A metabolite is an intermediate or end product of metabolism (catalyzed by various enzymes that occur naturally within cells). The term metabolite is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones).
A primary metabolite is directly involved in normal “growth”, development, and reproduction. They maintain the physiological functions of the body and are known as central metabolites.
A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Secondary metabolites are considered to be the end products of primary metabolites because they are derived by the pathways in which the primary metabolites involve. Examples include antibiotics and pigments such as resins and terpenes etc.
Adapted from Wikipedia