Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome

SIMPLE SUMMARY: Paleogenomic research has enhanced our understanding of past human populations and migrations. Moreover, ancient DNA can also provide information on the interactions between humans and their associated pathogens. Periodontitis, currently suffered by millions of people worldwide, is a gum infection that is caused by pathogenic oral bacteria, widely referred to as the “red complex”, which can lead to tooth loss and has been linked to an increased risk of oesophageal cancer. In this study we combine human population genetics with genomic analysis of the oral microbiome of 18th-century people from the Kazakh Khanate in Kazakhstan to gain insight into their health status and explore bacterial coadaptation to recent dietary changes. ABSTRACT: The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.