Microbial metabolomics in open microscale platforms

Abstract

The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria.

Aspergillosis and stem cell transplantation: An overview of experimental pathogenesis studies

“…A micrometabolomics platform has been developed which couples a microfluidic solid or liquid culture system to liquid chromatographymass spectrometry for the profiling and discovery of secondary metabolite production in response to environmental variations. 87 Use of this system revealed a clear relationship between A. fumigatus colony diameter and the secondary metabolite profile produced by the active culture that was independent of biomass. 87 Similarly, marked differences were observed in the metabolite profile of A. fumigatus grown in blood as compared with grown in standard culture media.…”

“…87 Use of this system revealed a clear relationship between A. fumigatus colony diameter and the secondary metabolite profile produced by the active culture that was independent of biomass. 87 Similarly, marked differences were observed in the metabolite profile of A. fumigatus grown in blood as compared with grown in standard culture media. 87 A similar system has been used to study the dynamics of germination in the pathogenic yeast Cryptococcus neoformans.…”

“…87 Similarly, marked differences were observed in the metabolite profile of A. fumigatus grown in blood as compared with grown in standard culture media. 87 A similar system has been used to study the dynamics of germination in the pathogenic yeast Cryptococcus neoformans. 88 The use of this and other similar microsystems may provide a useful tool to improve our understanding of the importance of the microenvironment on the expression and function of virulence factors of A. fumigatus.…”

Microbiome and metabolome data integration provides insight into health and disease

“…To circumvent these limitations, conventional approaches for microbiota growth have been modified to include environment specific media 103–106 , optimization of growth conditions based upon (meta)genomic information 106 , inclusion of helper organisms 107,108 and higher throughput cultivation strategies 105,109–112 . Efforts are also underway to cultivate both native and designer microbiome communities using in vitro and in vivo model systems 104 and new model systems continue to be developed 113,114 .…”

Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine

“…et al179 who used Aspergillus to demonstrate how MS-based metabolomics could be used together with microfluidic extraction to highlight modifications in the metabolome that are induced in microscale cultures by slight changes in the culture matrix. Using this methodology, the authors clearly…”