Microbial Metabolite Profiling

Microorganisms and in particular actinomycetes and microfungi are known to produce a vast number of bioactive secondary metabolites. Natural product research needs to continually improve the efficiency of the selection, screening, dereplication, isolation, and structure elucidation processes, in order for natural product chemistry to continue to be competitive with purely synthetic-based discovery methods. For industrially important fungal genera such as Penicillium and Aspergillus, the production of these compounds has been demonstrated to be very consistent at the species level. This means that direct metabolite profiling techniques such as direct injection mass spectrometry or NMR can easily be used for metabolomics of strains from both culture collections and natural samples using modern informatics tools. Metabolomics can be used for the identification and classification of filamentous fungi and for the discovery of novel compounds when used in combination with modern methods for dereplication. Such approaches will be important for future effective drug discovery strategies, especially for the dereplication of culture collections in order to avoid redundancy in the selection of species. This will maximize the chemical diversity of the microbial natural product libraries that can be generated from fungal collections.

Metabolomics aims to detect all small metabolites in a cell or organism. Rapid profiling techniques may determine all metabolites produced by a microorganism. These techniques are generally segregated into fingerprinting, footprinting, profiling, or target analysis.

  • Fingerprinting / Footprinting

Get a "chemical picture" of the sample where the signals cannot necessarily be used to detect/identify specific metabolites and depends strongly on the technique used.

  • Profiling Techniques

It requires that signals in the profile (e.g. peaks in a chromatogram) can be assigned to a specific metabolite whether it is of known structure or not.

  • Target analysis

Determine and quantify specific metabolites.

Fingerprinting, profiling or target analysis can be performed by e.g. thin-layer chromatography (TLC) screening, by mass-profiling using direct infusion ESI-MS, by NMR, or more by doing elaborate profiling and target analysis, using hyphenated analytical methodologies e.g. GC-MS(-MS), LC-UV(spectrometric), LC-MS(-MS), LC-NMR and other combinations. 

Mass spectrometer deviceFigure 1 Mass spectrometer device

Molecular genetics and metabolic engineering for microbial drug discovery

The genes coding for many natural products and in particular polyketide synthethase (PKS) genes are modular and produce multifunctional enzymes. This has lead to new possibilities to diversify unnatural microbial natural products since it is now possible to shuffle genes around within these clusters, or even to include genes from other pathways, thereby generating hybrid enzymes capable of synthesizing an unlimited set of new molecules that are difficult to make by traditional chemical methods.

It is a major challenge for future research due to the technical limitations of isolation and cultivation of organisms difficult to culture. An alternative approach to access unculturable organisms, and particularly prokaryotic species, is to access their DNA directly by cloning the metagenome. Isolated DNA is ligated into bacterial artificial chromosome (BAC) vectors, which are low copy plasmids that can contain relatively large DNA inserts. The BAC vectors are then subsequently transformed into host microorganisms such as E. coli. The resulting clones can then be screened for biological activity or alternatively be probed for sequences of interest. This approach is expected to become a powerful resource in the future from which new chemical entities can be accessed for lead discovery.

Creative Biogene is the premier institution to perform professional and comprehensive metabolomics profiling services for partners across the pharmaceutical and academic research segments. If you are interested in our microbial metabolite profiling services, please contact us for more details.

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