PHD Studentship: Adaptation and community dynamics of the human oral microbiome over centuries of evolution

The human microbiome is composed of two categories of microbes: commensals (beneficial to the host) and pathogens (detrimental to host health). While we know quite a lot about modern microbiomes in terms of what bacteria live there, how they enter the body and how the specific body site select for certain bacteria, little is known about the historical evolution of the human microbiome. How have commensals and pathogens interacted over the past thousand years in and on our bodies? What bacteria rely on what other bacteria for survival and has this changed over time?

Understanding three core aspects of the human microbiome (evolution, adaptation and interconnectedness) would better allow us to examine the effect of diet and human health on our resident microbes and in turn understand how shaping the microbial community in our bodies could better benefit our health.

This project aims to address these questions, focussing on the human oral cavity microbiome. Using dental calculus microbiome whole genome data collected over 5000 years from Yorkshire archaeological skeletons, we will reconstruct the evolution of the human oral microbiome in Northern England and examine the influence of diet, antibiotic exposure and urbanisation on this community. Next, by combining this dataset with modern global samples, we can extensively explore the human oral microbiome community ecology, including genetic exchange and metabolic handovers. This will allow us to investigate whether modern microbiomes interact and respond to change better than historical counterparts.