Antimicrobial resistance is a major threat to the future of human society with 10 million deaths projected in 2050. However, the search for new antimicrobials faces a setback in the rediscovery of the already known antibiotics. One strategy to mitigate this problem is the study of isolates from extreme environments, e.g. the Atacama Desert in Chile, adapted to those conditions and potentially encoding new specialised metabolites. Another method is to employ a multi-approach strategy for the discovery and elucidation of new metabolites combining genomics and metabolomics.This research project employed bioactivity assays, whole-genome analysis and metabolomics to determine the antibiotic potential from bioassays, identification of potential biosynthetic gene clusters and the elucidation of the compounds(s) responsible for the activity. Fourteen strains, closely related to Streptomyces phaeoluteigriseus by 16S rRNA, were isolated from two locations 30 km apart with similar altitude from the Atacama Desert. Further to taxonomic similarity the isolates showed also observable similarities, e.g. soluble pigment, despite inhabiting different locations.However, differential growth inhibition of several indicator strains, e.g. Staphylococcus aureus and Enterococcus faecalis was observed between isolates of both locations. Furthermore, phenotypic analysis and hyper-spectral imaging revealed hidden diversity of the isolates. Whole-genome analysis contradicted the phylogenetic relationship observed using 16S rRNA. Unique inter and intraspecific variations between isolates emerged with two distinct clades forming, revealing the possibility of soil 7 isolates to be a new species.Additionally, highly diverse plasmid profiles were observed instead of phages suggesting that the observed unique variations could result from horizontal gene transfer. Antibacterial activity was observed in solid and liquid cultures, especially in isolates from soil 7. Mass spectrometry analysis helped identify cinerubin B and unknown congeners of actinomycin (MW 1307.552). The latter were produced in large quantity by PH2 8 and further scale-up fermentation allowed the purification of an anti-E. faecalis metabolite.Actinomycin Y1 was its main constituent however further purification is required due to its low purity. In this study, the potential of the Atacama Desert to promote genetic and metabolomic diversification of closely evolutionary strains by niche specific pressures leading to production of known and, most importantly, bioactive metabolite production was demonstrated.
|Date of Award||8 Sep 2020|
- University Of Strathclyde
|Sponsors||University of Strathclyde|
|Supervisor||Paul Herron (Supervisor) & Ruangelie Edrada-Ebel (Supervisor)|