Microbial and Metabolic Flexibility in Response to Habitat Disturbance in an Ecologically Specialist Primate

In the Anthropocene, understanding what renders a species prone to extinction is critical to wildlife management. Ecological specialists are hypothesised to be at particular risk, given that morphological, physiological, and/or behavioural constraints are expected to impede their responses to rapid habitat degradation. Nevertheless, studies have found mixed support for this hypothesis, raising the question, 'how resilient are specialists to environmental change?' Here, we test the hypothesis that ecological specialists, limited by behavioural and physiological constraints, may be at an energetic disadvantage in degraded habitats. Specifically, we tested whether Critically Endangered dietary specialist primates, black-and-white ruffed lemurs (Varecia variegata), living in secondary forests suffered nutritional and energetic deficits compared to those in primary forest habitats over a 12-month period. To do this, we used mixed modelling approaches to examine relationships among behaviour, nutritional chemistry, 16S sequencing, metagenome functional predictions, metabolite profiles, and energetic outcomes. Compared to primary forest-living conspecifics, we found that animals in the degraded forest consumed slightly fewer calories from less diverse diets. These animals exhibited less diverse gut microbiota, reduced microbial functional potential, and altered metabolomic profiles. Nevertheless, despite apparent nutritional constraints, energetic outcomes were broadly similar across habitats. These findings suggest that an organism's gut microbiome may be able to regulate microbial metabolic potential to facilitate resilience under suboptimal conditions. These findings highlight host-microbiome interactions as an important component of resilience in ecological specialists, with broad implications for predicting species persistence amid ongoing environmental change.