Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus Philosophical Transactions of the Royal Society B Mark Achtman and Zhemin Zhou

% % bacteria % bacteria A 5 B C D Counts x 10 in modern plaque in ancient calculus in modern saliva A comparison of species Figure S5. 0.0 1.2 2.5 3.8 5.0 0 4 8 12 0 4 8 12 0 4 8 12 abundances between classical checker- board DNA-DNA hybridization and naeslundii 2 A. oris SPARSE. (A) Mean estimated cell counts by Prevotella nigrescens Prevotella intermedia DNA-DNA hybridization of 40 species in Veillonella parvula 20,247 samples from 776 individuals Tannerella forsythia Prevotella melaninogenica (periodontal disease: 592; healthy: 184). Capnocytophaga gingivalis Modified from figure 7 in Socransky and Porphyromonas gingivalis Actinomyces naeslundii 1 Haffajee, 2005 [28] to include subsequent Fusobacterium nucleatum ss nucleatum taxonomic name changes at the right. (B-D) Fusobacterium nucleatum ss vincentii Average percentage of bacterial species in Campylobacter gracilis metagenomic samples according to Neisseria mucosa SPARSE in modern dental plaque (B, 307 Campylobacter rectus metagenomes), ancient dental calculus (C, Fusobacterium nucleatum ss polymorphum 110) and modern saliva (D, 387). The 40 Peptostreptococcus micros Parvimonas micra Fusobacterium periodonticum species at the top correspond to those in Capnocytophaga sputigena part A. Sixteen other species accounted for Leptotrichia buccalis at least 1% of bacterial reads, and are Eubacterium nodatum Treponema denticola shown at the bottom. Five of those species Eikenella corrodens were first defined after 1998, and are Selenomonas noxia Campylobacter showae indicated by ‘Novel’ at the left. Actinomyces odontolyticus Capnocytophaga ochracea Eubacterium saburreum Lachnoanaerobaculum saburreum Gemella morbillorum Streptococcus sanguis Streptococcus sanguinis Aggregatibacter actinomycetemcomitans Streptococcus oralis Streptococcus gordonii Streptococcus mitis Propionibacterium acnes Streptococcus anginosus Treponema socranskii Streptococcus intermedius Streptococcus constellatus matruchotii Actinomyces sp. oral taxon 448 Novel Actinomyces dentalis Actinobaculum sp. oral taxon 183 Haemophilus parainfluenzae Rothia sp. HMSC08A08 Novel Lautropia mirabilis Neisseria elongata Novel Streptococcus cristatus Neisseria lactamica Rothia dentocariosa Actinomyces sp. oral taxon 877 Tannerella sp. oral taxon HOT-286 Novel Propionibacterium acidifaciens Porphyromonas sp. oral taxon 279 Novel Capnocytophaga leadbetteri