Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior.

Takahiro Segawa,Hiroshi Mori,Pierre Mbehang Nguema,Kazunari Ushida,Satoshi Fukuchi,Dylan Bodington,Sayaka Tsuchida

doi:10.3390/microorganisms7040099

Abstract

Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species.

Highlights

The gut microbiome is composed of an immense diversity of microorganisms [1], and recent studies have shown their essential roles in host health [2,3,4,5,6,7]
The human gut normally harbors Bifidobacterium as one of the most abundant bacterial genera (~10%) [14], and to date, 12 species belonging to B. adolescentis-group, B. longum-group or B. scardovi-group and B. bifidum have been recognized as human-associated bifidobacteria [15]
B. moukalabense was confirmed to be phylogenetically close to B. catenulatum and B. pseudocatenulatum and is a monophyletic species belonging to the B. adolescentis-group by 16S rRNA gene analysis (Figure S1)

Summary

Introduction

The gut microbiome is composed of an immense diversity of microorganisms [1], and recent studies have shown their essential roles in host health [2,3,4,5,6,7]. The genus Bifidobacterium is the unique Actinobacteria, which is adapted to animal intestinal tracts. Bifidobacteria have been commonly recognized as health-promoting gut bacteria in many health-oriented research studies [8,9,10,11,12]. The genus Bifidobacterium comprises 70 established species with 10 subspecies according to LPSN (http://www.bacterio.net/bifidobacterium.html). Within these 70 species, human-associated species of Bifidobacterium are abundant. The human gut normally harbors Bifidobacterium as one of the most abundant bacterial genera (~10%) [14], and to date, 12 species belonging to B. adolescentis-group, B. longum-group or B. scardovi-group and B. bifidum have been recognized as human-associated bifidobacteria [15]. The wide phylogenetic variety of human-associated Bifidobacterium spp. suggests their adaptation to the wide range of eating habits of humans [16]

Methods

Results

Conclusion