Ultra-resolved metagenomics of complex communities

HILDEBRAND_Q22DTP

We are looking for a highly motivated and scientifically minded student, to work in a hybrid wet lab (60%) and bioinformatics (40%) project on cutting edge metagenomics.

In the 4-year PhD project, the candidate will explore fungal and bacterial strains in the human gut, their evolution and persistence using metagenomics. We will be using the latest technologies to develop the experimental protocols as well as bioinformatic methods to unlock ultra-resolution metagenomics and improve species coverage. In the second part of the project, the candidate will analyse microbial transmission chains between human hosts, in a clinical as well as domestic setting.

If you are interested in the molecular biology used in metagenomics, understanding the evolutionary fate of bacteria in the human gut, learning and applying Oxford Nanopore and PacBio sequencing technologies, then this PhD will be right for you. The ideal candidate will enjoy developing wet lab protocols and have a strong interest in acquiring/improving their computational skills (R, python and Linux). The candidate will learn about different flavours of metagenomic sequencing, and how to analyse and interpret this data by using the latest bioinformatics tools. Visiting international conferences and training courses as well as exchanges with international collaborators are part of student training.

The candidate will be supervised by Dr Hildebrand (Quadram Institute), Prof Nieduszynski and Dr Leggett (both Earlham Institute) in Norwich. Both Institutes are part of the large, multinational Norwich Research Park (NRP), that hosts a vibrant and active research community adjacent to the University of East Anglia (UEA). Norwich is a mid-sized historical, medieval city with a large student community, situated at the Norfolk coast.

For further information and to apply, please visit our website: https://quadram.ac.uk/about/student-opportunities/how-to-apply/ or  https://www.falk.science/

References

1. Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P. 2021. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host Microbe 29:1167-1176.e9.

2. Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MT, Gossmann TI, Huerta-Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Aalvink S, Belzer C, Forslund SK, Sunagawa S, Hentschel U, Merten C, Patil KR, Benes V, Bork P. 2019. Antibiotics-induced monodominance of a novel gut bacterial order. Gut 68:1781–1790.

3. Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F. 2021. Metagenomic assessment of the global diversity and distribution of bacteria and fungi. Environ Microbiol 23:316–326.