Complete Genome Sequence of Pluralibacter gergoviae FB2, an N-Acyl Homoserine Lactone-Degrading Strain Isolated from Packed Fish Paste.

Pluralibacter gergoviae FB2, a bacterial strain isolated from packed food, has been found to exhibit quorum-quenching properties. Hence, we report the first, complete genome of P. gergoviae sequenced using the Pacific Biosciences single-molecule, real-time (SMRT) platform.

GENOME ANNOUNCEMENT

Microbial food spoilage has been reported to cause alarming economic losses in the food industry (1). In recent years, various studies have associated the event to quorum sensing (QS), a cell-to-cell communication strategy adapted by a wide range of proteobacteria (2). For instance, QS by means of N-acyl-homoserine lactone (AHLs) has been linked to the formation of biofilms, a known form of chronic contamination on food processing surfaces (3), as well as a number of proteolytic and lipolytic phenotypes (4, 5).

Pluralibacter gergoviae, formerly named as Enterobacter gergoviae, are Gram-negative, facultative anaerobic straight rods of 0.6–1.0 µm × 1.5–2.5 µm in size (6). As the genus name implies, this organism has been isolated from a wide range of sources (7). In this study, P. gergoviae FB2 was isolated from refrigerated packed fish paste, which is popular in East and Southeast Asia. A routine quorum-quenching (QQ) screening assay was performed as previously described (8), which indicated that this strain is able to degrade AHLs.

Genomic DNA of P. gergoviae FB2 was extracted using the MasterPure DNA purification kit (Epicentre, Inc., Madison, WI, USA) prior to sequencing via the Pacific Biosciences single-molecule, real-time (SMRT) sequencer (Pacific Biosciences, Menlo Park, CA, USA) sequencer. Routine quality checking on the DNA sample was performed using the NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA), the Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA), and gel electrophoresis. A SMRTbell library was prepared from sheared genomic DNA according to the 20-kb template library preparation workflow using P5 chemistry. The prepared library was sequenced on two SMRT cells, yielding output data with an average genome coverage of 93.65×. A single circular contig was obtained from de novo assembly of the insert reads performed with the Hierarchical Genome Assembly Process (HGAP) algorithm in the SMRT Portal (version 2.1.1). According to annotation via the NCBI Prokaryotic Genome Annotation Pipeline (PGAAP) (9), the genome size is 5.49 Mb with 59.1% GC content consisting of 4,856 open reading frames (ORFs), 4,692 protein-coding sequences, 22 rRNAs, 84 tRNAs, 1 other rRNA, and 57 pseudogenes.

Analysis of the genomic data via RAST (Rapid Annotation using Subsystem Technology) (10) revealed the presence of a putative AHL hydrolase gene. The sequence is 792 bp in length, encoding 264 amino acids that show 87% similarity to a reported attM gene of Agrobacterium tumefaciens (11). We hope that the finding of an AHL-degrading gene in P. gergoviae FB2 will provide an insight into the role of QQ in interspecies competition in the context of food spoilage.

Nucleotide sequence accession number.

This complete genome project has been deposited in DDBJ/ENA/GenBank under the accession number CP009450. The version described in this paper is the first version.