A comparative study of gut microbiomes in captive nocturnal strepsirrhines

Abstract

Feeding strategy and diet are increasingly recognized for their roles in governing primate gut microbiome (GMB) composition. Whereas feeding strategy reflects evolutionary adaptations to a host's environment, diet is a more proximate measure of food intake. Host phylogeny, which is intertwined with feeding strategy, is an additional, and often confounding factor that shapes GMBs across host lineages.Nocturnal strepsirrhines are an intriguing and underutilized group in which to examine the links between these three factors and GMB composition. Here, we compare GMB composition in four species of captive, nocturnal strepsirrhines with varying feeding strategies and phylogenetic relationships, but nearly identical diets.We use 16S rRNA sequences to determine gut bacterial composition. Despite similar husbandry conditions, including diet, we find that GMB composition varies significantly across host species and is linked to host feeding strategy and phylogeny.The GMBs of the omnivorous and the frugivorous species were significantly more diverse than were those of the insectivorous and exudativorous species. Across all hosts, GMBs were enriched for bacterial taxa associated with the macronutrient resources linked to the host's respective feeding strategy. Ultimately, the reported variation in microbiome composition suggests that the impacts of captivity and concurrent diet do not overshadow patterns of feeding strategy and phylogeny. As our understanding of primate GMBs progresses, populations of captive primates can provide insight into the evolution of host-microbe relationships, as well as inform future captive management protocols that enhance primate health and conservation.

Evolutionary development and co‐phylogeny of primate‐associated bifidobacteria

“…Furthermore, due to the advent of modern sequencing technologies, significant research effort has been aimed at disclosing the microbiota composition of non‐human primates and at investigating how this is influenced by ecological variation through time (Greene et al ., 2019; Orkin et al ., 2019). These studies described gut mirobiomes of several non‐human primate species in which Actinobacteria were outnumbered by Firmicutes and Bacteroidetes, being reminiscent of the human gut microbiota (Bornbusch et al ., 2019; Gomez et al ., 2019; Greene et al ., 2019). In contrast, reports on the gut microbiota of members of the Cebidae family highlighted a bacterial composition dominated by the genera Streptococcus and Bifidobacterium (Orkin et al ., 2019).…”

Longitudinal effects of antibiotics and fecal transplant on lemur gut microbiota structure, associations, and resistomes

“…Bacteroides -two, closely related taxa with similar functional potential 71 -dominated the observed relationships. The strength and quantity of relationships between Bacteroides and other bacterial taxa support the foundational membership of Bacteroides in the lemur gut microbiome 42,72,73 . Notably, increases in the log ratio abundance of Bacteroides during antibiotic treatment indicated that its members maintained or increased their relative abundances while other taxa were eliminated.…”

Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar

“…The increased similarity was evidenced in both the presence-absence and the abundance-weighted metrics of phylogenetic compositions (i.e., unweighted and weighted UniFrac), indicating that both rare and abundant microbes were driving the pattern of rewilding. We thus explored specific patterns in Bacteroides, Prevotella, and Ruminococcus-three dominant members of primate GMBs 8,[36][37][38] .…”