title: 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.
authors: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.|Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
authors: Layla J
authors: LJ
authors: Barkal
authors: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.|Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.|Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
authors: Ashleigh B
authors: AB
authors: Theberge
authors: Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles California 90089, USA.
authors: Chun-Jun
authors: CJ
authors: Guo
authors: Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
authors: Joe
authors: J
authors: Spraker
authors: Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
authors: Lucas
authors: L
authors: Rappert
authors: Department of Biotechnology, CEA-University Grenoble-Alpes, 17 Avenue des Martyrs, 38054 Grenoble, France.
authors: Jean
authors: J
authors: Berthier
authors: Department of Mathematics, Susquehanna University, Selinsgrove, Pennsylvania 17870, USA.
authors: Kenneth A
authors: KA
authors: Brakke
authors: Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles California 90089, USA.|Department of Chemistry, University of Southern California, Los Angeles California 90089, USA.
authors: Clay C C
authors: CCC
authors: Wang
authors: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.|Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
authors: David J
authors: DJ
authors: Beebe
authors: Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.|Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
authors: Nancy P
authors: NP
authors: Keller
authors: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.|Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
authors: Erwin
authors: E
authors: Berthier
mesh_terms: D001230:Aspergillus / Q000378:metabolism*; D001231:Aspergillus flavus / Q000378:metabolism; D001232:Aspergillus fumigatus / Q000378:metabolism; D001233:Aspergillus nidulans / Q000378:metabolism; D002851:Chromatography, High Pressure Liquid; D018920:Coculture Techniques; D046508:Culture Techniques; D005670:Fusarium / Q000378:metabolism*; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D044085:Microfluidics; D011550:Pseudomonas aeruginosa / Q000378:metabolism*; D043368:Ralstonia solanacearum / Q000378:metabolism*; D053719:Tandem Mass Spectrometry