Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

Abstract

Background: Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. Results: Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species. Furthermore, in silico analyses allowed the reconstruction of the genome sequences of five ancient bacterial genomes, including apparent pathogenic ancestor strains of Clostridium perfringens and Pseudomonas veronii species present in the gut of the Tyrolean Iceman. Conclusions: Genomic analyses of the reconstructed C. perfringens chromosome clearly support the occurrence of a pathogenic profile consisting of virulence genes already existing in the ancient strain, thereby reinforcing the notion of a very early speciation of this taxon towards a pathogenic phenotype. In contrast, the evolutionary development of P. veronii appears to be characterized by the acquisition of antibiotic resistance genes in more recent times as well as an evolution towards an ecological niche outside of the (human) gastrointestinal tract.

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

“…A recently applied approach to infer the gut microbiota composition at high resolution down to the strain level without performing any isolation and cultivation of bacterial strains involves the reconstruction of a genome sequence of an individual microbiota member from shotgun metagenomic data (52). Such an NGS approach not only provides taxonomic information about strain identity but also provides very useful data related to the genetic makeup of the organism, thereby providing metabolic and evolutionary insights (52).…”

Multi-proxy analyses of a mid-15th century ‘Middle Iron Age’ Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

“…To gain insight into the taxonomic and functional (metabolic) differences between the BRS IM ( n = 4) and other ancient and modern (including ‘traditional’) IMs, we compared BRS with data derived from the shotgun metagenome sequencing of Malawian agro-pastoralists ( 51 ) (MG-RAST http://metagenomics.anl.gov/ accession number ‘qiime:621’), Tanzanian Hadza hunter-gatherers ( 26 ) (NCBI SRA SRP056480 Bioproject ID PRJNA278393), contemporary Italians ( 26 ) and the Copper Age (dated to c . 3,250 BC) Alpine (Tyrolean) Iceman (Ötzi) ( 109 ) (European Nucleotide Archive accession number ERP012908). For comparison, four metagenome samples (comprising two males and two females) were randomly selected from each of the comparative cohorts ( n = 12).…”

Egyptian Canopic Jars at the Crossroad of Medicine and Archaeology: Overview of 100 Years of Research and Future Scientific Expectations

“…On a different track, focusing on the microbiome, various studies were successful in reconstructing microbial communities in South American Mummies [72,73]; much more well-known is Ötzi's (i.e., the Tyrolean Ice Man) gut microbiome retrieved from colon and stomach content and whole-genome reconstruction of Helicobacter pylori [74,75]. All of these studies prove that genetic-derived disease, pathogen presence and microbiomes can be inferred from mummified soft tissues -including canopic jars, when DNA preservation is sufficient.…”