Taxonomic and Functional Profiles of the Gastrointestinal Microbiome Across Digestive Tract Segments in Growing Water Buffaloes

Abstract

Gastrointestinal segments in ruminants differ in physiological environment and substrate availability. This study characterized taxonomic and gene-encoded functional profiles in 54 shotgun metagenomes from 30 growing male water buffaloes assigned to five dietary formulations. The dataset comprised 30 rumen-fluid samples, six per group, and 24 post-slaughter samples from six gastrointestinal sites in five animals. Comparisons among groups A–E yielded p = 0.9816 for final body weight, p = 0.9315 for overall average daily gain, and p = 0.2832 for rumen-fluid pH. Genus-level principal coordinate analysis (PCoA) used Bray–Curtis dissimilarities calculated from Hellinger-transformed relative abundances. In the 30 rumen-fluid samples, PERMANOVA yielded R2 = 0.1554, pseudo-F = 1.1499, and p = 0.327. The cross-site profiles were described separately from the dietary-group comparison. Post-slaughter rumen contents had larger proportions of Bacteroidota than the other sampled sites, whereas Bacillota accounted for the largest proportions in the cecum and colon. Kyoto Encyclopedia of Genes and Genomes (KEGG) Level 2 profiles and carbohydrate-active enzyme (CAZyme) profiles described the distribution of annotated functions across sites. These data characterize taxonomic assignments and carbohydrate-utilization-related gene profiles from the rumen to the colon in growing water buffaloes.