Metabolic profiling as a tool for prioritizing antimicrobial compounds

Journal of Industrial Microbiology & Biotechnology
Changsheng WuGilles P van Wezel

Abstract

Metabolomics is an analytical technique that allows scientists to globally profile low molecular weight metabolites between samples in a medium- or high-throughput environment. Different biological samples are statistically analyzed and correlated to a bioactivity of interest, highlighting differentially produced compounds as potential biomarkers. Here, we review NMR- and MS-based metabolomics as technologies to facilitate the identification of novel antimicrobial natural products from microbial sources. Approaches to elicit the production of poorly expressed (cryptic) molecules are thereby a key to allow statistical analysis of samples to identify bioactive markers, while connection of compounds to their biosynthetic gene cluster is a determining step in elucidating the biosynthetic pathway and allows downstream process optimization and upscaling. The review focuses on approaches built around NMR-based metabolomics, which enables efficient dereplication and guided fractionation of (antimicrobial) compounds.

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Citations

Jan 8, 2016·Journal of Industrial Microbiology & Biotechnology·Leonard Katz, Richard H Baltz
Jun 14, 2016·Journal of Medicinal Chemistry·Michel FrédérichPascal de Tullio
Dec 19, 2016·Journal of Industrial Microbiology & Biotechnology·Pingping TianQiang Gao
Feb 1, 2018·Metabolites·Pollen K Yeung
Oct 3, 2018·Marine Drugs·Emiliana TortorellaDonatella de Pascale
Feb 26, 2019·Protein and Peptide Letters·Dan ZhangShufang Liang
Feb 8, 2019·Journal of Industrial Microbiology & Biotechnology·Nataliia V MachushynetsGilles P van Wezel
Jul 30, 2019·International Journal of Microbiology·Periyasamy SivalingamKandasamy Prabakar
Jun 30, 2019·Folia Microbiologica·Phuong-Anh NguyenAngélique Fontana
Oct 7, 2015·Journal of Natural Products·Changsheng WuGilles P van Wezel

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Methods Mentioned

BETA
nuclear magnetic resonance
ChIP-chip
NMR
glycosylation
RNAseq

Software Mentioned

ADEQUATE
Pep2Path
antiSMASH
NRPSPredictor
DasR
SMURF ( Secondary Metabolite Unknown Regions Finder )
BAGEL
SBSPKS ( Based Sequence Analysis of Polyketide Synthases
antiSMASH ( ANTIbiotics & Secondary Metabolite Analysis SHell

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