range vs. captive yaks, Gut microbiomes, metabarcoding, functional prediction.

How to cite this article: Ye B, Liu R, Li R, Md Roduan MR, Wan Mohd Noor WSA, Sairi F. Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens). Vet. World, 2026;19(2):864-876.

Received: 30-09-2025 Accepted: 27-01-2026 Published online: 28-02-2026

Corresponding author: Fareed Sairi E-mail: fareed@ukm.edu.my

DOI: 10.14202/vetworld.2026.864-876

Copyright: Ye, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.