Comparative genomics and taxonomy of bacterial predators in soil and a genetic response of potential prey organisms

  • Natashia Sydney

Student thesis: Doctoral ThesisDoctor of Philosophy


With the emergence of antibiotic resistance and the decreasing effectiveness of antibiotics, there is a growing need for a solution with an environmentally safe nature. Bacterial predation has gained a lot of attention over the past decade and can be explored to provide a safe solution to the rise in antibiotic resistance. The field of genomics too is progressing rapidly and has attracted a growing interest amongst microbiologists. A recent highlight in the microbial genomics is the continually understanding of evolution and microbial diversity with the application of the latest sequencing techniques, as a result allowing us to expand and update the databases of genome sequences of old and novel species. In this dissertation, the objective is to investigate the genomics of predatory bacteria by using microbiology techniques to isolate and grow predatory bacterial strains, and observe their interaction with imminent pathogens, thereby increasing our knowledge on anti-biotic resistance. Pan-genomes of micro- organisms provide an insight into the secondary metabolite profile of a species, enabling us to expand the database of natural products. The research has taken a comparative genomic approach and has delved into annotating and creating pan-genomes of 11 Myxoccoccus and 10 Coralloccus sp.. The results from which have shown that the pan genome of Myxococcus/Pyxidicoccus is large and more diverse
than that of Corallococcus, with secondary metabolites present in the accessory genomes. On the taxonomy front, six novel species have been isolated and given a taxonomic rank. A similar approach was done whilst comparing the pan-genomes of another soil predator Streptomyces belonging to the Actinomycetota genus , indicating that though both the groups of organisms belonging to completely different taxonomic groups and with one being a Gram-positive and the other Gram-negative, the pan-genomes are both large and open with a tremendous scope for secondary metabolite production The study has added a species to the database of phyla Actinobacteria also known as Actinomycetota.,with 88.73% similarity to Streptomyces albidoflavus. Predation assays of the isolated Streptomyces strains show that they predate very differently from Myxococcus xanthus DK1622 on Escherichia coli and the plant pathogens: Pantoea gglomerans, Pseudomonas syringae, Pectobacterium atrosepticum, Rhodococcus rhodochrous, Xanthomonas campestris indicating that C5A and DK1622 prey efficiently across all these pathogens. The number of metabolites and compound class secreted across the 14 genomes of Streptomyces has been documented, re-affirming the validity on anti-SMASH as a potential tool for metabolite characterization. To combat infections caused by the antibiotic resistant Pseudomonas aeruginosa PA14, the work done has screened Pseudomonas aeruginosa transposon mutagenesis library to identify potential traits that might allow prey bacteria evade destruction by myxococcus, including bioinformatics approaches to identify the genes knocked out in ‘resistant mutants’. Interestingly, the COG analysis has provided the community with a comprehensive list of gene subsets that indicate resistance mechanisms to predation by M. xanthus. Conclusively, to eradicate contamination, there can be an application of a concoction of antibiotics which when used in the right proportion can kill potential pseudonomads in a myxobacteria cultures. The experiment has isolated and purified clean strains from glycerol stocks which have carried cross contaminants, thereby making it a reliable purification protocol in laboratory contamination stocks.
Date of Award2023
Original languageEnglish
Awarding Institution
  • Aberystwyth University
SupervisorGareth Griffith (Supervisor) & David Whitworth (Supervisor)

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