Antibiotics from the Abyss - Establishing the Bristol Sponge Microbiome Collection as an Antibiotic Discovery Pipeline

Student thesis: Doctoral ThesisDoctor of Philosophy (PhD)


Antibiotic resistance is one of the gravest threats that humanity faces today. Discovering new classes of antibiotics effective against resistant infections is vital. Most of the antibiotics currently used in the clinic were discovered as the natural products of microorganisms, and returning to these sources could provide the next generation of drugs. The main obstacle to this goal is the rediscovery of known compounds from nature, but underexplored environments may host undiscovered species that produce new bioactive compounds. This thesis describes how we established the Bristol Sponge Microbiome Collection (BISECT) - a collection of deep-sea sponges from a region never studied before - as a platform for antibiotic discovery. We adopted an iterative design approach, drawing lessons from our previous work to improve each step of the pipeline, from sponge processing to antibiotic purification. In the first iteration, we identified five sponge bacteria with apparent antibacterial activity. On further examination, we showed that they were false positives, although one of the strains is the new species Psychrobacter noctis. For the second iteration, we improved our bacterial isolation and antibacterial screening procedures and identified our first two strains with reproducible activity. Micromonospora ferruginea sp. nov. produces the cytotoxic compound kosinostatin, and we better defined its proposed biosynthetic pathway and antibacterial activity. Bacillus nautilus sp. nov. likely produces a cyclic lipopeptide related to surfactin, although we haven’t yet isolated the compound. These strains validated our approach and confirmed that BISECT is a source of new species that can produce antibiotics. For the third iteration, we explored ways to activate the silent biosynthetic gene clusters of our BISECT bacteria in the hope of discovering new antibiotics. We altered the culture conditions of our strains using ‘One Hit Many Compound’ (OSMAC) screening, which improved our hit rate 30-fold. Stappia quadratibracata sp. nov. produces the siderophore agrochelin and its newly discovered epimer stappiachelin; we show that these compounds have antibacterial activity for the first time. Two Kocuria rhizophila strains with potent activity against Gram-negatives may produce a new poly-amino acid, the purification of which is underway. We have also started the process of expressing silent biosynthetic gene clusters in heterologous hosts using TAR cloning. Finally, I discuss the lessons to draw from our work to date, and make recommendations for future work.
Date of Award28 Sep 2021
Original languageEnglish
Awarding Institution
  • The University of Bristol
SupervisorChris L Willis (Supervisor), Paul R Race (Supervisor) & Angela Essex-Lopresti (Supervisor)

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