Persistence and decay of the intestinal microbial flora’s DNA in frozen bodies from the Alps

The study of the DNA of ancient microorganisms in human remains represents one of the newest and most promising branches of molecular archaeoanthropology. Despite the growing number of papers addressing this subject, however, the analysis of ancient bacterial DNA is still a contentious issue. The indigenous microbiota of the gastrointestinal tract of man represents a community characterized by relative constancy in species composition and proportion. As a model system, we studied the preservation of the intestinal microbiota DNA in two naturally freeze-dried human mummies found on the Alps. This kind of mummy is an ideal subject for ancient DNA investigations. The first is a male body historically dated 1918 A.D. while the second is the famous Tyrolean Iceman (3.350-3.100 B.C.). The screening of bacterial 16S rRNA gene libraries from colon samples of the two mummies (49 clones for the 1918 mummy, 119 clones for the Iceman) showed that the characteristic composition of the intestinal microbiota of man (Alpha-, Beta-, Gammaproteobacteria, Bacteroides, Clostridia) is still kept in the library from the recent mummy while the Iceman's library is almost entirely composed by the DNA of clostridia. Comparison of the intestinal data with those from the literature describing the screening of 16S rRNA gene libraries from other parts of the Iceman's body and from permafrost specimens indicates that the changes in library composition may partly be attributed to the proliferation of clostridia inside the corpses, as described in forensic literature, and partly to the differential persistence of the DNA of gram-negative bacteria and endospore-former low-GC gram-positive bacteria. The present results contribute to the issue of the authentication of claims of pathogen DNA identification in archaeological human remains.