Analysis of the bacterial communities in ancient human bones and burial soil samples: Tracing the impact of environmental bacteria

Publication date: September 2019

Source: Journal of Archaeological Science, Volume 109

Author(s): Alisa Kazarina, Guntis Gerhards, Elina Petersone-Gordina, Janis Kimsis, Ilva Pole, Egija Zole, Viktorija Leonova, Renate Ranka


In our attempts to reveal the hidden fragments of the history of the natural world, ancient DNA (aDNA) is the precious missing key that allows us to discover hidden truths about ourselves and the world around us. Not only does aDNA encrypt genetic data from a particular individual, it also carries information about the microbial communities that were present in the individual. However, the process of such data mining has many intrinsic challenges. One of the main challenges in aDNA research is the contamination of archaeological material with environmental bacteria from the surrounding soil and postmortem microbial sources.

The goal of this study was to identify the microbial communities in human archaeological bone samples dated 15th – 17th century AD and to compare the microbiome patterns with the corresponding soil samples of the burial environment. Samples were analysed by 16S rRNA-based profiling of bacterial communities using Ion Torrent technology. The results showed that the most represented phyla in the bone samples were Firmicutes followed by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Nitrospirae, Planctomycetes, Gemmatimonadetes and Bacteroidetes.

All identified microbial taxa of the bone samples coincided with the corresponding soil samples, indicating significant infiltration and contamination of archaeological remains with microbial species of the burial environment. However, differences in microbial community composition between the bone and soil samples were observed at both the phylum and genus levels, as indicated by statistically significant beta-diversity analysis results. A deeper investigation of the Firmicutes phylum showed significant differences between the bone and soil samples by alpha- and beta-diversity analyses. Several genera belonging to Firmicutes were significantly more abundant in the soil samples than in the bone samples and vice versa.

In conclusion, the analysis of the microbiome profiles of archaeological bone and corresponding soil samples revealed significant diversity in microbial compositions. It appeared that some bacteria may infiltrate the bone matter through the process of tissue decomposition and remain trapped inside for a longer period of time. Archaeological human bone samples might provide significant data on the investigation of ancient human microbiomes; however, environmental bacteria from the surrounding soil must be considered an important contamination factor.