Host Phylogeny Shapes Gut Microbiota and Predicted Functions in Captive Artiodactyls

Host phylogeny can imprint the gut microbiota, but it is often masked by diet and environment. Leveraging the standardized husbandry of a zoological collection, we profiled fecal microbiota from 55 captive artiodactyls representing 12 species in Bovidae, Cervidae, and Camelidae using 16S rRNA amplicon sequencing targeting the V3-V4 region on the Illumina MiSeq platform. Community composition differed significantly among host families (Bray-Curtis PERMANOVA, R² = 0.1075, <i>p</i> = 0.001). A host-microbiota tanglegram, which juxtaposes the host phylogeny with a dendrogram of microbiota similarity, recovered a topology congruent with the host phylogeny, with camelids forming a distinct branch separate from true ruminants in both trees. The linear discriminant analysis effect size (LEfSe; LDA ≥ 3.5) identified family-specific biomarkers, including enrichment of <i>Acinetobacter</i>/Moraxellaceae in Bovidae, Rikenellaceae (the <i>Rikenellaceae_RC9_gut_group</i>) in Cervidae, and <i>Rummeliibacillus</i> together with the <i>Christensenellaceae_R-7_group</i> in Camelidae. Functional inference with PICRUSt2 revealed significant differences in KEGG level-2 pathways (e.g., carbohydrate metabolism and xenobiotics biodegradation), consistent with taxonomic shifts. Altogether, these findings show that-even under uniform captive conditions-host evolutionary history remains a primary determinant of both the structure and the predicted functions of the artiodactyl gut microbiota, refining the scope of phylosymbiosis and providing actionable baselines for veterinary monitoring and conservation management in zoo settings.