Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota

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.

Keywords: Bifidobacterium; genomics; metagenomics; microbiota.

Figure 1

Bifidobacterial profiling of 23 fecal samples of human and animals. Panel (a) displays the relative abundance of each genus by means of 16S rRNA microbial profiling. Only genera that display at least one sample with a relative abundance of at least 5% were included in the heat map. Panel (b) shows the relative abundance of each species belonging to the genus Bifidobacterium by means of ITS bifidobacterial profiling. Only species that display at least 0.01% of the total amount of the sequencing data were included in the heat map.

Figure 2

Bifidobacterium adolescentis AS-ADO unique loci. B. adolescentis AS-ADO reconstructed contig sequences are ordered based on the genome of the type strain B. adolescentis ATCC 15703 complete genome and its genes reported as a circular genome atlas (orange circles). Internal circles illustrate B. adolescentis AS-ADO GC% deviation and GC skew (G−C/G+C). Genetic maps exhibit two unique loci of B. adolescentis AS-ADO compared to B. adolescentis strains retrieved from the database. Loci positions in the genome are highlighted with the relative color. Each arrow indicates an open reading frames (ORF), whereas the length of the arrow is proportional to the length of the predicted ORF.