Too rare to see? Investigating microbes overlooked by metagenomics


Microbial communities consist of thousands of species, some abundant but most actually very rare.

Such rare microbes are underrepresented in metagenomic sequencing and therefore little researched. Within the Hildebrand group we love looking at these – largely ignored – microbes, because often they play key roles in health and disease, and because there is still a lot to discover.

In this project, you will have the chance to develop novel protocols that can enrich the pathogen Listeria (causative of listeriosis), relying on 3rd generation (Oxford Nanopore) sequencing and CRISPR-CAS9 systems.

Later we will expand this method to investigate fungi and low abundant bacteria in metagenomes.

During this PhD you will learn about complex molecular biology techniques, metagenomics, bioinformatics, and microbial ecology.

The project is directly related to human health and wellbeing, looking not only at detecting and preventing listeriosis, but also investigating how health-promoting microbes can be inherited in families, and how they evolve and adapt during this process.

The ideal candidate will enjoy science and be very curious about biology, want to develop wetlab protocols and have an interest in strengthening their computational skills (R and Linux).

We will teach different flavours of metagenomic sequencing, and how to analyse and interpret this data using bioinformatics.

Visiting international conferences and training courses as well as a planned 3-month exchange with collaborators are part of student training.

The candidate will be supervised by Dr Hildebrand, Prof Nieduszynski and Dr Gilmour (Quadram and Earlham Institutes) in Norwich. Both Institutes are part of the large, multinational Norwich Research Park, that hosts a vibrant and active research community adjacent to the University of East Anglia.

Norwich is a mid-sized historical, medieval city with a large student community, situated on the Norfolk coast.

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[1] M. Bahram, S. Anslan, F. Hildebrand, P. Bork, and L. Tedersoo, “Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment,” Environ. Microbiol. Rep., vol. 5, Jul. 2018, doi: 10.1111/1758-2229.12684.

[2] C. Frioux, D. Singh, T. Korcsmaros, and F. Hildebrand, “From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes,” Comput. Struct. Biotechnol. J., vol. 18, pp. 1722–1734, 2020, doi: 10.1016/j.csbj.2020.06.028.

[3] L. Tedersoo et al., “Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi,” MycoKeys, vol. 10, pp. 1–43, May 2015, doi: 10.3897/mycokeys.10.4852.

[4] F. Hildebrand et al., “Dispersal strategies shape persistence and evolution of human gut bacteria,” Cell Host Microbe, vol. 29, no. 7, pp. 1167-1176.e9, Jul. 2021, doi: 10.1016/j.chom.2021.05.008.