Draft Genome Sequence of Lactobacillus brevis Strain EW, a Drosophila Gut Pathobiont.

Lactobacillus brevis strain EW, a gut pathobiont, was isolated from the fruit fly Drosophila melanogaster. Here, we report the draft genome sequence of L. brevis EW.

GENOME ANNOUNCEMENT

Lactobacillus brevis is a Gram-positive rod-shaped species of lactic acid-producing bacteria. Many strains of L. brevis, such as ATCC 367 (1), KB290 (2), and L. brevis subsp. gravesensis ATCC 27305, have been shown to exert a probiotic effect in humans and animals. L. brevis strain EW was originally isolated from the gut epithelia of Drosophila melanogaster (3). Although the presence of lactobacilli is generally considered to be beneficial to the host, L. brevis EW acts as a pathobiont (i.e., a resident gut bacterium that is generally benign within a normal community structure but is pathogenic under certain deregulated conditions) in the Drosophila gut (4). A recent study showed that germfree Drosophila monoassociated with L. brevis EW exhibited severe gut cell apoptosis and early host death (4). The L. brevis EW-induced host pathology is a result of the chronic activation of a reactive oxygen species-producing enzyme, dual oxidase (DUOX). Since bacterium-derived uracil acts as a ligand for DUOX activation in Drosophila gut immunity (4), it has been hypothesized that L. brevis EW releases uracil in a constitutive manner, which in turn induces chronic DUOX-dependent reactive oxygen species (ROS) generation in the gut. However, it is unclear as to why L. brevis EW secretes uracil, as certain other lactobacilli do not. In the current study, the genomic information for L. brevis EW is presented, which is essential for elucidating the mechanism by which L. brevis EW provokes gut-microbe dysbiosis through chronic DUOX activation.

The genome sequence of L. brevis EW was determined using a 3-kb paired-end library (175,405 reads, ~10.92-fold coverage) with the Genome Sequencer FLX system (Roche Diagnostics, Branford, CT) and a 100-bp paired-end library (6,924,211 reads, ~362.4-fold coverage) with the Illumina HiSeq 2000 (Illumina, San Diego, CA). The 38 contigs were generated using the CLC Genomics Workbench 5.1 (CLC bio, Denmark). The functional annotation of the predicted genes was performed using the RAST server (5) and the COG database (6). The draft genome sequence is 2,885,101 bp in length and contains 2,892 open reading frames (ORFs). Eleven rRNA genes and 68 tRNA genes were also identified. The G+C content of the genome is 45.26 mol%. Using comparative genomics for the various L. brevis strains with different characteristics, i.e., regarding their roles as symbionts or pathobionts within the Drosophila gut, it is now feasible to dissect the molecular principles governing gut-microbe symbiosis and pathogenesis.

Nucleotide sequence accession numbers.

The result of this whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AUTD00000000. The version described in this paper is the first version, AUTD01000000.