Lemur gut microeukaryotic community variation is not associated with host phylogeny, diet, or habitat

Gut prokaryotic (GP) community variation is often associated with host evolutionary and ecological variables; whether these factors drive variation in other gut taxa remains largely untested. We present a one-to-one comparison of GP (16S rRNA metabarcoding) and microeukaryotic (GME) (18S rRNA metabarcoding) community patterning among 12 species of lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological diversity. We found that while lemur GPs vary with host taxonomy, diet, and habitat, GMEs have no association with these factors. As a mechanism, we suggest purifying selection purges microbes with negative and commensal associations, while positive selection promotes the persistence of beneficial microbes. It is therefore likely that a greater proportion of GMEs comprise taxa with commensal, transient, and parasitic symbioses compared with GPs, many of which are mutualists. Our study reveals different microbial taxa are shaped by unique selective pressures.