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Nature is an attractive source of new therapeutic compounds as a tremendous chemical diversity is found in millions of species of plants, animals, marine and microorganisms. The exploitation of microorganisms to produce food ingredients has been going on since antiquity. These are being employed for the large scale production of a variety of bio-chemicals ranging from alcohol to antibiotics and processing of foods and feeds. Microorganisms have great potential as nutraceuticals and can be used to combat diseases like protein energy malnutrition (PEM), anaemia, diarrhoea, cancer, obesity, ulcerative colitis, Crohn's disease, irritable bowel syndrome and gluten therapy resistant celiac. They are also potential sources of antioxidants, natural colours, vitamins, enzymes, antibiotics and can be used as synbiotics. Microbes also have tremendous potential for the management of diseases like diabetes and can cure even allergies and alleviate stress problems.