The Gut Microbiome of Exudivorous Wild and Captive Marmosets

Abstract Among mammals, captive dietary specialists like primate folivores are prone to gastrointestinal distress and suffer the greatest gut microbiome diversity losses relative to wild individuals. Less is known about the gut microbiome of mammalian exudivores, which exploit tree gums and sap, and increased knowledge could improve management of wild exudivores and facilitate captive exudivore welfare. A number of primates, including Callithrix marmosets, represent key mammalian exudivores. Captive marmosets commonly develop gastrointestinal distress symptoms that in human diseases are linked to microbiome dysbiosis. Thus, we studied wild and captive Callithrix gut microbiome composition and predictive function through 16S V4 ribosomal subunit sequencing of 59 wild, translocated, and captive pure and hybrid Callithrix. We found that host environment had a stronger effect on the gut microbiome than host taxon. Captive marmosets showed relatively reduced gut microbiome diversity. Wild Callithrix gut microbiomes were enriched for carbohydrate function and Bifidobacterium, which process host-indigestible carbohydrates. Captive marmosets had the highest relative abundance of Enterobacteriaceae, a family containing several pathogenic bacteria. Captive marmosets also showed gut microbiome composition aspects seen in human gastrointestinal diseases. Thus, captivity may perturb the exudivore gut microbiome, which raises implications for captive exudivore welfare and calls for modified husbandry practices.