Mutations, selection and speciation in human microbiomes

Bacterial strains in the human gut microbiome can associate to their host for decades. During this time, mutations accumulate in their genomes that are either adaptive, neutral, or deleterious. 

In this project, we will investigate these mutations - and their evolutionary impact - using metagenomic time series data of dietary interventions, family cohorts, and our own experimental evolution trials in mice. 

The student will explore the evolution and spread of important genes, such as virulence factors and antibiotic resistance, and revisit the current bacterial species definitions in light of multiple species cooperating within a community. 

The project will create a robust basis for modelling evolutionary forces at play in high-performing, natural microecosystems. The project also aligns with the Earlham Institute’s BBSRC-funded strategic programme Decoding Biodiversity, providing access to resources, mentorship, and expertise.

The student will learn about high-resolution metagenomics, advanced sequencing techniques, host-associated bacteria, and applied evolutionary theory.

Knowledge of and/or willingness to advance in metagenomics, population genetics, machine learning, DNA sequencing, and the human gut microbiome will be required. Exposure to statistics and programming languages (either R, python, Perl, C++, or equivalent) is expected, though specialised skills will be taught and developed through mentorship and collaborations.  A research visit with collaborators in France, 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, Dr Wilfried Haerty and Dr Falk Nagies. 

The Hildebrand group uses metagenomics to research the diversity, community interactions, and evolution of microbes in communities, developing bioinformatic solutions to complex microbial questions and is based at both the Earlham Institute and Quadram Institute in Norwich, UK. 

For further information, please visit our website: https://www.falk.science/.

Norwich is home to vibrant research and student communities, with plenty of history, pubs and cafes, and access to the Norfolk coast.

Further Reading:

• Hildebrand, et al. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host Microbe (2021).
• Benoit, et al. Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs. biRxiv (2023).
• Özkurt, et al. LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis. Microbiome (2022).
• 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).

Further Information:

Application deadline: Monday 20 November 2023 (23:59 i.e.,midnight).

Shortlisted applicants will be interviewed on 23, 24 or 25 January 2024.

Visit the NRPDTP website for further information on eligibility and how to apply.

Our partners value diverse and inclusive work environments that are positive and supportive. Students are selected for admission without regard to gender, marital or civil partnership status, disability, race, nationality, ethnic origin, religion or belief, sexual orientation, age or social background.

This project is awarded with a 4-year Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP) PhD studentship.

The studentship includes payment of tuition fees (directly to the University), a stipend to cover living expenses (2023/4 stipend rate: £18,622), and a Research Training Support Grant of £5,000pa for each year of the studentship.

Entry requirements:
At least UK equivalence Bachelors (Honours) 2:1 or UK equivalence Master's degree. English Language requirement (Faculty of Science equivalent: IELTS 6.5 overall, 6 in each category).