Abstract
BackgroundBifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents exploration of their genomic functions, including those that convey (human) health benefits.MethodsPacBio SMRT sequencing was used to determine the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree was constructed using a maximum-likelihood based approach in PhyML v3.0. M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned into pORI19 for insertion mutagenesis.ResultsIn this study we present the complete genome sequences of two Bifidobacterium longum subsp. longum strains. Comparative analysis with thirty one publicly available B. longum genomes allowed the definition of the B. longum core and dispensable genomes. This analysis also highlighted differences in particular metabolic abilities between members of the B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic analysis of the B. longum core genome indicated the existence of a novel subspecies. Methylome data, coupled to the analysis of restriction-modification systems, allowed us to substantially increase the genetic accessibility of B. longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed mutagenesis.ConclusionsComparative genomic analysis of thirty three B. longum representatives revealed a closed pan-genome for this bifidobacterial species. Phylogenetic analysis of the B. longum core genome also provides evidence for a novel fifth B. longum subspecies. Finally, we improved genetic accessibility for the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a mutant of this strain.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1968-4) contains supplementary material, which is available to authorized users.
Highlights
Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human gastro intestinal tract (GIT), while revealing genetic diversity among members of a given bifidobacterialspecies
General features of B. longum genomes The complete genome sequence was determined for two B. longum subsp. longum strains that had been isolated from infant faeces (B. longum subsp. longum NCIMB 8809) or a human adult intestine (B. longum subsp. longum CCUG 30698)
The observed G + C% content of both B. longum genomes (60.1 % G + C% content for B. longum subsp. longum NCIMB 8809 and 60.22 G + C% content for B. longum subsp. longum CCUG 30698) is consistent with that reported for other bifidobacterial genomes [3]
Summary
Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while revealing genetic diversity among members of a given bifidobacterial (sub)species. In order to map the evolutionary development of the Bifidobacterium genus, an extensive comparative study was recently performed on individual representatives of 47 bifidobacterial (sub)species [9, 10]. One of these comparative studies suggests that bifidobacteria and their animal hosts co-evolved, and that this co-evolution was facilitated by both gene loss and acquisition events to allow for (sub)species-specific adaptations to a glycan-rich environment [9]
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