Metabolomic strategies to investigate biochemical interactions in microbiomes
Jean-Luc Wolfender, Léonie Pellissier, Abdulelah Alfattani, Thilo Kohler, Gerard Gdaniec Bartosz, Emerson Ferreira Queiroz, Pierre-Marie Allard
Section des Sciences Pharmaceutiques, Institut des Sciences Pharmaceutiques de Suisse Occidentale, Université de Genève, CH-1211 Genève
Microorganisms play an important role in host-pathogen interactions. This is true in natural ecosystems, for example in plants that harbor communities of endophytes or in mammals with their diverse microbiota. The pharmaceutical industry is also very interested in micro-organisms as the source of important drugs produced by fermentation.
In this context, we are developing analytical strategies that aim to characterize the metabolome of micro-organisms as efficiently as possible and to highlight the chemical variations that may be caused by their interactions.
In particular, we have studied how microorganisms interact through co-culture experiments and the study of the induction of natural antifungal products produced during confrontation. To do this we have developed chemical profiling methods based on mass spectrometry and metabolomic data analysis for the detection of biomarkers. We are also interested in trying to decipher how secondary metabolites might act within endophyte communities in plants by analyzing the metabolome of the host plant and the cultured strain set. The methods developed also allowed us to understand how microbial strains of clinical interest interact.
In order to successfully identify the antimicrobial molecules responsible for these interactions an innovative strategy has been developed. It integrates mass spectrometry profiling of the extracts and allows to guide the rapid isolation on a small scale of the metabolites of interest for complete characterization by nuclear magnetic resonance.