Bacterial DNA Not Found in Neanderthal Whole Genome Shotgun Sequencing Reads in a Preliminary Study

Abstract

The field of ancient hominids and ancient DNA research has primarily focused on studying the subject matter, hominids, in detail. Less focus has been put on investigating the microbiome of these hominids. Theoretically, such microbial DNA should persist together with the hominid DNA in the environment if the skeleton is well-preserved. It is with this notion that I undertook a preliminary study to investigate if Helicobacter pylori, Escherichia coli, and Bacillus subtilis DNA could be found in Neanderthal whole genome shotgun sequencing reads. Alignment of the sequenced reads to the genes of the different bacterial species in an in-house MATLAB software reveals no bacterial genes is amidst the Neanderthal sequenced reads in a 40000 reads dataset. The results reported here are preliminary, but it suggests that it may be difficult to profile for microbial DNA in ancient DNA samples as the shorter length of the microbial genome (millions of base pair) compared to the billions of base pair in the ancient hominid genome is vulnerable to larger extent of hydrolysis and degradation.

Keywords: ancient DNA, Neanderthal, alignment of genes, hydrolysis and degradation, bacterial DNA