The role of natural products in modulating the microbial secondary metabolome

The biological role of many natural products remains unknown. Even compounds with a clear mode of action, such as the antibiotics, have weak translation of that activity to an ecological context, highlighting the complexities of natural product mechanisms in Nature. Microbial interactions are useful for the study of such natural products, and coupled with secondary metabolomics, the production of secondary metabolites can be profiled spatially and temporally in response to a microbial interaction.

In the first half of this thesis (Chapter 1-3), microbial interactions were explored as a tool for understanding the natural dynamics of secondary metabolomes. Specifically, interactions involving fungi and actinomycetes were investigated (Chapter 2), as well as the differences between interactions of microorganisms derived from the same or different ecological niches. Chemical inductions were found to be 1) twice as likely to result from interkingdom rather than intrakingdom interactions; 2) independent of the ecological source of the interacting microbes; and 3) more common in the diffusible chemistry range (35-55% acetonitrile/water by reversed phase HPLC elution). Physical observations defining key interactions (e.g., inhibition) could also be correlated to specific metabolomic effects. Lastly, a specific co-culture between Penicilliumbrasilianum and Aspergillus nomius was investigated in more detail (Chapter 3) whereby the isolation and characterisation of three new compounds was outlined.

In the second half of this thesis (Chapter 4-6), “forgotten antibiotics”, which were not pursued at their time of discovery due to modest biological activity, stability, or toxicity, were further explored in order to understand the biological relevance for their production. Chapter 4 details the large-scale cultivation of Penicillium turbatum and the subsequent isolation and characterisation of analogues of the forgotten antibiotic, A26771B, a macrocyclic polyketide with modest Gram-positive antibacterial activity. In addition to A26771B, nine novel and three previously reported berkeleylactones were isolated. The majority of the berekeleylactones isolated constitute a diverse set of berkeleylactone F stereoisomers highlighting an usually broad degree of substrate specificity for hydroxylation across the fungal macrolide. Chapter 5 details the investigation of a unique rearrangement pathway that the polyketide, enterocin, undergoes in relatively mild conditions, resulting in six novel isomeric compounds, arising from transformations of its tricyclic core. Rearrangements of the enterocin scaffold resulted in loss of its weak bacteriostatic activity, calling into question what role the rearrangement products might have in Nature. The ability for antibiotics and other non-biologically active natural products to manipulate or influence microbial metabolomes was also investigated (Chapter 6), highlighting the unique induction of dehydrorabelomycin upon treatment of Streptoverticilliumorinoci with the antibiotic, novobiocin. Microbial metabolomes were also shown to be influenceable by specific natural product classes, even those bereft of demonstrable biological activity, providing insight into their ecological roles in Nature.