Double- v. single-stranded Neanderthal and Chalcolithic oral microbiomes
DNA library construction methods can strongly affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few systematic studies have examined how library protocols shape ancient microbial community reconstruction. In our study, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from twelve Neanderthals and two Chalcolithic humans sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication, and taxonomic profiles across multiple normalization strategies to assess protocol-specific biases. All newly sequenced data for this project can be found here, while previously published data included in this study can be found under the project PRJEB34569.
DNA library construction methods can strongly affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few systematic studies have examined how library protocols shape ancient microbial community reconstruction. In our study, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from twelve Neanderthals and two Chalcolithic humans sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication, and taxonomic profiles across multiple normalization strategies to assess protocol-specific biases. All newly sequenced data for this project can be found here, while previously published data included in this study can be found under the project PRJEB34569.
Max Planck Institute for Evolutionary Anthropology