Genetic characteristics and functional genes of Bifidobacterium animalis subsp. lactis Probio-M8 from breast milk

Abstract:

[Objective] Breast milk-derived Bifidobacterium animalis subsp. lactis Probio-M8 has excellent probiotic properties. We analyzed the genetic characteristics of Probio-M8 at the genome-wide level and compared the genomes between Probio-M8 and other B.animalis subsp. lactis strains with probiotic efficacy. [Methods] We constructed the core gene set and pan gene set based on the genome data of 21 strains and 1 model strain DSM10140^T of B.animalis subsp. lactis in the NCBI database. Further, we constructed a phylogenetic relationship of this population and analyzed the genetic characteristics and functional genes of Probio-M8. [Results] The pan gene set of the 22 strains contained 1 618 genes, including 1 514 (93.57%) core genes, which indicated the core gene set was highly conserved. A phylogenetic tree was constructed based on the 1 514 core genes, which showed that AD011 was in a single branch, while Probio-M8 and the other strains were in the same clade with the type strain DSM10140^T. Probio-M8 had short genetic distance with V9, BB-12, Bi-07, and HN019. The genomes of Probio-M8, V9, BB-12, Bi-07, and HN019 carried three inherent resistance genes dfrA43, tetW, and rpoB with the same copy number among strains and did not contain virulence genes, which indicated the virulence and resistance genes were conserved. Furthermore, Probio-M8, V9, BB-12, and HN019 all had 47 carbohydrate metabolism-related genes. Bi-07 lacked GH49 gene and one GH13 gene copy, while Probio-M8 had an extra copy of GH49 gene, which indicated that the 5 probiotic strains had similar genes for carbohydrate metabolism. [Conclusion] The core gene set is highly conserved among the 22 strains of B.animalis subsp. lactis. The strains Probio-M8, V9, BB-12, Bi-07, and HN019 have similar genetic characteristics. This article supplies data support for the follow-up studies of Probio-M8.

Key words:Bifidobacterium animalis subsp. lactis;comparative genomics;carbohydrase