Complete Genome Sequence of the Probiotic Strain Lactobacillus casei BD-II

Abstract

Lactobacillus casei BD-II, a patented probiotic strain (U.S. patent 7,270,994 B2), was isolated from homemade koumiss in China and has been implemented in the industrial production as starter cultures. Here we report the complete genome sequence of BD-II, which shows high similarity with the well-studied probiotic BL23.

TEXT

Lactobacillus casei is a remarkably adaptable lactic acid bacterium (LAB) that has been isolated from a variety of environmental niches, including dairy and plant materials as well as the gastrointestinal tracts of humans and animals (1). L. casei BD-II is a novel probiotic strain isolated from homemade koumiss in China which exhibits the ability to reduce the blood lipid level and regulate the cardiovascular system (2).

Whole-genome sequencing of BD-II was performed with a combined strategy of Roche 454 and Solexa paired-end sequencing technology. A genomic library containing a 8-kb insert was constructed, and 240,974 paired-end reads and 73,074 single-end reads were generated using the GS FLX system, giving 21.60-fold coverage of the genome. The analysis with the 454 Newbler (454 Life Sciences, Branford, CT) showed that 92.90% of the reads were assembled into three large scaffolds, including 349 contigs. A total of 12,410,962 reads (3-kb library) were generated to reach a depth of 381-fold coverage with an Illumina Solexa GA IIx (Illumina, San Diego, CA) and mapped to the scaffolds using the Burrows-Wheeler alignment (BWA) tool (3). Most of the gaps within the scaffolds were filled by local assembly of 454 and Solexa reads. The gaps between scaffolds were filled by sequencing PCR products using an ABI 3730 capillary sequencer. Comparative genomic analysis was performed with the published genomes of L. casei strains ATCC 334 (1), BL23 (4), and Zhang (8).

The complete genome sequence of BD-II is composed of a circular 3,069,926-bp chromosome and a 57,362-bp plasmid named pBD-II, with mean GC contents of 46.34% and 43.70%, respectively. There are 3,139 coding genes, 5 rRNA operons, and 59 tRNAs in the chromosome and 65 coding genes in the plasmid.

Comparative genome analysis showed that BD-II carries most of the core genes of L. casei, with no known pathogenic genes identified. Among the four genomes, BD-II and BL23 show the highest similarity with respect to genome structure and gene order, while only a few differential genes are identified in BD-II and BL23. The differential genes all belong to multicopy genes of the two strains and are mainly involved in transposition, sugar transport, ion transport, and redox.

Like BL23, many regions with novel properties are identified in BD-II, mostly involved in carbohydrate utilization and transcriptional regulation. In particular, a region of 12.8 kb forming the iolRTABCDG1G2EJK operon, which is involved in the catabolism of myoinositol, was found in BD-II. In LAB, the iol cluster was first discovered in BL23 (6), and Zhang et al. (7) determined that it was not a common feature among dairy L. casei strains by investigating its distribution in 24 dairy L. casei isolates. In addition, a region covered by the genes LCBD_2197 to LCBD_2210 of BD-II show high homology with the genes for the biosynthesis of cell wall-associated polysaccharides of L. casei Shirota (5), suggesting the potential ability to produce polysaccharide for BD-II.

In conclusion, the genome sequence of BD-II proves its safety and stability in commercial use and reveals many potential properties for further elucidation.

Nucleotide sequence accession numbers.

Genome information for the chromosome and the plasmid of Lactobacillus casei BD-II has been deposited in the GenBank database with accession numbers CP002618 and CP002619.