Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry

Abstract

To meet the increase in demand for food and health-related products, there was a promptly growing trend in the food and pharmaceutical manufacturing industries in recent years. Microbial process plays main role in the manufacturing of food products for enhancement of taste, aroma, shelf- life and other probiotic applications. Microbes and microbial enzymes were used for manufacturing of pharmaceutical ingredients/products through biocatalysis and biotransformation and also for degradation of toxic chemical compounds in pharmaceutical industry waste. From a chosen environment, only small fraction of microbes can be cultured in the laboratory conditions, afore mentioned industries critically depends on these cultivable microbial communities to make use of microbes and microbial metabolites/enzymes. The microbial metagenomics, a culture independent technique has become a revolutionary tool for biotechnological applications, especially in food and pharmaceutical industries, which takes an advantage of identification of all the possible genomic information from chosen microbiome and to apply them for needs of an industry. In the recent years, metagenomics has been adopted to screen antimicrobial resistant genes, enzymes used for biotransformation of pharmaceutical ingredients and degradation of toxic chemicals from pharmaceutical industry wastes. In this book chapter, we discuss application of metagenomics on probiotics, detection and resistance developed by pathogens present in natural/ packed foods. Also we discuss various metagenome derived enzymes (nitrilases, β-glucosidase, lipases and esterases) applied for chiral synthesis of pharmaceutical ingredients and degradation of recalcitrant chemical compounds (nitroaromatic, Cyanide) from pharmaceutical industry and an overview on predicting novel antimicrobial resistance genes from uncultivable microbiome.