Metabolomics is an emerging and quickly evolving as one of the new 'Omics' technique joining after genomics, transcriptomics and proteomics as a science employed towards the understanding of global system biology. Metabolomics is comprised of two words: Metabolome and Omics. Metabolome also referred as Small Molecule inventory (SMI) is defined by entire complement of low molecular weight, non-peptide metabolite within a cell or tissue or organism at a particular physiological rate which are required for maintenance, growth and normal function of a cell. Metabolites are the result of interaction of systems genome with its environment and are not merely end product of gene expression but also from part of regulatory system in an integrated manner and thus can define biochemical and phenotypes of a cell or tissues.

There are two classes of metabolites:
(1) Primary or basic metabolite is the source of backbone precursors for the production of secondary metabolites such as carbohydrates, amino acids and lipids and;
(2) Secondary metabolite refers to compounds that are not necessary for the survival and propagation but are considered to play a role in the continued existence and adaptation to the ever changing environmental conditions.

SMs formed both as part of normal plant developmental pathways and upon diverse endogenous and environmental stimuli. "Omics" is a high-through put screening based on biochemical and molecular characterization of an organ, tissue, or cell type.

What is Metabolomics?

“Metabolomics can be defined as a comprehensive quantitative and qualitative analysis of all small molecules (i.e., metabolites) present in a specific cell, tissue, or in an organism”. Small molecules means, which are less than or equal to about 1500 daltons (Da). The study of metabolomics therefore excludes polymers of amino acids and sugars. Metabolomics deals with the quantification of all or a substantial fraction of all metabolites within a biological sample and simultaneously identifying and quantifying their respective classes of biomolecules- mRNAs, proteins and metabolites. Measurement of metabolite provides basic information about biological response to physiological or environmental changes and thus improves the understanding of cellular biochemistry as networks of metabolite feedback regulate gene and protein expression and mediate signal between organisms.

Techniques used in the Metabolome analysis

Metabolome analysis can mainly be grouped in to four categories:

(i) Metabolic fingerprinting: This is used to classify samples according to their biological relevance and origin. This high throughput approach is normally utilized in tissue comparison or discrimination analysis;

(ii) Metabonomics: refers to “the quantitative measurement of the time-related multi-parametric metabolic response of living systems to pathophysiological stimuli or genetic modification”. This approach is generally restricted to microbiological and other non-botanical studies;

(iii) Metabolite profiling: can be defined as quantitative and qualitative analysis of complex mixtures of physiological origin is employed to study the number of compounds belonging to a selected biochemical pathway;

(iv) Metabolite target analysis: It refers to the study of primary effects of any alteration; analysis can be restricted to a particular metabolite or enzyme that would be directly affected by abiotic or biotic perturbation, mainly used for screening purpose.

Merits of Metabolomics over other Omics technology

The size of genome, transcriptome and proteome are estimated to be quite large, as compared to the metabolome and is tightly conserved across organisms. There are estimated to be about 25,000 genes, 100,000 transcripts and more than one million proteins in humans but, there are only approximately 2,500 metabolites in the human metabolome. Unlike the transcripts and proteome, metabolites share no direct link with genetic code and are instead products of concerted action of many networks of enzymatic reactions in cell and tissue.

Challenges/ Limitations of Metabolomics:

The major challenge faced by metabolomics is unable to comprehensively profile all of the metabolites and metabolome analysis is difficult due to widely differing structures, functional groups, physicochemical properties and concentrations of metabolites.

Biological variance is inherent in most living organisms and to capture this dynamic range of most instrumental approaches is insufficient.

Applications of Metabolomics:

Metabolomics including both targeted and global metabolite profiling strategies is rapidly becoming the approach of choice across a broad range of sciences including systems biology, drug discovery, diagnosis, toxicology, phytomedicines, molecular and cell biology, and other medical and agricultural sciences.

Applications in Plant Sciences:

• Plant metabolomics strategies are providing new and crucial insights for medicinal herb research for quality control of medicinal plants or herb products and linking putative bioactivity with the constituent phytocompounds of herbal medicines.

• It is also useful in the development of active secondary metabolites from medicinal plants as novel or improved phytotherapeutic agents.

• It is utilized in studies relating to biomass accumulation, stress resistance and secondary metabolite production.

• Metabolomics is a vital component of the systems biology approach, in which it at once reflects and connects the genotype with the diverse and yet specific phenotypes of cells, tissues, or organs.

• Breeding of resistant or genetically modified plants can be a long and time taking task, metabolite analyses promise to provide early indication for increased utility in the field via the presence of metabolic biomarkers.

• It offers a quick way to elucidate the function of novel genes and play an important role in future plant nutrition health and drug toxicity etc.

• In order to elucidate the function of unknown gene, genetic alteration is introduced in system by analyzing phenotyping effect of such a mutation by analyzing the metabolome functions may be assigned to respective genes.

• Comparative metabolomics platforms are evolving into novel technologies for monitoring disease development, drug metabolism and chemical toxicology.


Metabolomics is a very young science as compared to genomics, transcriptomics and proteomics, showing great potential for providing insights into the identification and quantification of metabolites. Metabolomics offers a promising approach to biomarker-driven drug discovery, development and identification of bioactive compounds from medicinal plants. Thus, metabolomics should contribute to a more fundamental understanding of the underlying biology and, hopefully, have a major impact on human healthcare and quality control of phytomedicines.

About Author / Additional Info:
I am Biotechnology professional with Ph.D in Plant Molecular Biology and Biotechnology and working as Scientist, Biotechnology