Abstract
Bifidobacteria are among the most prevalent gut commensals in mammals, playing crucial functional roles that start from their early colonization of the infant gastrointestinal tract and last throughout the life span of their host. Metagenomic approaches have been employed to unveil the genetic features of bifidobacteria in order to understand how they participate in the correct development of a healthy microbiome. Nevertheless, their low relative abundance in many environmental samples may represent a major limitation for metagenomics approaches. To overcome this restriction, we applied an enrichment method that allows amplification of bifidobacterial DNA obtained from human or animal fecal samples for up to 26,500-fold, resulting in the metagenomic reconstruction of genomes belonging to bifidobacterial strains, present at very low abundance in collected samples. Functional predictions of the genes from these reconstructed genomes allows us to identify unique signatures among members of the same bifidobacterial species, highlighting genes correlated with the uptake of nutrients and adhesion to the intestinal mucosa.
Highlights
The human body, as well as that of non-human animals, is inhabited by a plethora of microbial species that reside in specific microbial communities in and on their host [1]
In order to investigate the bifidobacterial composition of the mammalian gut microbiota, we inspected the taxonomic composition of the bacterial community harbored by seven human beings and 16 non-human animals through 16S rRNA-based profiling (Table S1)
Nucleotide sequences were grouped in clusters of operational taxonomic units (OTUs) and taxonomically classified
Summary
The human body, as well as that of non-human animals, is inhabited by a plethora of microbial species that reside in specific microbial communities in and on their host [1]. The gastrointestinal microbial community, known as gut microbiota, represents the most numerous host-associated community, with an estimated 1014 bacterial cells located in the large intestine [2]. The microbial population exerts many important activities to sustain host health, including a breakdown of otherwise indigestible food components, pathogen protection, promotion of host cell differentiation, and stimulation/modulation of the host immune system [3,4]. For this reason, the gut microbiota is the most scrutinized host-associated community in terms of large scale metagenomic studies [5,6]. Reconstruction of a complete bifidobacterial genome from the gut microbiota of adults can be quite a challenge due to the relatively low abundance of members of this genus
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