The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism (such as amino acids, organic acids, nucleic acids, fatty acids, amines, sugars, vitamins, co-factors, pigments, antibiotics, etc.) as well as exogenous chemicals (such as drugs, environmental contaminants, food additives, toxins and other xenobiotics) that are not naturally produced by an organism. In other words, there is both an endogenous metabolome and an exogenous metabolome. The endogenous metabolome can be further subdivided to include a "primary" and a "secondary" metabolome (particularly when referring to plant or microbial metabolomes). A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has important ecological function.  Secondary metabolites may include pigments, antibiotics or waste products derived from partially metabolized xenobiotics. To qualify as a metabolite, or to be considered to be part of the metabolome, a small molecule must typically have a molecular weight <1500 Da. This means that molecules such as glycolipids, polysaccharides, short peptides (<14 amino acids) and small oligonucleotides (<5 bases) can be regarded as metabolites or constituents of the metabolome. On the other hand, very large macromolecules such as proteins, messenger RNA, ribosomal RNA, microRNA and DNA are definitely not metabolites and are not considered to be part of the metabolome. The study of the metabolome is called metabolomics. See Figure 1 for a picture of the relationship between different “omes”.

The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism (such as amino acids, organic acids, nucleic acids, fatty acids, amines, sugars, vitamins, co-factors, pigments, antibiotics, etc.) as well as exogenous chemicals (such as drugs, environmental contaminants, food additives, toxins and other xenobiotics) that are not naturally produced by an organism. In other words, there is both an endogenous metabolome and an exogenous metabolome. The endogenous metabolome can be further subdivided to include a "primary" and a "secondary" metabolome (particularly when referring to plant or microbial metabolomes). A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has important ecological function.  Secondary metabolites may include pigments, antibiotics or waste products derived from partially metabolized xenobiotics. To qualify as a metabolite, or to be considered to be part of the metabolome, a small molecule must typically have a molecular weight <1500 Da. This means that molecules such as glycolipids, polysaccharides, short peptides (<14 amino acids) and small oligonucleotides (<5 bases) can be regarded as metabolites or constituents of the metabolome. On the other hand, very large macromolecules such as proteins, messenger RNA, ribosomal RNA, microRNA and DNA are definitely not metabolites and are not considered to be part of the metabolome. The study of the metabolome is called metabolomics. See Figure 1 for a picture of the relationship between different “omes”.