PT  - JOURNAL ARTICLE
AU  - Mark Achtman
AU  - Zhemin Zhou
TI  - Analysis of the human oral microbiome from modern and historical samples with SPARSE and EToKi
AID  - 10.1101/842542
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 842542
4099  - http://biorxiv.org/content/early/2019/11/15/842542.short
4100  - http://biorxiv.org/content/early/2019/11/15/842542.full
AB  - Elsewhere we have provided details on a program for the probabilistic classification of sequence reads from metagenomes to microbial species (SPARSE) [1]. Similarly, we have also provided details on a stand-alone set of pipelines (EToKi) that are used to perform backend calculations for EnteroBase [2]. We have also provided examples of analyses of genomes reconstructed from metagenomes from ancient skeletons together with genomes from their modern relatives [3], which can also be visualized within EnteroBase. Finally, we have also described GrapeTree [4], a graphic visualizer of genetic distances between large numbers of genomes. Here we combine all of these approaches, and examine the microbial diversity within the human oral microbiome from hundreds of metagenomes of saliva, plaque and dental calculus, from modern as well as from historical samples. 1591 microbial species were detected by these methods, some of which differed dramatically in their frequency by source of the metagenomes. We had anticipated that the oral complexes of Socransky et al. [5] would predominate among such taxa. However, although some of those species did discriminate between different sources, we were unable to confirm the very existence of the oral complexes. As a further example of the functionality of these pipelines, we reconstructed multiple genomes in high coverage of Streptococcus mutans and Streptococcus sobrinus, two species that are associated with dental caries. Both were very rare in historical dental calculus but they were quite common in modern plaque, and even more common in saliva. The reconstructed genomes were compared with modern genomes from RefSeq, providing a detailed overview of the core genomic diversity of these two species.