Ancient metagenomes

Metagenomic analyses of ancient specimens tell us much about the social history, as well as the evolutionary paths, of present-day organisms. Although many bioarcheological studies have targeted specific organisms using PCR-based amplification followed by sequencing of specific genes or regions of the genome, the direct sequencing approach to metagenomes allows investigators to detect organisms that they would not have predicted were in the sample.

It is very difficult to identify organisms in fossilized or mummified archeological specimens, and the DNA contained within them is often fragmented. But massively parallel sequencing methods are well suited for short, denatured DNA fragments, and sequencing many-fold can improve coverage, and therefore the confidence in identifying each nucleotide base. The tools and methods of metagenomics have therefore seen wide application in bioarcheology. 

A case in point is a medieval skeleton recovered from Geridu, close to Sardinia in Italy, which contained calcified nodules, a common feature of tuberculosis arising from infections by Mycobacterium tuberculosis. Part of the skeleton and the calcified nodules are shown in Figure A(i). The investigators used whole-genome sequencing to analyze DNA recovered from one of the nodules and assembled the genome of a Brucella strain, in addition to the fourteenth-century human DNA. Brucella is a less common cause of infected nodules, and very little is known about the epidemiology of this infectious agent before modern times.

After omitting single-nucleotide polymorphisms (SNPs) likely due to the types of DNA damage common in ancient specimens and those for which sequence coverage was insufficient, the investigators compared the medieval sequence to that of modern Brucella strains from Italy; this produced the tree shown in Figure A(ii). As can be seen in the tree, the ancient Geridu strain shares a common ancestor with the progenitor of modern-day strains from Italy. The Italian strains fall within a specific western Mediterranean phylogenetic cluster that is distinct from other Brucella strains, so the fact that the ancient genome clusters with them suggests that this western Mediterranean lineage is a long-standing one.

(i)

(ii)

Figure A: An example of analysis of an ancient metagenome. (i) Part of the skeleton dating from the fourteenth century, found in Geridu, Italy, with calcified nodules shown in the image on the right. (ii) Phylogenetic tree created with genomic data, showing the relationship between the Geridu Brucella strain and other known strains. Each strain has a letter and/or number code designation.