Development, diet and dynamism: longitudinal and cross‐sectional predictors of gut microbial communities in wild baboons

Abstract

Summary Gut bacterial communities play essential roles in host biology, but to date we lack information on the forces that shape gut microbiota between hosts and over time in natural populations. Understanding these forces in wild primates provides a valuable comparative context that enriches scientific perspectives on human gut microbiota. To this end, we tested predictors of gut microbial composition in a well-studied population of wild baboons. Using cross-sectional and longitudinal samples collected over 13 years, we found that baboons harbor gut microbiota typical of other omnivorous primates, albeit with an especially high abundance of Bifidobacterium. Similar to previous work in humans and other primates, we found strong effects of both developmental transitions and diet on gut microbial composition. Strikingly, baboon gut microbiota appeared to be highly dynamic such that samples collected from the same individual only a few days apart were as different from each other as samples collected over 10 years apart. Despite the dynamic nature of baboon gut microbiota, we identified a set of core taxa that is common among primates, supporting the hypothesis that microbiota codiversify with their host species. Our analysis identified two tentative enterotypes in adult baboons that differ from those of humans and chimpanzees.

Gut microbiota of a long‐distance migrant demonstrates resistance against environmental microbe incursions

“…Finally, we found only weak shifts in gut microbiota composition within the flock over the nonbreeding season, and individual stints underwent large, seemingly random, fluctuations in their gut microbiota composition and diversity, demonstrating a remarkably changeable microbiota within individuals even during sedentary periods. Such dramatic shifts have also been found in other wild species such as anolis lizards (Ren, Kahrl, Wu, & Cox, ) and baboons (Ren, Grieneisen, Alberts, Archie, & Wu, ), suggesting microbial fluctuations in community composition, potentially in response to short‐term shifts in host diet or physiology, may be the norm in wild animals, independent of being sedentary or migratory. However, our findings suggest these changes are likely to be due to short‐term shifts in diet or physiology, rather than exposure to altered environmental microbiota.…”

“…Such dramatic shifts have also been found in other wild species such as anolis lizards (Ren, Kahrl, Wu, & Cox, 2016) and baboons (Ren, Grieneisen, Alberts, Archie, & Wu, 2016), suggesting microbial fluctuations in community composition, potentially in response to short-term shifts in host diet or physiology, may be the norm in wild animals, independent of being sedentary or migratory. However, our findings suggest these changes are likely to be due to short-term shifts in diet or physiology, rather than exposure to altered environmental microbiota.…”

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards

“…In similar fashion, pronounced temporal variation in the microbiota of individuals was also observed in faecal samples from wild baboons (Ren et al . ). In Burmese pythons, bacterial diversity and community composition in the gut changed rapidly and dramatically within hours to days of feeding, and these changes were primarily due to shifts in the abundance of endogenous gut bacteria, rather than the introduction of new bacteria from the rodent meal (Costello et al .…”

Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors

“…The associations between age and sex and the gut microbiome have been described for a handful of NHP species: black howler monkeys ( A. pigra ) (Amato et al, , ), yellow baboons ( P. cynocephalus ) (Ren, Grieneisen, Alberts, Archie, & Wu, ), ring‐tailed lemurs ( L. catta ) (Bennett et al, ), rufous mouse lemurs ( M. rufus ) (Aivelo, Laakkonen, & Jernvall, ), captive lemurs ( V. variegata , L. catta , P. coquereli ) (McKenney, Rodrigo, & Yoder, ), and chimpanzees ( P. t. schweinfurthii ) (Degnan et al, ). In general, some of these studies have suggested that individuals in early stages of development and females exhibit gut microbiome patterns associated with higher metabolic demands (e.g., higher abundance of fermentative taxa) during juvenile development, female pregnancy, and lactation (Amato et al, ; Mallott, Amato, Garber, & Malhi, ).…”