Draft Genome Sequence of Lactobacillus zeae KCTC 3804

Abstract

We announce the draft genome sequence of the type strain Lactobacillus zeae KCTC 3804 (3,110,326 bp, with a G+C content of 47.8%), which is one of the most prevalent lactic acid bacteria present during the processing of raw cow's milk. The genome consists of 113 large contigs (>100 bp). All of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).

GENOME ANNOUNCEMENT

Cow's milk has all 8 essential amino acids in varying amounts, depending on the stage of lactation. About 80% of the proteins in milk are caseins, which are reasonably heat stable and, for the most part, easy to digest. The remaining 20% or so are classed as whey proteins, many of which have important physiological effects (bioactivity). Also easy to digest, but very heat sensitive (6), these include key enzymes (specialized proteins) and enzyme inhibitors, immunoglobulins (antibodies) (10), metal-binding proteins, vitamin-binding proteins, and several growth factors.

Our laboratory received the strain Lactobacillus zeae KCTC 3804, which is known to be present in raw cow's milk (2), from the Korean Collection for Type Cultures (KCTC), and it was grown under standard conditions (lactobacillus MRS broth [Difco 0881], 30°C, and 200 rpm). The genomic DNA was extracted using the alkaline lysis method (3) from the cultured bacteria. We then sequenced the genome of L. zeae KCTC 3804; genome sequencing of this organism had not been completed or initiated when our sequencing project was begun, according to the Genomes OnLine Database (GOLD) (8).

Here we report the genome sequence of L. zeae KCTC 3804, which was obtained using a whole-genome shotgun strategy (5) using Roche 454 GS (FLX Titanium) pyrosequencing (507,651 reads totaling ∼67.9 Mb; ∼26-fold coverage of the genome) at the Genome Resource Center, KRIBB (Korea Research Institute of Bioscience and Biotechnology). Genome sequences from pyrosequencing were processed by Roche's software according to the manufacturer's instructions. All of the reads were assembled using the Newbler assembler 2.3 (454 Life Science), which generated 113 large contigs (>100 bp). The annotation was done by merging the results obtained from the RAST (Rapid Annotation using Subsystem Technology) server (1), the Glimmer 3.02 modeling software package (4), tRNAscan-SE 1.21 (9), and RNAmmer 1.2 (7). In addition, the contigs were searched against the KEGG, UniProt, and Clusters of Orthologous Groups (COG) databases to annotate the gene descriptions. The G+C content (moles percent) was calculated using the genome sequence. The DNA base composition was calculated using Java.

The uncompleted draft genome includes 3,110,326 bases and is comprised of 2,965 predicted coding sequences (CDSs), with a G+C content of 47.8%. There are single predicted copies of the 5S, 16S, and 23S rRNA genes and 57 predicted tRNAs. There are 310 subsystems represented in the genome, and we used this information to reconstruct the metabolic network (determined using the RAST server). There are many carbohydrate subsystem features, including genes involved in metabolism of mono-, di-, and oligosaccharides, central carbohydrate metabolism, B, and fermentation. In particular, the ability to ferment cow's milk is a special feature of this strain.

Nucleotide sequence accession numbers.

The draft genome sequence of Lactobacillus zeae KCTC 3804 is available in GenBank under the accession numbers BACQ01000001 to BACQ101000113.