Bacterial evolution in gut microbiomes

Bacterial strains in the human gut microbiome can live for decades in association to us. During this time their genomes mutate, we assume that this happens partly to adapt to our own lifestyles.

In this project, we will investigate such mutations and their evolutionary impact, using metagenomic time series data of dietary interventions, family cohorts and experimental evolution trials in mice, created in the hosting research groups. The project will investigate the evolution and spread of important genes (such as virulence factors, antibiotic resistance etc), and revisit the current bacterial species definitions in light of multiple species cooperating within a community. The project aims at creating the robust basis for modelling evolutionary forces at play in high-performing, natural microecosystems.

During the PhD, the student will learn about high-resolution metagenomics, advanced sequencing techniques, host-associated bacteria and applying evolutionary theory. Exposure to statistics and programming languages (either R, python, Perl, Rust, C++, or equivalent) is expected, specialized skills will be taught and developed through mentorship and collaborations. During this 4-year DTP programme, a research visit with collaborators in France, visiting international conferences and training courses and a 3-month industrial placement are planned as part of a broad and interdisciplinary education.

The project will be supervised by Dr Falk Hildebrand, Dr Christopher Quince, and Dr Anthony Duncan and is located at the Earlham/Quadram Institute in the Norwich Research Park, UK. The Hildebrand group uses metagenomics to research the diversity, community interactions, and evolution of microbes in communities, developing bioinformatic solutions to complex microbial questions. Norwich hosts a vibrant and active research community, large student community and multiple startups. It is a mid-sized historical, medieval city with an active pub and coffee scene, situated at the Norfolk coast.

For further information and to apply, please visit: https://www.falk.science/.

References

Frioux, et al. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host & Microbe (2023).

Belcour, Frioux, et al. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. eLife 9, (2020).

Lee, K. et al. Population-level impacts of antibiotic usage on the human gut microbiome. Nat Commun 14, 1191 (2023).

Benoit, G. et al. High-quality metagenome assembly from long accurate reads with metaMDBG. Nat Biotechnol 1–6 (2024) doi:10.1038/s41587-023-01983-6.

Sidorczuk, K. et al. adhesiomeR: a tool for Escherichia coli adhesin classification and analysis. BMC Genomics 25, 609 (2024).