Dr Hugh Cross1, Mrs. Meriam van Os, Dr. Gert-Jan Jeunen, Mrs. Olga Kardailsky, Dr. Catherine Collins, Professor Hallie Buckley, Professor Lisa Matisso-Smith, Dr. Michael Knapp
1University Of Otago, Dunedin, New Zealand
The human microbiome contains a great wealth of biodiversity. Advances in next-generation sequencing over the last decade have led to a greater understanding of the ecosystem within us. We used ancient DNA samples to add a dimension of time to metagenomic studies and provide a window into past microbial environments. From human burials ranging in age from a few hundred to three thousand years, DNA was extracted and shotgun sequenced using Illumina short-read technology. After filtering out the human DNA component, sequence reads were assembled into longer contigs, annotated, and binned according to the closest taxonomic group. The biggest challenge was to separate the truly ancient microbes from subsequent contamination to the grave sites. We used several methods to verify the ancient DNA community, including sequence damage, read length decay distribution, and comparisons to taxonomic communities of modern microbiome studies. We utilised phylogenetic placement and other tree-based methods to more accurately place each contig within its taxonomic group. The combination of methods was able to verify much of the read data as ancient and, though significant challenges remain, some insight into these past microbial communities and their hosts were obtained. We present our conclusions on how these microenvironments compare across time and space and provide recommendations for future research.
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