Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04

Abstract

Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two Bifidobacterium animalis subsp. lactis strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three Bifidobacterium species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium B. animalis subsp. lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.

FIG. 1.

Alignment of B. animalis subsp. lactis genomes. Differences observed between the two B. animalis subsp. lactis genomes are shown in the figure. (A) SNPs are indicated using bars, with noncoding SNPs at the top, synonymous SNPs in the middle, and nonsynonymous SNPs at the bottom. INDELs are shown by arrows, with insertions in the Bl-04 genome shown on top and insertions in the DSM 10140 genome shown on the bottom. (B) Optical maps of various B. animalis subsp. lactis strains, visualized using OpGen MapViewer, based on a NotI digest. The first two optical maps were generated in silico (indicated by asterisks) based on the genome sequences. The other optical maps represent experimental data.

FIG. 2.

Comparative genomic analysis of bifidobacteria. Sequences homologous to B. animalis subsp. lactis (Bla) proteins are shown in black, whereas the absence of a homolog in the B. adolescentis ATCC 15703 (Bad) or B. longum NCC2705 (Blo) genome appears in white, represented using MeV. (Left) Data are presented in chromosomal ORF order, with the origin of replication at the top and with numbers indicating locations of areas of unique content in B. animalis subsp. lactis. (Right) Hierarchical representation of homologs across the three genomes.

FIG. 3.

Overview of B. animalis subsp. lactis CRISPR locus. The Bala1 CRISPR locus, as it appears in the genome, is shown at the top, with the repeat-spacer region on the left (repeats are represented as black diamonds, and spacers are represented as gray boxes) and cas genes on the right. The repeat-spacer region is shown below for Bl-04 and DSMZ 10140, with repeats shown as black diamonds, spacers shown as numbered gray boxes, the leader shown as a white box, and the terminal repeat shown as a black diamond annotated with a “T.” The bottom panel shows a CRISPR spacer overview where repeats are not included and only spacers are represented, using two-color combinations.