Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics

Abstract

De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n=238) and Porphyromonas (n=976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa. Significance statementPangenome analyses have been primarily applied to clinically significant species that are abundant and easy to culture, leaving a substantial number of human commensal microbes uninvestigated. De novo assembly of commensal microbial metagenomes is a significant resource for generating metagenome assembled genomes (MAGs) of difficult-to-culture species, which can be used for pangenome analyses. We investigated the ecological niches and geographic localization of multiple species of the human oral commensal genera Tannerella and Porphyromonas using MAGs assembled from globally diverse modern and ancient populations. While much work on these genera comes from Europe and North America, we note distinctions in ecological niches and species prevalence globally, highlighting how MAGs overcome limitations set by culture-based approaches that dominate currently available data. Additionally we demonstrate how improved taxonomic representation of diverse oral species through MAGs can clarify the evolutionary history of commensals and their virulence factors associated with oral disease.