A BRIEF OVERVIEW OF METABOLOMICS: WHAT

IT MEANS, HOW IT IS MEASURED, AND ITS

UTILIZATION
By Genoa Barchet

What is metabolomics?

Metabolomics is a relatively new member to the ‘-omics’ family of systems biology

technologies (Bino et.al. 2004). The term ‘metabolome’ was coined in 1998 and was used
to describe the metabolite complement of living tissues (Oliver et.al. 1998). Despite its
relative youth (in comparison to genomics and proteomics), metabolomics as a field of
study is now firmly established as a functional genetics approach to understanding the
molecular complexity of life (Wagner et.al. 2003). Today, it even has a journal with its
namesake, Metabolomics, dedicated to scribing its tribulations and advances (available at
www.springeronline.com). This paper will briefly describe some important aspects of the
innovative field of metabolomics, namely, some working definitions for metabolomics in
a scientific setting, measurement methods of the metabolome, and some current
applications of metabolomic research.

What is metabolomics and why is it an important addition to the study of biological

systems? Metabolomics is the comprehensive, qualitative, and quantitative study of all
the small molecules in an organism (Oliver et.al. 1998). By small, I mean molecules that
are less than or equal to about 1500 daltons (Da). Recall that a dalton (or, equivalently, an
atomic mass unit, u) has a mass approximately equal to one hydrogen atom (Lodish et.al.
2004). The study of metabolomics therefore excludes polymers of amino acids and
sugars. The focus is instead on intermediary metabolites used to form the macromolecular
structures and other small molecules participating in important metabolic functions and
fulfilling critical roles such as signaling molecules or secondary metabolites.

Because metabolomics encompasses such an extensive network of biochemical

interactions, many of which have not yet been fully characterized in terms of
participating reactants, different approaches to metabolome analyses have arisen.
Depending on the goal of one’s experiment, the approach used will differ. The three
principal approaches for the analysis of the metabolome are metabolite profiling,
metabolic fingerprinting, and metabonomics (Hall 2006).

Metabolite profiling is an approach that aims to identify and quantify metabolites, but
does so on a biased scale due to methodological limitations and differences in analytical
platforms (Dunn and Ellis 2005, Hall 2006). Much of the bias in this technique is
introduced when extracting the sample from the organism or tissue of interest, and is due
to differential affinities for extraction solvents. Despite the introduced bias, this technique
is, at present, the closest one can get to a true and complete visualization of the
metabolome (Bino et.al. 2004).
Another approach in metabolomic technology is metabolic fingerprinting. This high-
throughput approach is normally utilized in tissue comparison or discrimination analysis,
and so is simpler and coarser in its technique (sample preparation, separation, and
detection) in comparison to metabolic profiling.

Metabonomics is yet another aspect of metabolomics, which focuses on the metabolic

response of organisms to pathophysiological stimuli or genetic modification. This
approach is generally restricted to microbiological and other non-botanical studies.

Though these three different approaches to metabolomic analysis all generate copious
amounts of useful information, they do not compensate for the ultimate goal: the
comprehensive analysis of the metabolome. However, they do enable scientists to obtain
a snap-shot of the metabolic state of an organism at a given time. When used in
combination with physiological assays and/or genomics, proteomics, or transcriptomics,
this technology could lead to a deeper understanding about an organism’s organization
and function.

How is the metabolome measured?

Achieving the ability to visualize the metabolome, of any organism, is currently still a
dream because the metabolome is vastly complex. Just imagine all the metabolic
pathways that need to be mapped, every intermediate to be accounted for, the amounts of
chemical compounds to be determined, and the method or mechanism by which they flow
through their various cycles on their way to biomass accumulation, excretion, exudation,
etc. This picture is enormous and is difficult to envision in its entirety. The complexity of
the whole picture increases particularly when considering the cooperative nature of the
different levels of organization of biological systems and the effect that the environment
can produce on the metabolism of an organism.

The method by which metabolic complexity is sorted is usually through hyphenated

analysis platforms such as chromatography-mass spectrometry. In fact, gas
chromatography-mass spectrometry (GC/MS) is probably the most popular analytical
platform used in metabolic analyses and will be used as the paradigm method of analysis
in this paper (Dixon et.al. 2006). Biological extracts to be analyzed via GC/MS must first
be chemically derivatized with agents that make the chemical constituents present in the
sample more volatile (Seger and Sturm 2006, Wagner et.al. 2003). Once the sample is
injected into the gas chromatograph, there is two-fold separation of sample components
based on differences in volatility and size of molecules. Larger molecules take a longer
time to move through the column than do small molecules and amongst molecules of
similar size, different molecular species display different volatilities.

Upon outflow from the chromatograph column, individual volatilized chemicals are
funneled into the mass spectrometer where identification and quantification of individual
chemical compounds are determined. Data obtained by the GC/MS is deconvoluted by
special software to produce two graphs corresponding to the chromatogram and mass
spectra of the sample. Graphs from different samples can be overlaid to aid in comparison
and detection. Individual chemicals can be identified based on the retention time (the
time it takes for the compound to become vaporized and to flow through the
chromatographic column) and the mass spectrum.

One problem that persists in metabolomic analyses is the dearth of comprehensive

identification of metabolic components, particularly in pathways outside of primary
carbon metabolism (Wagner et.al. 2003). Therefore, there is movement in the scientific
community towards a cooperative approach for creating open-access libraries of
compounds based on standardized analytical procedures (Bino et.al. 2004, Dixon et.al.
2006). Several libraries already exist and are immensely helpful in chromatogram
analysis, though they are far from being comprehensive.

Mass spectroscopy systems coupled with nuclear magnetic resonance systems are ideally
the best platforms for identification of unknown chemical compounds, but are
prohibitively expensive for most scientific laboratories (Dixon et.al. 2006).

What is metabolomic technology used for?

Metabolomics is said to be a critically important technique in a systems biology

framework. Systems biology is a term that envelopes the various ‘-omics’ technologies,
of which metabolomics is just one. Studies in systems biology aspire to integrate the
structures and functions of various levels of encoded information of the organism (Kitano
2002). If one considers that many proteins, encoded by genes, are in fact enzymes that
catalyze chemical reactions, then by extension, metabolomics can be seen as another
level of information encoded by the organism but more subject to manipulation by its
environment (Seger and Sturm 2006). In a sense, metabolomics represents the meeting of
phylogenetics and phenetics.

Currently, metabolomics research is being applied to myriad different uses, from plant
science to medicine. In the plant science community, for instance, metabolomic research
is utilized in studies relating to biomass accumulation, stress resistance, and secondary
metabolite production (Hall 2006, Meyer et.al. 2007). Biomass accumulation and
resistance to certain environmental stressors are important in plant science as plants are
sought as a potential source of alternative energy production such as biofuel (Meyer et.al.
2007). Breeding resistant or genetically modified plants can be a long and arduous task,
and metabolite analyses promise to provide early indication for increased utility in the
field via the presence of metabolic biomarkers (Dixon et.al. 2006).

Additionally, plants are an exceedingly rich source of nutrients and secondary metabolites
useful in nutritional and medicinal research. Recently, there has been resurgence in the
interest for plant-based pharmaceutical compounds (Hall 2006). A conservative estimate
places the number of plant metabolic compounds at 200,000, which provides for an
extensive searching ground for new and improved medicinal and nutritional products
(Bino et.al. 2004, Dunn and Ellis 2005). On a related note, comparative metabolomics in
humans may provide for enhanced diagnostic power and individualized treatment for
illness and disease (Bino et.al. 2004).
In conclusion, metabolomics represents the interface between genetic pre-disposition and
environmental influence. It is because of this unique position in the systems biology
hierarchy that metabolomics could prove invaluable in our quest to understand the
function of genes, to be able to control and/or design novel organisms that may benefit
our health or lifestyles, and to understand more fully the molecular physiology of
ourselves and that of other organisms.

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