New Research on Ancient Microbiomes Published

Posted on 13 November 2015

Publication in Scientific Reports reveals community compositions of ancient microbiomes biased by the age of sample.

A team of scientists including several researchers from York's Department of Archaeology and Department of Biology published a groundbreaking paper in Scientific Reports: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

New research on ancient human microbiomes (the genes of all of the microbes that dwell within us) reveals the ​problem of assessing complexity of ​communities by targeted amplification of DNA​. This is because the same regions of DNA, when targeted in different bacteria, is of different length. As time goes by there is an increasing chance that the DNA will be damaged, and the longer fragments are more likely to be damaged than shorter ones as they have more targets. ​The result is that in older samples the pattern of community can appear to change because ​those with the longer targets drop out of the analysis first, and the community from older samples therefore looks simpler. The older the sample the less complex it will look, as longer 16s rRNA target sequences are less likely to survive. Therefore community compositions of ancient microbiomes are biased by the age of sample.

One of the authors of the paper, Christina Warinner, highlights the importance of this study:

"The emerging field of ancient microbiome science is revealing dramatic insights into the fundamental evolutionary relationships between humans, microbes, and chronic disease. A key step in this research is establishing the best methods for accurately reconstructing the state of the ancestral human microbiome using ancient DNA and paleoprotein technologies. Through Next-Generation Sequencing (NGS) analysis of more than a hundred ancient microbiome samples drawn from sites and cultures spanning three continents and more than 4,000 years, this study advances and refines ancient microbiome analytical methods and provides a framework for future ancient microbiome investigations."

This research was part funded through a C2D2 Research Priming Grant.

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

Kirsten A. Ziesemer, Allison E. Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters- Rist, Menno Hoogland, Domingo C. Salazar-García, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. MacDonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis, Corinne Hofman, Christina Warinner. Nature Scientific Reports 2015; DOI: 10.1038/srep16498. Published 13 November 2015.