UCLA

Taxonomic studies using rRNA and protein coding genes as molecular markers have been used to study the heterogeneity of Fusobacterium nucleatum. Efforts have been made to determine differences between fusobacterial strains and prevalence of subspecies in sites of health or disease, but a conclusive correlation between the different subspecies and virulence factors still has not been found. Previously used molecular markers have been internal, cytoplasmic markers. However, when looking at strains and subspecies involved in disease, it is important to look at virulence factors, which are often external markers. In this study, we chose the major outer membrane protein FomA of Fusobacterium nucleatum as a phylogenetic molecular marker because of its suggested role in virulence. To determine the fomA gene's utility as a phylogenetic molecular marker, the fomA gene was amplified in 24 strains of Fusobacterium. The corresponding nucleotide sequences and deduced FomA amino acid sequences were used to create alignments and phylogenetic trees for analysis of Fusobacterium subspecies. It was found that the resulting clade distribution does not follow the subspecies clade distribution determined previously by using internal molecular markers such as 16S rRNA and gyrB. The variability from the FomA surface-exposed loops within and between subspecies is responsible for the clade distribution of the strains, and there is no correlation between clade distribution and body site of strain isolation. It is suggested that variable regions could account for the specificity of binding to other species and targets that F. nucleatum experiences, and its affect on virulence, and the functions of each strain may be dictated by the composition of the FomA surface exposed loops, versus the actual subspecies. Therefore, FomA may not be a relevant phylogenetic molecular marker for F. nucleatum subspecies classification, but it may be reflective of functional relationships in strains of F. nucleatum.