Helicobacter pylori in ancient human remains

Abstract

The bacterium Helicobacter pylori (H. pylori) infects the stomachs of approximately 50% of all humans. With its universal occurrence, high infectivity and virulence properties it is considered as one of the most severe global burdens of modern humankind. It has accompanied humans for many thousands of years, and due to its high genetic variability and vertical transmission, its population genetics reflects the history of human migrations. However, especially complex demographic events such as the colonisation of Europe cannot be resolved with population genetic analysis of modern H. pylori strains alone. This is best exemplified with the reconstruction of the 5300-year-old H. pylori genome of the Iceman, a European Copper Age mummy. Our analysis provided precious insights into the ancestry and evolution of the pathogen and underlined the high complexity of ancient European population history. In this review we will provide an overview on the molecular analysis of H. pylori in mummified human remains that were done so far and we will outline methodological advancements in the field of ancient DNA research that support the reconstruction and authentication of ancient H. pylori genome sequences.

Keywords: Helicobacter pylori; Ancient DNA; Ancient gut contents; Coprolites; Evolution; Iceman.

Figure 1

Molecular workflow applied to the Iceman intestinal content samples. Both “untargeted” shotgun metagenomic next generation sequencing and “targeted” capture-enrichment have been used to identify endogenous Helicobacter pylori DNA and to reconstruct the ancient pathogen genome.

Figure 2

Ancient DNA characteristics used for authenticating endogenous sequences. Visualised with Helicobacter pylori (H. pylori) sequences enriched from the gut of the Iceman and aligned to the H. pylori 26695 reference genome[20]: A: Read length distribution. B: C to T substitutions towards the 5’ end of sequence reads (Enriched H. pylori reads, metagenomic H. pylori reads, human Iceman genomic reads). C: Mean genome coverage and distribution of the aligned sequences. H. pylori: Helicobacter pylori.

Figure 3

Population assignment of the ancient Helicobacter pylori strain using multilocus sequence typing. A: Comparison of the Iceman strain to a collection of strains representing the worldwide Helicobacter pylori (H. pylori) populations. The proportion of the Iceman strain is displayed on the right. B: Comparison of the Iceman strain to the H. pylori populations hpNEAfrica, hpEurope, hpAsia2. C: STRUCTURE linkage model analysis showing the proportion of Ancestral Europe (AE) 1 (from Central Asia) and AE2 (from northeast Africa).

Figure 4

Helicobacter pylori core genome tree based on 1121 core genes with 375 publicly available Helicobacter pylori genomes from Europe, Asia and Africa including the Iceman (in bold). The core genome analysis was performed using the Roary pan-genome analysis tool[44] followed by phylogenomic analysis using the PhyML tool v 3.1[45].