The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity

Abstract

Strain NI1060 is an oral bacterium responsible for periodontitis in a murine ligature-induced disease model. To better understand its pathogenicity, we have determined the complete sequence of its 2,553,982 bp genome. Although closely related to Pasteurella pneumotropica, a pneumonia-associated rodent commensal based on its 16S rRNA, the NI1060 genomic content suggests that they are different species thriving on different energy sources via alternative metabolic pathways. Genomic and phylogenetic analyses showed that strain NI1060 is distinct from the genera currently described in the family Pasteurellaceae, and is likely to represent a novel species. In addition, we found putative virulence genes involved in lipooligosaccharide synthesis, adhesins and bacteriotoxic proteins. These genes are potentially important for host adaption and for the induction of dysbiosis through bacterial competition and pathogenicity. Importantly, strain NI1060 strongly stimulates Nod1, an innate immune receptor, but is defective in two peptidoglycan recycling genes due to a frameshift mutation. The in-depth analysis of its genome thus provides critical insights for the development of NI1060 as a prime model system for infectious disease.

Fig 1. Phylogenetic placement.

Phylogenetic placement of NI1060 using the 16S gene (A) and a set of 400 most conserved bacterial genes using Phylophlan (B). The scale indicates the number of nucleotide or amino acid substitutions per site. Both methods show that NI1060 is closest to P. pneumotropica ATCC 35149 but with a branch length suggesting that NI1060 represents a novel species.

Fig 2. Comparative analysis between NI1060 and P. pneumotropica ATCC 35149.

The putative protein-coding genes on forward (outside) and reverse (middle) strands are show by blue bars. Red bars represent tRNA and purple bars represent rRNA. The protein-coding genes, which are conserved in the related bacterium P. pneumotropica ATCC 35149, are indicated by green bars.