Design of Pathway-Level Bioprocess Monitoring and Control Strategies Supported by Metabolic Networks - Measurement, Monitoring, Modelling, and Control of Bioprocesses - page 201

Table 1 Different levels of metabolome analysis
Metabolite target analysis Identification and quantification focused on one or a few

metabolites related to a specific pathway [ 34 ]

Metabolite profiling (or
metabolic profiling)

Identification and quantification of a selected group of
metabolites, e.g., metabolites from a specific metabolic
pathway or a specific compound class, such as amino acids,
organic acids, or carbohydrates [ 34 ]

Metabolomics Identification and quantification of all metabolites in a biological

system. Sample preparation method must retain all
metabolites. Analytical technique must be suited to measure
metabolites over a broad range of concentrations and needs
high discriminatory power

Metabonomics Analysis of tissues and/or biological fluids to detect changes

caused by disease or therapeutic treatments [ 35 ]

Metabolic fingerprinting Fast, high-throughput analysis of intracellular metabolites to

provide a characterization of the cells for sample
classification. Analytical technique must allow sample
discrimination, but it is not required to identify and quantify
all the metabolites individually [ 34 ]

Metabolic footprinting Fast, high-throughput analysis of the surrounding medium to

characterize the cells based on their exometabolome. As with
fingerprinting, it is not necessary to identify and quantify all
the metabolites individually to allow sample discrimination
[ 6 ]

metabolites, of which some are provided by the culture medium and many others
are produced inside the cells and then secreted or excreted into the environment.
The ''metabolome'' was defined by Oliver et al. [ 32 ] as the qualitative and
quantitative collection of all metabolites, that is, all the low-molecular-weight
molecules present in a cell, which are also participants in general metabolic reac-
tions and that are required for the maintenance, growth, and normal function of the
cell. The metabolome can be subdivided into the endometabolome (intracellular
metabolites) and exometabolome (extracellular metabolites) [ 33 ]. Depending on
whether the analysis is being targeted for the endo- or exometabolome and
depending on the analytical detail and quantitative power desired, there are several
measurement strategies available (Table 1 ); some such strategies have the potential
for real-time monitoring and are therefore suitable for process control.
Measuring the endometabolome (metabolic fingerprinting) is not as straight-
forward as measuring the exometabolome (metabolic footprinting) given the
complex sample preparation protocols and the higher number of intracellular
metabolites. Endometabolome analysis requires separation of cells from extra-
cellular medium followed by cell breakage. In addition, the rapid turnover inherent
to intracellular metabolites, which can be under one second for microbial systems
[ 36 ], results in the need for a rapid quenching step to halt metabolism. In contrast,
the turnover rates of exometabolites are much lower given the low volume ratio
between the intracellular and extracellular phases.