Genome Sequence of Fusobacterium nucleatum Subspecies Polymorphum — a Genetically Tractable Fusobacterium

Abstract

Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique to F. nucleatum subsp. polymorphum ATCC 10953 were identified. A large percentage of these mapped within one of 28 regions or islands containing five or more genes. Seventeen percent of the clustered proteins that demonstrated similarity were most similar to proteins from the clostridia, with others being most similar to proteins from other gram-positive organisms such as Bacillus and Streptococcus. A ten kilobase region homologous to the Salmonella typhimurium propanediol utilization locus was identified, as was a prophage and integrated conjugal plasmid. The genome contains five composite ribozyme/transposons, similar to the CdISt IStrons described in Clostridium difficile. IStrons are not present in the other fusobacterial genomes. These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common.

Fap2 of Fusobacterium nucleatum Is a Galactose-Inhibitable Adhesin Involved in Coaggregation, Cell Adhesion, and Preterm Birth

“…vincentii, and F. nucleatum subsp. polymorphum (56,61,62) have opened new avenues of research. However, though site-directed mutagenesis (40,60,65) and complementation assays (36) have been performed with this bacterium, research has been hindered by the lack of genetic systems to induce random insertion mutagenesis.…”

“…Though two shuttle vectors have been developed for fusobacteria (58-60) and several strains have been sequenced and annotated (56,61,62), research on this bacterium has been hindered by the lack of genetic systems to induce random mutations.…”

Application of rpoB and Zinc Protease Gene for Use in Molecular Discrimination of Fusobacterium nucleatum Subspecies

“…polymorphum) of F. nucleatum were sequenced completely or incompletely and compared to the data for F. nucleatum subsp. polymorphum (17)(18)(19). According to the analysis, 919 genes account for the differences between the three strains.…”

Maternal oral origin of Fusobacterium nucleatum in adverse pregnancy outcomes as determined using the 16S–23S rRNA gene intergenic transcribed spacer region

“…nucleatum was identified by the three libraries, as the genome sequence is available for this strain (Kapatral et al, 2002), although this was not the case with subsp. polymorphum whose genome has also been characterized (Karpathy et al, 2007). Certainly, bacterial genome data will become accessible exponentially as a result of the developing genome projects and emerging next-generation sequencing; however, as part of these advances, more precise and simplified techniques are also necessary to evaluate the strains of F. nucleatum in a greater number of samples, such as in clinical trials.…”