Draft Genome Sequence of Fusobacterium nucleatum ChDC F128, Isolated from a Periodontitis Lesion

Abstract

Fusobacterium nucleatum is classified into five subspecies. F. nucleatum ChDC F128 was isolated from a periodontitis lesion and proposed as a new subspecies based on the comparison of the nucleotide sequences of the RNA polymerase beta subunit and zinc protease genes. Here, we report the draft genome sequence of the strain.

GENOME ANNOUNCEMENT

Fusobacterium nucleatum is a Gram-negative, nonmotile, obligately anaerobic rod bacterium which is frequently isolated from the oral cavity (3, 4). Fusobacterium nucleatum is classified into 5 subspecies (nucleatum, polymorphum, vincentii, animalis, and fusiforme) based on the polyacrylamide gel electrophoretic pattern of the whole-cell proteins and DNA homology (2) or electrophoretic patterns of glutamate dehydrogenase and 2-oxoglutarate reductase and DNA-DNA hybridization patterns (4). Recently, 4 strains (ChDC F128, ChDC F145, ChDC F174, and ChDC F206) of F. nucleatum were isolated from periodontitis or gingivitis lesions and a 5th strain (ChDC F300) from a healthy site, and a new subspecies was proposed based on the comparison of the nucleotide sequences of the RNA polymerase beta subunit gene (rpoB) and the zinc protease gene (7). We propose ChDC F128 (= KCOM 1249 = KCTC 5108) as the type strain for the new subspecies of F. nucleatum.

In this report, we present the draft genome sequence of F. nucleatum ChDC F128. Draft sequencing was performed by SolGent, Co., Ltd. (Daejeon, Republic of Korea), using the 454 GS-FLX Titanium system (Roche Diagnostics, Basel, Switzerland). Following an initial round of shotgun pyrosequencing, 30 contigs with a size range between 255 and 463,726 bp were assembled using the Newbler Assembler software-gsAssembler version 2.5.3 (454 Life Sciences, Branford, CT), and the percentage of GC content was 26%. Open reading frames were predicted and annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The predicted protein sequences were annotated in Gene Ontology using the basic local alignment search tool (BLAST) (1). Then, the GO classes were grouped into a total of 124 GO-Slim terms using the web tool CateGOrizer (5).

A total of 67.2% (1, 479) of ORFs were annotatable with known proteins. The genome contained 2,200 protein-coding genes, 3 copies of 23S rRNA, 1 copy of 5S rRNA, and 43 tRNA genes.

The draft genome sequence contains several key pathways for amino acids, carbohydrates, lipids, and organic acids. Biosynthetic pathways exist for at least 7 amino acids: aspartate, asparagine, threonine, methionine, glutamate, glutamine, and cysteine (from serine). The amino acid biosynthesis activity is different from the known activity in F. nucleatum strains. For example, F. nucleatum subsp. nucleatum ATCC 25586^T and F. nucleatum subsp. nucleatum ATCC 51190^T can synthesize just 3 amino acids (glutamate, aspartate, and asparagine) and at least 4 amino acids (aspartate, asparagine, glutamate, and glutamine), respectively (6, 8). The draft genome sequence also contains virulence factors, such as hemolysin, zinc metalloprotease, collagenase, serine protease, butyrate fermentation-related genes, 5-nitroimidazole antibiotic resistance proteins, beta-lactamase, macrolide-efflux protein, toxin YoeB, zeta toxin, virulence factor MviN, and TonB and TolC proteins. The genome also contains oxidative stress-response genes, such as glutathione peroxidase and NADH oxidase, but not superoxide dismutase.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number ALVD00000000. The version described in this paper is the first version, ALVD01000000. The Bioproject designation for this project is PRJNA171181.