Exometabolomics
Exometabolomics, also known as 'metabolic footprinting',[1][2] is the study of extracellular metabolites and is a sub-field of metabolomics.[3]
While the same analytical approaches used for profiling metabolites apply to exometabolomics, including
Exometabolomics is also used as a complementary tool with genomic, transcriptomic[5] and proteomic data, to gain insight into the function of genes and pathways. Additionally, exometabolomics can be used to measure polar molecules being consumed or released by an organism, and to measure secondary metabolite production.[6][7]
History
The study of extracellular metabolites has been prevalent in scientific literature.[8][9][10] However, global exometabolite profiling was only realized with recent advances allowing for improved chromatographic separation and detection of hundreds to thousands of compounds by the mid-2000s.[7] The first work to demonstrate the biological relevance of comparative profiling of exometabolite pools was not until 2003, when the term "metabolite footprinting" was coined by Jess Allen and coworkers.[1][7] This work attracted a great deal of interest in the community, particularly for characterization of microbial metabolism.[2] The idea of the "exometabolome" encompassing the components of the exometabolite pool was not introduced until 2005.[11]
Recent advances in
Analytical technologies
In principle, any technologies used for metabolomics can be used for exometabolomics. However, liquid chromatography–mass spectrometry (LC–MS) has been the most widely used.[3] As with typical metabolomic measurements, metabolites are identified based on accurate mass, retention time, and their MS/MS fragmentation patterns, in comparison to authentic standards. Chromatographies typically used are hydrophilic interaction liquid chromatography for the measurement of polar metabolites,[16] or reversed-phase (C18) chromatography for the measurement of non-polar compounds, lipids, and secondary metabolites.[17] Gas chromatography–mass spectrometry can also be used to measure sugars and other carbohydrates, and to obtain complete metabolic profiles.[18]
Because LC–MS does not give spatial data on metabolite localization, it can be complemented with mass spectrometry imaging (MSI).[3]
Applications
Exometabolomic techniques have been used in the following fields:
Functional genomics
Metabolite utilization to annotate function of unknown genes.[19]
Bioenergy
In lignocellulosic feedstock studies.[20]
Agriculture and food
Characterization of plant root exometabolites to determine how exometabolites affect
Metabolic footprinting of yeast strains for identification of yeast strains optimal for enhancing fermentation performance and positive attributes in wine.[22]
Health
Differentiating healthy versus cancerous bladder cells with metabolic footprinting.[23]
Footprinting, in combination with other techniques, for early recognition of outbreak and strain characterization.[24]
Studying aging with C. elegans exometabolomics.[25]
Extracellular metabolite analysis to evaluate pathogenic mechanism of intracellular protozoal parasite.[26]
Analysis of carbon cycling
Global carbon fixation, phytoplankton/dinoflaggelate interactions, and exometabolomics.[27]
Microbial communities
Interaction of E. coli exometabolites with C. elegans affects life span.[28]
Bacteria and yeast in dairy systems.[13]
Bioremediation
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Metabolic niche partitioning
In 2010, exometabolomics analysis of the cyanobacterium, Synechococcus sp. PCC 7002 by Baran, et al. revealed that this photoautotroph could deplete a diverse pool of exogenous metabolites.[29] A follow-up exometabolomics study on sympatric microbial isolates from biological soil crust, which exist in communities with cyanobacteria in the desert soils of the Colorado Plateau, suggested that metabolite niche partitioning exists in these communities, where each isolate only utilizes 13-26% of metabolites from the soil [30]
Secondary metabolites
Metabolic footprinting for determination of antifungal substances' mode of action[31]
See also
- Mass spectrometry
- Metabolomics
- Metabolome
- Metabolite fingerprinting
- Mass spectrometry imaging
References
- ^ S2CID 15800623.
- ^ PMID 18675480.
- ^ PMID 25855407.
- ISBN 978-3-319-10320-4.
- PMID 18990252.
- PMID 24616891.
- ^ S2CID 18217591.
- S2CID 13766961.
- JSTOR 2389307.
- PMID 16346073.
- PMID 16154652.
- PMID 24111681.
- ^ S2CID 21031529.
- PMID 26885935.
- PMID 19116616.
- PMID 22628210.
- S2CID 30421756.
- PMID 21890679.
- PMID 23082955.
- PMID 24957893.
- S2CID 6321050.
- PMID 23528123.
- S2CID 10422166.
- PMID 23135942.
- PMID 23929107.
- PMID 24973017.
- hdl:1912/8760.
- ^ Correia, Gonçalo dos Santos. "Coupling metabolic footprinting and flux balance analysis to predict how single gene knockouts perturb microbial metabolism". repositorio.ul.pt. Retrieved 2016-04-23.
- PMID 21935552.
- PMID 26392107.
- PMID 15466562.