The gut microbiome of nonhuman primates: Lessons in ecology and evolution

Abstract

The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa. Finally, we highlight how studying the gut microbiome offers new insights into primate nutrition, physiology, and immune system function, as well as enhances our understanding of primate ecology and evolution. Microbiome approaches are useful tools for studying relevant issues in primate ecology. Further study of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health.

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

“…Due to this critical role, research has focused on the environmental and ecological factors that shape the composition and function of this microecosystem. Among these factors geographic range, anthropogenic pressure, group identity, and type of diet, have all been shown to influence the gut microbiome composition of nonhuman primates (NHP) (Barelli et al, ; Clayton et al, ; Gomez et al, ). However, the impact of individual host traits such as age and/or sex on bacterial community composition has received considerably less attention.…”

A descriptive analysis of gut microbiota composition in differentially reared infant rhesus monkeys (Macaca mulatta) across the first 6 months of life

“…The gut microbiome is receiving increased recognition as a critical component in host immune function, physiology, and even behavior. This is evidenced by the recent uptick in studies of the microbiome in both human and non‐human primates (NHP) in various settings (Chernikova et al, ; see also Clayton et al, , for a review of NHP gut microbiome studies). Collectively, the literature demonstrates that early experiences shape infant gut microbial colonization, literature that is best described in human neonates.…”

“…Collectively, the literature demonstrates that early experiences shape infant gut microbial colonization, literature that is best described in human neonates. This colonization appears to be influenced by the mode of birth (Frese & Mills, ; Rautava, ), gestational age at birth (Chernikova et al, ), time spent in the neonatal intensive care unit (NICU; Chernikova et al, ; Hartz, Bradshaw & Brandon, ), bacterial transmission by various maternal body sites (Ferretti et al, ), infant feeding practices (Allen‐Blevins, Sela, & Hinde, ; Bode, ; Cong et al, ; Sela, ), and social environments, including early caregiving settings (Clayton et al, ; Thompson, Monteagudo‐Mera, Cadenas, Lampl & Azcarate‐Peril, ). Moreover, gut microbial composition and diversity in infancy have long‐term impacts on infant health and behavior (Allen‐Blevins et al, ; Carlson et al, ; Kostic et al, ; Martin & Sela, ; Tamburini, Shen, Wu & Clemente, ; Thomas et al, ).…”

“…As such, this is the first study to characterize gut microbiota profiles in infant macaques beginning at birth and continuing throughout infancy, thereby integrating the gut microbiome into the literature on the consequences of the early life environment. We conducted amplicon (16S rRNA gene) sequencing analyses to examine the gut microbiome, with a particular focus on the relative abundances of Lactobacillus, Clostridium, Bacteroides , Streptococcus , Prevotella , and Bifidobacterium based on previous reports that these taxa predominate in the macaque gastrointestinal tract (Clayton et al, ), and that they also have health and developmental consequences in human primates (Martin & Sela, ; Thomas et al, ). These bacteria have important roles in shaping infant development, including stimulating the infant immune system, producing nutrients and energy for host cells, and serving as a barrier to invading pathogens (see Martin & Sela, , for a review).…”

The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs

“…A major goal of GMB researchers is to improve our understanding of the evolutionary and ecological mechanisms by which consortia are established and mediated (Clayton, Gomez, et al, ; Groussin et al, ). One topic of discussion involves the respective roles of host phylogenetic relationships and feeding ecology (Delsuc et al, ; Groussin et al, ; Ley et al, ; Nishida & Ochman, ).…”