Differential Microbial Composition and Fiber Degradation in Two Sloth Species (Bradypus variegatus and Choloepus hoffmanni).

Sloths have the slowest digestion among mammals, requiring 5-20 times longer to digest food than other herbivores, which suggests differences in their gut microbiota, particularly in plant-fiber-degrading microorganisms. Bradypus variegatus has a lower metabolic rate and moves less than Choloepus hoffmanni. However, no comprehensive studies have compared the microbiota (e.g., fungi) of these species. We hypothesized that differences in digestion and metabolism between the two species would be reflected in their microbiota composition and functionality, which we characterized using metagenomics, metabarcoding, and cellulose degradation. Results revealed significant differences in microbiota composition and functionality. Both species are dominated by bacteria; fungi comprised only 0.06-0.5% of metagenomic reads. Neocallimastigomycota, an anaerobic fungus involved in fiber breakdown in other herbivores, was found in low abundance, especially in B. variegatus. Bacterial communities showed subtle differences: C. hoffmanni was dominated by Bacillota and Bacteroidota, while B. variegatus showed higher Actinomycetota. Expected herbivore bacterial taxa (e.g., Fibrobacter and Prevotella) were scarce. Functional analysis showed a low abundance of carbohydrate-active enzymes essential for polysaccharide breakdown. Cellulose degradation assays confirmed that sloths digest only ~ 3-30% of ingested plant material. This research sheds light on the potential multidirectional links between the gut microbiota, metabolism, and digestion.