UC San Diego

Microbial metabolic exchange mediates microbial interactions and plays key roles in regulating biology and has shaped modern healthcare, agriculture and other commercial processes. In this thesis, cutting edge mass spectrometry techniques, new genome mining approaches, and innovative bioinformatics tools were coupled and developed into investigating microbial metabolic exchange and led to the identification and characterization of biological active molecules that may have therapeutic values. The thesis begins by informing the reader current understanding of microbial metabolic exchange as well as the emergence of new technologies that are allowing us to eavesdrop on microbial conversations. Chapter 2 describes the use of imaging mass spectrometry (IMS) to study a microbial intraspecies interaction which led to the identification and structural elucidation of two complex metabolites, sporulation killing factor (SKF) and sporulation delaying protein (SDP), that are active in a Bacillus subtilis cannibalism system. Further bioassays investigate the cannibalistic activity of SDP and also reveal SDP inhibits Staphylococci pathogens with comparable IC50 to vancomycin. Chapter 3 introduces a new genome-mining approach (peptidogenomics), and when combined with IMS leads the discovery of anti-infective agent arylomycin and its biosynthetic gene cluster in S. roseosporus. Chapter 4 goes beyond studying one or two metabolites at a time, presents the systematic characterization of microbial metabolic profile by the combination of peptidogenomics and an innovative bioinformatics tool (MS/MS spectral molecular networking) that is capable of clustering molecules of similar structure classes which leads to efficient characterization of the molecular universe of S. roseosporus. One of the molecules, stenothricin, after further investigations suggest it appears to be unique in its mechanism of antibiotic activity. Lastly, chapter 5 puts forth future directions envisioning how these tools and approaches described in the thesis can be further extended into investigating more complex microbial interactions that are of significant biological or clinical importance. Here, a proposal for investigating the molecular insight of fecal transplantation for the treatment of Clostridium difficile-associated diarrhea was presented. Similar approach could be undertaken to investigate other important human microbiota associated diseases/disorders such as Crohn's diseases, obesity, and diabetes