Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shōchū Residue.

Here, we report the draft genome sequences of two type strains of Lactobacillus, Lactobacillus farraginis JCM 14108(T) and Lactobacillus composti JCM 14202(T), isolated from the compost of distilled shōchū residue. Their genome information will be useful for studies of ecological and physiological functions of these Lactobacillus species.

GENOME ANNOUNCEMENT

Lactobacillus strains have been isolated from various environments and are frequently used as probiotics. Strains NRIC 0676 and NRIC 0689 (also available from the Japan Collection of Microorganisms as JCM 14108 and JCM 14202, respectively) were isolated from the compost of distilled shōchū (traditional Japanese spirits) residue as the type strains of the novel species L. farraginis and L. composti, respectively (1, 2). They are heterofermentative lactic acid bacteria. The 16S rRNA gene sequence analyses indicate that L. farraginis is closely related to Lactobacillus hilgardii, isolated from wine, and Lactobacillus buchneri, isolated from silages (1). The 16S rRNA gene sequence identities of L. composti to known Lactobacillus species are <93% (2, 3).

The genomes of L. farraginis JCM 14108T and L. composti JCM 14202T were sequenced using an Ion Torrent PGM system. The sequence reads, totaling 567,815 for JCM 14108T and 484,069 for JCM 14202T, were assembled using Newbler version 2.8 (Roche) into 129 and 94 contigs, with N50 lengths of 51,335 and 87,613 bp, respectively. These assemblies resulted in draft genome sequences of 2,884,682 bp for JCM 14108T and 3,449,704 bp for JCM 14202T, with 46.2× and 28.2× redundancies and G+C contents of 42.1 and 43.9%, respectively. A total of 3,079 and 3,863 protein-coding genes and 61 and 49 RNA-coding sequences for JCM 14108T and JCM 14202T, respectively, were identified using the RAST server (4) and with the manual inspections detailed below.

The phosphoenolpyruvate:carbohydrate phosphotransferase (PTS) system is involved in the transport and phosphorylation of numerous carbohydrates (5, 6). L. composti JCM 14202T has at least 17 genes related to the PTS system, whereas L. farraginis JCM 14108T has only 6 genes. Analyses in the CAZy database (7) revealed that L. composti JCM 14202T has genes encoding β-glucosidases belonging to the glycoside hydrolase 1 (GH1) and GH3 families, whereas L. farraginis JCM 14108T has only those of GH3. Both strains have genes encoding α-galactosidases of GH36. L. composti JCM 14202T has genes encoding β-galactosidases of GH2 and GH42, whereas L. farraginis JCM 14108T has only those of GH2. In addition, L. composti JCM 14202T has genes encoding xylanase of GH43, α-mannosidase of GH38, and α-N-arabinofuranosidase of GH51. Detailed analyses of the genomes of these strains will facilitate studies on the functions of Lactobacillus spp. in the compost of distilled shōchū residue.

Nucleotide sequence accession numbers.

The genome sequences of L. farraginis JCM 14108T and L. composti JCM 14202T have been deposited at DDBJ/EMBL/GenBank under accession no. BAKI01000001 to BAKI01000129 and BAMK01000001 to BAMK01000094, respectively.