Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities

We develop, test, and apply a hybridisation enrichment technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We first simulated enriched data sets, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enriched approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Comparing 16S rRNA amplification to unenriched methods also suggest that targeted enrichment using hybridization capture is less prone to the effects of background contamination, yielding a higher percentage of on-target recovery.