Metabolomics: Concept, methods and potential prospect in marine biology

SPECIAL TOPIC Omics in Marine Biotechnology 0 1 ZHANG Xuan 0 1 CHEN Hao ) 0 1 0 metabonomics, metabolomics, biosynthetic pathway, NMR, LC/GC-MS 1 Key Laboratory of Marine Biological Active Substances, The First Institute of Oceanography , State Oceanic Administration, Qingdao 266061, China The term omics refers to the comprehensive analysis of a specific biological system. With the development of omics, a number of omics subdisciplines have emerged, which play an important role in system biology. As a subdiscipline of omics, metabolomics provides a comprehensive analysis of the metabolome and has been widely applied to various fields of biology. In this paper, we introduce the concept, approaches, applications, and promising prospects of metabolomics. - The complete sequencing of the human genome has introduced a new field of systems biology, known as omics. In biology, the term omics, which means the totality of sorts, refers to the comprehensive analysis of a specific biological system. For example, genomics is the study of all the genes of a cell or tissue at the DNA (genotype), mRNA (transcriptome) or protein (proteome) level [1]. Omics is an integrated concept that combines all the information acquired from the different levels at which biological systems are controlled to investigate the nature of biological phenomena at the molecular level. Compared with traditional biological ideology, omics places more emphasis on the integration of diverse bioinformation. Thus, it provides a general view of processes rather than detailed information on the independent behaviors of specific cells or tissues. To date, a range of omics subdisciplines have emerged, including genomics and proteomics, each of which has its own set of instruments, techniques, reagents, and software. Omics technology has driven the development of new research approaches, including DNA and protein chips, mass spectrometry, and instruments that enable high-throughput analysis. Omics not only offers the advantage of understanding biological processes, but the prospect of more accurate diagnoses, improvements in nutrition and other new applications in biological fields. Nicholson first propounded the concept of metabonomics in 1999. The primary definition of metabonomics is the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification [2]. Metabonomics focuses on understanding the global biological system by the study of metabolic compounds. The early study of metabonomics was focused primarily on the application of nuclear magnetic resonance spectroscopy (NMR) to analyze the changes of metabolic compounds in biological fluids, cells, and tissues, and was aimed at the augmentation and complementation of the information provided by measuring the genetic and proteomic responses to xenobiotic exposure [2]. Another important subject in the study of metabolic compounds is metabolomics. The focus of metabolomics is the compositional analysis of low molecular-weight substance in biological samples. This approach traditionally uses MS (Mass Spectrometry) in combination with a separation technique such as gas chromatography (GC) or liquid chromatography (LC) to analyze information from low molecular-weight compounds. To avoid interaction between The Author(s) 2012. This article is published with open access at Springerlink.com the compounds being measured in the matrix, sample preparation and analysis is focused on a series of compounds that share similar properties. The comprehensive identification and quantification of the metabolic compounds synthesized by an organism means that metabolomics is one of the most important approaches to study genetic expression and proteomics. Although there is conceptual similarity between the fields of metabonomics and metabolomics, there are some significant differences in the approaches and objectives of the research. The former is dedicated to comprehensive metabonomics profiling at a given scale, whereas the latter is primarily concerned with the history of time-dependent metabolic profiles in an integrated system [3]. However, associated with the development of bioinformatics, the two concepts will likely be integrated. For convenience, we use the term metabolomics in the following discussion. An organism is an integrated and networked system with a bioinformatics transport chain consisting of genes-proteinsmetabolic compounds. Genes and proteins provide information about what will happen, whereas metabolic compounds provide information about what has happened. In comparison with other omics subdisciplines, metabolomics is defined by the following unique characteristics: (1) Metabolic data do not provide the information produced by the independent behaviors of specific cells or tissues but, instead, documents the global changes of metabolome under the external interference, which reflect the metabolic response to exogenous stimuli in a general view. (2) Metabolic compounds are the endpoint of functional gene activity. According to Johnsons research, metabolic throughput is not only controlled by genetic expression, but also adjusted by the exogenous environment [4]. The changes in concentrations of metabolic compounds illustrate the biological response to perturbation from outside. Therefore, metabolic compounds are more sensitive compared with genes and proteins. (3) During a biochemical reaction, the concentration of enzymes and metabolic throughput is generally unchanged, whereas the concentration of some low-molecular weight compounds will change significantly. Being the endpoint of the bioinformatic transport chain, the signal generated by alteration of the metabolome is magnified and can provide insight and accurate characterization of the cells function [5]. Progress in metabolomics Pharmacotoxicology involves studying the toxicity of drugs, their effect on target organs, their latency, and the relationship between structure and toxicity. After being taken into an organism, a heterologous substance acts directly on the metabolome, but has no apparent effect on the genome or proteome. Thus, there is little value in using genomics and proteomics to evaluate the mechanisms of drug toxicity. Traditional drug screening depends primarily on biological screening, which is reliant on large sample sizes and is time consuming. The advent of high throughout metabolomics technologies means it is now possible to analyze large numbers of samples in a relatively short period of time. Using metabolomics technologies, we are able to detect abnormal changes in trace materials in biofluids such as urine, serum, and tissue biopsies following exposure to a heterologous substance. In addition, these technologies allow for simultaneous quantification of total metabolic compounds. For example, Zhou et al. [6] injected dexamethasone into a group of mice at day 17.5 of pregnancy then collected (...truncated)