Comparative genomics of Bifidobacterium species isolated from marmosets and humans

Abstract

The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced. There were six B. reuteri strains, two B. callitrichos strains, one B. myosotis sp. nov. and one B. tissieri sp. nov. among our isolates. Phylogenetic analysis showed that three of the four species we isolated were most closely related to B. bifidum, B. breve and B. longum, which are species found in high abundance in human infants. There were 1357 genes that were shared by at least one strain of B. reuteri, B. callitrichos, B. breve, and B. longum, and 987 genes that were found in all strains of the four species. There were 106 genes found in B. reuteri and B. callitrichos but not in human bifidobacteria, and several of these genes were involved in nutrient uptake. These pathways for nutrient uptake appeared to be specific to Bifidobacterium from New World monkeys. Additionally, the distribution of Bifidobacterium in fecal samples from captive adult marmosets constituted as much as 80% of the gut microbiome, although this was variable between individuals and colonies. We suggest that nutrient transporters may be important for the maintenance of Bifidobacterium during adulthood in marmosets.

The Gut Microbiome of Exudivorous Marmosets in the Wild and Captivity

“…The genomes of three isolates of Bifidobacterium callitrichos from a captive C. jacchus fecal sample contained predicted genes associated with galactose and arabinose metabolism, which are major constituents of tree gums eaten by C. jacchus [70]. In 3 US captive facilities, C. jacchus collectively shared four species of Bifidobacterium which possessed genes encoding ATP-binding cassette proteins, which are important for nutrient transport that may be specific to marmoset gut [32].…”

“…Thus, comparing GMC of wild and captive conspecifics is an important step for such approaches. Up to now, Callithrix gut microbiome studies have focused on captive C. jacchus to identify specific bacterial strains [30][31][32][33] and on how life history, social, or laboratory conditions affect the GMC [34][35][36]. Here, we determine gut microbiome profiles of wild and translocated/captive Callithrix sampled throughout Brazil.…”

Evolutionary development and co‐phylogeny of primate‐associated bifidobacteria

“…Furthermore, a combination of whole metagenome shotgun sequencing coupled with cultivation approaches allowed the isolation of novel bifidobacteria from faecal samples of monkeys (Lugli et al ., 2019). A comparative genomic study, involving genomes of four species of bifidobacteria isolated from marmosets and four species isolated from humans, unveiled apparently species‐specific genes predicted to be involved in nutrient uptake (Brown et al ., 2019).…”

Generation of germ-free common marmosets

“…The comparison of faecal bacterial composition in this study indicated that intestinal bacterial flora in conventional marmosets is similar to that in humans, such as Bifidobacterium colonisation, which did not occur in SPF mice. Spontaneous Bifidobacterium colonisation was also consistently observed in marmosets from other facilities 30,31 . Furthermore, the inoculation of the intestinal bacterial strains obtained from humans showed that marmosets underwent significantly steady colonisation by all these strains, suggesting similar colonisation milieu for intestinal bacteria with humans.…”