Ancient British and London Oral Microbiome Study

Identifying factors that shape human microbiome diversity in Industrialized populations is key to understanding chronic disease origins. Microbiomes from Indigenous peoples are commonly used as proxies for non-Industrialized ancestors, but this is problematic, as different human groups have their own unique histories, identities, genetics, and practices. Here, we reconstruct 235 ancient oral microbiomes spanning 8,000 years in Great Britain- including 127 incredibly well provenanced individuals from London (1066-1853) CE- to trace the direct microbial history of an Industrialized population for the first time. Using a novel sampling approach that controls for biases (e.g., oral geography), two distinct oral microbial communities were reconstructed form ancient British people, including one not commonly found today in Industrialized societies. Functional analysis suggests that these communities may reflect past differences in diet, including access to milk and sugar. Within London, oral microbiome composition was also linked to the presence of chronic, inflammatory diseases and the arrival of the Black Death, suggesting that past pandemics may have also shaped human microbiomes in the past. this study reveals unpredicted factors that contribute to Industrialized microbial histories and demonstrates how paleogenomic studies may be used to uncover microbial correlates of modern chronic disease origins.