Research Progress and Challenges of Microbial Metabolomics

Genomics and proteomics explore life activities from the level of genes and proteins respectively. In fact, many life activities in cells occur at the level of metabolites, such as cell signal release, energy transfer, and cell-to-cell communication, which are all regulated by metabolites. Gene and protein expression are closely related, and metabolites can better reflect the environment in which the cell is located, which in turn is closely related to the nutritional status of the cell, the effects of drugs and environmental pollutants, and the influence of other external factors. So some people think that genomics and proteomics tell you what might happen, while metabolomics tells you what actually happened.

Metabolomics is the simultaneous qualitative and quantitative analysis of all metabolites of a certain biological component or cell in a specific physiological period or condition to find different target metabolites. Metabolomics appeared in the post-genomics era, and its main goal is to quantify the multiple dynamic responses of graduate students to external stimuli, pathophysiological changes and their own gene mutations. The study of the metabolome (the full set of metabolites produced in organisms) reflects the enzymatic pathways and networks encoded in the genome. In addition, the entire composition of metabolites conveys the interaction between the developmental process and the changing environment during the life cycle of the organism.

Metabolomics is the study of the overall metabolite profile of cells under given conditions. It is an important part of systems biology and is considered a living system, and emergency characteristics cannot be predicted by a single part. On the contrary, biological results require an integrated approach to study the sum of all systems. Since metabolites reflect the interaction between the cell's genome and its environment, metabolomics provides a fair assessment of the state of the cell under specific conditions.

Because the concentration of metabolites in a cell usually reveals aspects of biochemical regulation that cannot be detected by other methods, metabolomics fills a gap in more traditional studies of the interaction between genes, proteins, and metabolites in a single cell. It also resolves the ambiguity caused by the influence of the environment on cell expression. In addition, changes in metabolites usually lead to changes in phenotype and cell function, which can then be analyzed by the metabolome. Metabolomics has proven its key role in bioenergy, environmental interactions, functional genomics and gene discovery, secondary metabolism, genome-wide association mapping, and metabolic modeling in higher biological and microbial systems.

Although significant progress has been made, some researchers believe that metabolomics is still in its infancy or emerging stage. The time that others advocated has come to integrate it as one of the important components of systems biology, which provides a complementary role to genomics and proteomics. Regardless of various opinions, metabolomics has undeniably used the knowledge and experience gained from other "omics". Significant advances in the three areas have made metabolomics research and analysis feasible.

Microorganisms are ideal for systems biology research because they are easy to manipulate and play a vital role in human health and the biosphere. Microbial metabolomics is one of the platforms that integrate biological information into system microbiology to promote the understanding of microbial interactions and cell functions. The next decade of genomics will continue to emphasize functional analysis and promote systematic and integrated methods of life science research. Microbiological research has adopted this view, producing results and insights that cannot be achieved by traditional methods. Microorganisms are no longer regarded as isolated organisms in the system, but as integrated components for understanding functional biology.

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