Mixed peoples, mixed microbes: Human and Helicobacter pylori coevolution in the European-African population of Cape Verde

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Helicobacter pylori (HP) infection is one of the most common bacterial infections in the world, and is known to have been co-evolving with humans since their origins in Africa ~100,000 years ago. Due to this, bacteria from around the world are genetically stratified as their hosts are. HP has a dynamic genome exhibiting intra-host genomic variation as it evolves in response to the selective pressures of the host, which can inclusively lead to the expression of specific types and combinations of virulence factors and ultimately disease. Several studies on within-host evolution showed the pivotal role of recombination in genomic diversification of HP, especially in the presence of infection with multiple strains. These studies have also shown that recombination rates are different among stains. Although these studies have only started to disclose general patterns of microevolution of HP. The aim of this project is to investigate the patterns of HP microevolution in a cohort from Cape Verde, a population that derives mixed ancestry from Europe and West Africa. Due to the random recombination that occurs over the generations since the first admixture event, present day admixed genomes (both host and HP genomes) in Cape Verde consist of mosaics of segments with European and African ancestry that are relatively easily to trace computationally. We can explore this property to characterize the history of recombination of HP and its role in the generation of diversification in HP. The specific aim is to characterize the genomic variation of up to 5 bacterial isolates from each of 80-100 infected Cape Verdeans and to use this data to infer the haplotypic structure of the isolates in terms of the number of blocks of African and European ancestry (so called inference of local ancestry), and to evaluate the role of admixture and recombination in generating bacterial diversity within and among individuals in the general population of Cape Verde.