Draft Genome Sequence of Fusobacterium nucleatum subsp. nucleatum ChDC F316, Isolated from a Human Peri-implantitis Lesion in the Republic of Korea.

Fusobacterium nucleatum is a Gram-negative anaerobe and is one of the causative agents of periodontal diseases, including peri-implantitis. Fusobacterium nucleatum subsp. nucleatum ChDC F316 (KCOM 1322) was isolated from a human peri-implantitis lesion. Here, we report the draft genome sequence of this strain.

GENOME ANNOUNCEMENT

Fusobacterium nucleatum is a Gram-negative anaerobe and is one of the causative agents of periodontal diseases, including peri-implantitis (1–3). F. nucleatum was classified as five subspecies, nucleatum, polymorphum, vincentii, fusiforme, and animalis, based on the polyacrylamide gel electrophoresis pattern of the whole-cell proteins and DNA homology (4), 2-oxoglutarate reductase and glutamate dehydrogenase electrophoretic patterns, and DNA-DNA hybridization patterns (5). F. nucleatum subsp. nucleatum ChDC F316 (KCOM 1322) was isolated from a human peri-implantitis lesion. In this report, we present the draft genome sequence of F. nucleatum ChDC F316.

Draft sequencing was performed by the Macrogen Co., (Seoul, South Korea) using the Illumina Hiseq 2000 system sequencing technology. We constructed 101 paired-end sequencing libraries with insert sizes of about 200 bp and generated 35,690,994 bp of usable sequence. We assembled the reads using SOAPdenovo (http://soap.genomics.org.cn). SOAPdenovo v. 1.05 was run with option K79 and configuration options reverse_seq of 0 (standard mate-pair orientation), asm_flags of 3 (try harder to build large contigs), rank of 1 (reads were used while scaffolding). The reads were assembled into 83 contigs with a size range between 202 and 22,979 bp (total 2,162,122 bp), and the GC content was 26.95%. Open reading frames were predicted and annotated using the Glimmer-3.02 modeling software package (6). The predicted protein sequences were annotated as Gene Ontology (GO) by the basic local alignment search tool (BLAST). Then, the GO classes were grouped into a total of 124 GO-Slim terms using the web tool CateGOrizer (7).

The genome contained 2,077 protein-coding genes, three copies of 5S rRNA and 323 tRNA genes, and several key pathways for amino acids, carbohydrates, lipids, and organic acids. Biosynthetic pathways exist for four amino acids: glutamate, glutamine, aspartate, and asparagine. The strain might biosynthesized at least one more amino acid (glutamine) than the type strain (ATCC 25586) of F. nucleatum subsp. nucleatum (3). The draft genome sequence also contains virulence factors such as butyrate fermentation-related genes, hemolysin, zinc metalloprotease, serine protease, 5-nitroimidazole antibiotic resistance proteins, beta-lactamase, multidrug resistance proteins, multi-antimicrobial extrusion proteins, macrolide-efflux protein, outer membrane porin F, TonB protein, and tolC. The genome also contained oxidative stress-response genes such as glutathione peroxidase, glutaredoxin, NADH oxidase, and rubrerythrin (confers superoxide dismutase-like activity). The genome contained four two-component systems and one unmatched sensor histidine kinase.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number ATKC00000000. The version described in this paper is the first version, ATKC01000000.