The inside tract: The appendicular, cecal, and colonic microbiome of captive aye‐ayes

Objectives The aye‐aye ( Daubentonia madagascariensis ) is famous for its feeding strategies that target structurally defended, but high‐quality resources. Nonetheless, the influence of this digestible diet on gut microbial contributions to aye‐aye metabolism and nutrition remains unexplored. When four captive aye‐ayes were unexpectedly lost to persin toxicity, we opportunistically collected samples along the animals' gastrointestinal tracts. Here we describe the diversity and composition of appendicular, cecal, and colonic consortia relative to the aye‐aye's unusual feeding ecology. Materials and methods During necropsies, we collected digestive content from the appendix, cecum, and distal colon. We determined microbiome structure at these sites via amplicon sequencing of the 16S rRNA gene and an established bioinformatics pipeline. Results The aye‐ayes' microbiomes exhibited low richness and diversity compared to the consortia of other lemurs housed at the same facility, and were dominated by a single genus, Prevotella . Appendicular microbiomes were differentiated from more homogenized cecal and colonic consortia by lower richness and diversity, greater evenness, and a distinct taxonomic composition. Discussion The simplicity of the aye‐aye's gut microbiome could be attributed to captivity‐induced dysbiosis, or it may reflect this species' extreme foraging investment in a digestible diet that requires little microbial metabolism. Site‐specific appendicular consortia, but more similar cecal and colonic consortia, support the theory that the appendix functions as a safe‐house for beneficial bacteria, and confirm fecal communities as fairly reliable proxies for consortia along the lower gut. We encourage others to make similar use of natural or accidental losses for probing the primate gut microbiome.