PHD Project

October 4, 2022

The effect of environmental metals on the spread of antimicrobial resistance genes in the stickleback skin microbiome


Antimicrobial resistance (AMR) is a major threat to humans, animals, and our environment. Often associated with overuse of antibiotics in human and livestock dominated environments, its wider environmental occurrence is poorly understood. Emerging evidence suggests that AMR genes (ARGs) are frequently identified in commensal organisms, such as members of host-associated and environmental microbiomes. To effectively combat AMR, we need to understand how environmental variation encourages the spread of ARGs between bacteria (i.e., horizontal gene transfer (HGT)). It has shown that resistance to metals (e.g., copper, zinc, lead etc.) and AMR are often co-selected for in bacterial genomes, and that they directly correlate with environmental metal levels (Pal C et al 2017 Adv Micro Physio).

Three-spined stickleback are a well-studied model organism native to fresh and oceanic northern waters. While a variety of environmental factors have been associated with the composition of their gut microbiome (Rennison et al 2019 Proc Royal Soc B), the skin microbiome remains under-explored. The skin of fish, a mucus membrane in direct contact with the environment, is an important mechanism in infection prevention (Reverter et al 2018 Fish Sahul).

This project asks whether environmental variation in metal concentrations on the island of North Uist, Scotland leads to increased presence, abundance, and spread (via HGT) of ARGs in stickleback skin microbiomes. To answer this question, we will:

  • sequence the skin microbiome (and water to determine background bacterial contamination (Krotman et al. 2020 Microbiome)) of stickleback populations, controlling for genotype/environmental differences
  • culture the microbiome and determine AMR bacteria
  • in the Nottingham aquariums, colonize gnotobiotic (i.e., germ-free) fish with a skin microbiome from low- vs. high-metal environments; longitudinally sample the skin microbiome to identify new HGT events

Applicants should have an interest in ecology, microbiology, and bioinformatics. They should hold a minimum of a UK Honours degree at 2.1 or equivalent in a biological or environmental subject. Candidates with additional (e.g., Masters) qualifications will be looked on favourably. Bioinformatic or computational experience would be an asset but not a requirement. A driving licence, experience of remote fieldwork and SCUBA/snorkelling would be valuable.

Further reading:

Magalhaes IS et al. The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland. 2016. Mol Ecol. 25(17), 4319-36.

Krotman Y et al. Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system. 2020 Microbiome 8(9).

Whelan FJ et al. Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota. 2020 Nat Microbiol 5(2), 379-90.

Milligan-Myhre K et al. Innate immune responses to gut microbiota differ between oceanic and freshwater threespine stickleback populations. 2016 Dis Model Mech 9(2), 187-98.

For further details please contact Fiona Whelan,