Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

Abstract

ABSTRACTMany strains ofBifidobacterium animalissubsp.lactisare considered health-promoting probiotic microorganisms and are commonly formulated into fermented dairy foods. Analyses of previously sequenced genomes ofB. animalissubsp.lactishave revealed little genetic diversity, suggesting that it is a monomorphic subspecies. However, during a multilocus sequence typing survey ofBifidobacterium, it was revealed thatB. animalissubsp.lactisATCC 27673 gave a profile distinct from that of the other strains of the subspecies. As part of an ongoing study designed to understand the genetic diversity of this subspecies, the genome of this strain was sequenced and compared to other sequenced genomes ofB. animalissubsp.lactisandB. animalissubsp.animalis. The complete genome of ATCC 27673 was 1,963,012 bp, contained 1,616 genes and 4 rRNA operons, and had a G+C content of 61.55%. Comparative analyses revealed that the genome of ATCC 27673 contained six distinct genomic islands encoding 83 open reading frames not found in other strains of the same subspecies. In four islands, either phage or mobile genetic elements were identified. In island 6, a novel clustered regularly interspaced short palindromic repeat (CRISPR) locus which contained 81 unique spacers was identified. This type I-E CRISPR-cassystem differs from the type I-C systems previously identified in this subspecies, representing the first identification of a different system inB. animalissubsp.lactis. This study revealed that ATCC 27673 is a strain ofB. animalissubsp.lactiswith novel genetic content and suggests that the lack of genetic variability observed is likely due to the repeated sequencing of a limited number of widely distributed commercial strains.