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Secondary metabolism (also called specialized metabolism) is a term for pathways and small molecule products of metabolism that are not absolutely required for the survival of the organism. These molecules are produced by specific cells, that do not need these metabolites by themselves, but rather can be beneficiary for the whole organism. It is expected that in nature secondary metabolism helps organism to become more competitive for nutrients with other organisms by either their ability to obtain and purify necessary nutrients or by killing competitive organisms. There is no necessity for an organism to produce secondary metabolites if it is grown under normal laboratory conditions. Examples of the products include antibiotics, pigments and scents. To distinguish non-secondary ("ordinary") metabolism, the term basic metabolism is sometimes used.

Secondary metabolites are produced by many microbes, plants, fungi and animals, usually living in crowded habitats, where chemical defense represents a better option than physical escape. It is very hard to distinguish primary and secondary metabolites due to often overlapping of the intermediates and pathways of primary and secondary metabolism. As an example can serve sterols, that are products of secondary metabolism, and, at the same time, represent a base for a cell structure.

scents, such as ionone