The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut

Abstract

Bifidobacterium is a diverse genus of anaerobic, saccharolytic bacteria that colonize many animals, notably humans and other mammals. The presence of these bacteria in the gastrointestinal tract represents a potential coevolution between the gut microbiome and its mammalian host mediated by diet. To study the relationship between bifidobacterial gut symbionts and host nutrition, we analyzed the genome of two bifidobacteria strains isolated from the feces of a common marmoset (Callithrix jacchus), a primate species studied for its ability to subsist on host-indigestible carbohydrates. Whole genome sequencing identified these isolates as unique strains of Bifidobacterium callitrichos. All three strains, including these isolates and the previously described type strain, contain genes that may enable utilization of marmoset dietary substrates. These include genes predicted to contribute to galactose, arabinose, and trehalose metabolic pathways. In addition, significant genomic differences between strains suggest that bifidobacteria possess distinct roles in carbohydrate metabolism within the same host. Thus, bifidobacteria utilize dietary components specific to their host, both humans and non-human primates alike. Comparative genomics suggests conservation of possible coevolutionary relationships within the primate clade.

Targeted Diet Modification Reduces Multiple Sclerosis–like Disease in Adult Marmoset Monkeys from an Outbred Colony

“…In marmosets, Bifidobacteria facilitate the fermentation of the long-chain carbohydrates in gum, which is a main factor in their diet in the wild and in captivity. The high percentage of Actinobacteria contrasts with a recent paper in which marmoset gut microbiota were found to be dominated by Proteobacteria and Firmicutes (49). The differences may be explained by different food or technical differences, as we could confirm the high percentage of Bifidobacteria by FISH.…”

The Gut Microbiome of Exudivorous Marmosets in the Wild and Captivity

“…Actinobacteria was not the most abundant gut bacterial taxa for most captive Callithrix and there is increased abundance of gut Proteobacteria among captive marmosets here and other studies [36,70]. One study of captive C. jacchus uniquely compared gut microbiome composition between a specific pathogen free colony, housed under conditions that minimized outside contamination, with a Bifibacterium (approximately 1% to 80%), while Fusobacterium B (phylum Fusobacteria) was dominant in conventionally housed hosts [34].…”

“…While wild and captive/translocated marmosets possessed similar classes of bacterial phyla (Table 3), bacterial abundance differed starkly between host environment. Unlike non-captive marmosets, wild marmosets had a GMC enriched for the Bifidobacteriaceae family (Actionobacterium), which includes genera like Bifibacterium that are common in animal gastrointestinal tracts and metabolize host-indigestible carbohydrates [70,71]. Wild marmosets gut microbiomes were also enriched for other bacteria involved in carbohydrate metabolism like Megasphaera and Pectinatus (both Firmicutes), which are actually known as important beer spoilage bacteria [72].…”

The gut microbiome and metabolome of saddleback tamarins (Leontocebus weddelli): Insights into the foraging ecology of a small‐bodied primate

“…A recent comparative study of nonhuman primate gut microbiomes suggests that host physiology has a larger influence on gut microbiome than dietary niche; however, in the case of most fruit‐eating primates, the gut microbiome is enriched for functions related to starch and sucrose metabolism (Amato et al, ). Although the few studies of small‐bodied primates such as the rufous mouse lemur ( Microcebus rufus ), whose diet is composed of insects, lipid‐rich fruits, floral nectar, and plant exudates (Atsalis, ), indicates broad similarities in gut microbial composition with saddleback tamarins (Aivelo et al, ) as do microbial adaptations to carbohydrate metabolism in exudate, fruit, and invertebrate/vertebrate feeding common marmosets ( Callithrix jacchus ; Albert, Rani, & Sela, ), it is difficult to make robust predictions about the influence of both the metabolic demands and short gut retention times in understanding the gut microbiome of these small‐bodied primates.…”