Integrated ‘omics for accelerated antibiotic discovery for abyssal Actinomycetota

About the Project

Antimicrobial Resistance (AMR) is predicted to cause more than 10 million deaths annually by 2050, making it the greatest threat, globally, to human health. The WHO defined the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) as critical based on their multidrug resistance (MDR) profiles. We urgently require new chemistry. In terms of antibiotics, microbial natural products produced, by the bacterial phyla Actinomycetota, are unsurpassed, and are responsible for 70% of all antibiotics. However, biodiscovery of natural products has historically been of terrestrial origin. In fact, marine environments, due to logistical reasons, have only been investigated for biomedicine since the 1970s, meaning many of these ecosystems are vastly understudied for antibiotics.

Microbes living at the extremes are testing out possibilities and carving out a niche to survive. These microbial pioneers are pushing limits; as a microbiologist the questions are exciting, challenging and represent a fascinating world of discovery. Deep sea ecosystems are some of the most extreme on Earth, yet bacterial species have been evolving to inhabit these extreme environmental niches. Through this project, you will be uncovering the biological and chemical diversity of Actinomycetota isolated from marine sediment. These bacterial pioneers have been trapped in sediment, up to 3000 meters (the abyssal zone) below the Ocean surface for decades, representing an incredible opportunity for assessing their antibiotic potential!

Here, you will investigate the extent the metals they encounter in the deep-sea, such as manganese and copper, affect their genetic composition (biosynthetic and metal genes), their ability to express the products of those genes and how metals effect their microbially-produced chemistry. Linking ecosystem parameters to antibiotic production is a new frontier of biodiscovery, here you will generate multi-‘omics datasets (genomics and metabolomics datasets) to assess the impact metals on microbial metabolism as well as extreme pressure, for the switching on (elicitation) of novel chemistry in the quest to discover new antibiotics from biotechnologically understudied environments. You will assess the ability of your strains to kill clinically relevant bacterial pathogens, such as Pseudomonas aeruginosa and Staphylococcus aureus and characterise the novel metabolites responsible for the observed antibiotic activity.

This exciting work combines leading experts in marine antibiotic biodiscovery, metals biology, microbiology, molecular biology, genomics, transcriptomics and metabolomics across three Universities. This new interdisciplinary training network on multi-‘omics approaches to antibiotic discovery will be highly collaborative with student skills training as the central feature.

Funding

Students who have, or are expecting to attain, at least an upper second-class honours degree (or equivalent) in a relevant subject, are invited to apply. Funding is available for Home (UK) students to cover tuition fees, a tax-free stipend at the UKRI rate (indicative amount in year 1 in 2026-27, £21,805) and research costs, for four years. Applicants normally required to cover International fees will have to cover the difference between the Home and the International tuition fee rates. There is no additional funding available to cover NHS Immigration Health Surcharge (IHS) costs, visa costs, flights etc.

Funding for this studentship is awarded on a competitive basis and is not guaranteed; availability will depend on the outcome of the selection process and subject to final approval by the University.