Fibrolytic capacity of the gut microbiome in captive African elephants (Loxodonta africana): a pilot study.

African elephants (Loxodonta africana) depend on the fibrolytic capacity of their gut microbiome (GMB) to efficiently utilize fibrous plant material. However, knowledge is missing on the temporal stability and functional dynamics (especially fibrolytic capacity) of their GMB. Likewise, information on the associated volatile fatty acids (VFA) production in the elephant's hindgut is scarce. In this pilot study, we collected feces from five captive African elephants on two occasions separated by 12 months to explore the GMB composition and its changes over time. We characterized the GMB's fibrolytic potential based on total microbial numbers and metagenome composition, including carbohydrate-active enzymes (CAZy), and fecal VFA, at individual and group level. Elephants received a roughage-based diet, which contained more carrots at the second than at the first sampling. Bacteria, specifically fibrolytic Prevotella, Bacteroides, Ruminococcus and Fibrobacter dominated the GMB, while archaea, fungi and protozoa were less present. Treponema was highly abundant, which might be an adaptation to maximize energy gain from cellulose-rich food. The elephants showed individual shifts in GMB composition from the first to second sampling. The shift in functional gene composition from the first to the second sampling was similar among elephants. It showed distinct clustering of CAZy families between fecal collections and discriminated features related to breakdown of carrot pectin for the second sampling. Sparse partial least squares-discriminant analysis identified (hemi-)cellulolytic genera within Prevotellaceae as discriminant taxa, which positively associated with CAZy families but negatively with VFA. At group level, fecal VFA concentrations were similar among elephants. However, opposite shifts from the first to the second sampling were detected among elephants at individual level. It may be speculated whether feeding decisions of three related females might explain the increase of VFA in their feces at the second compared to the first sampling, whereas VFA were lower in feces of the non-related female at the second sampling. We assert that this pilot study on GMB taxonomy and carbohydrate breakdown in captive African elephants may be helpful for feeding management at zoological gardens.