Comparative Analysis of Fecal Microbiome Composition in Zoo-Housed Colobines: The Influence of Dietary Macronutrients, Browse Provisioning, and Phylogeny

This study investigated the interplay between dietary macronutrient composition, browse provisioning frequency, and host phylogeny in shaping the gut microbiome of zoo-housed colobine monkeys. We focused on four species (Colobus guereza, Colobus angolensis, Trachypithecus cristatus, and Trachypithecus francoisi) housed across 20 AZA-accredited institutions and integrated detailed dietary records with fecal microbiome profiling. Diets were categorized using Partition Around Medoids clustering based on macronutrient content, while browse offerings were classified by provisioning frequency (low, moderate, and high). Microbial diversity and community composition were evaluated using high-throughput 16S rRNA sequencing. The results revealed that browse provisioning frequency was the strongest predictor of microbiome alpha diversity, with moderate and high browse categories supporting significantly greater microbial richness and evolutionary breadth than low browse frequency. While diet cluster and phylogeny did not significantly affect alpha diversity metrics, all three factors significantly influenced the overall microbiome composition, as indicated by the unweighted and weighted UniFrac analyses. Notably, diet clusters with the highest relative crude fat (16.33%) or protein (23.27%) content, as well as sugar-rich diets promoted distinctive shifts in microbial community structure and function, fostering bacteria linked to dietary macronutrient processing, and in low-fiber contexts, reduce the abundance of key fiber-degrading taxa. These findings emphasize the necessity of frequent browse provision and an appropriate fiber balance to maintain gut microbial diversity and ecosystem stability in zoo-housed colobines. These results provide evidence-based recommendations for husbandry practices to promote nutritional and microbiome health in managed primate populations.