**Abstract**

Some microorganisms (MOs) such as bacteria, fungi and aquatic creatures synthesize bioactive secondary metabolites synthesis that known as natural products. A series of landmark metabolomics studies by using mass spectrometry (MS) or nuclear magnetic resonance (NMR) analysis to identify potentially important microbial metabolites that derive from the intestine microbes. Vital roles for numerous microbial metabolic pathways in host physiology had been long established, such as in the synthesis of vitamin K and the synthesis of water-soluble B vitamins including biotin, folates, nicotinic acid, pyridoxine, riboflavin, cobalamin and panthotenic acid, the degradation of nutritional oxalates, and amendment of bile salts. These metabolites have biological and medical activities. The medical activities including antimicrobial, immunosuppressive, anticancer, and anti-inflammatory, antibiotic, antitumor, antioxidant activities, etc. Also biological activities derive from metabolites microbial transformation have effects on physiological processes such as gut and immune homeostasis, energy metabolism, vascular function, and neurological behavior such as short-chain fatty acids, trimethylamine N-oxide, tryptophan and tyrosine derivatives, and oxidized fatty acids. Using recombinant DNA technology synthesize a wide array of biopharmaceutical products, such as recombinant proteins, offering significant advances in treating a broad spectrum of medical. Such interventions will require modulating either bacterial species or the bacterial biosynthetic enzymes required to synthesis these metabolites.

**Keywords:** microorganism, metabolism, biosynthesis, metabolite, biological activities
