Industrial biotechnology applies microorganisms in industrial fermentation processes to produce bioproducts such as food and feed ingredients, vitamins, enzymes, pharmaceutical ingredients, biomaterials and biofuels. Fermentation has been traditionally used for thousands of years to make products such as beer, wine, bread and cheese. Such traditional processes have gradually improved in an empirical manner based on knowledge built up over generations, trial-and-error approaches and selection of the physical characteristics of the fermentation products. Advances in sequencing technologies over the past twenty years accelerated research and development in industrial biotechnology in many ways: from speeding up microbial strain development to the discovery of novel bio-products and their metabolic routes, and from optimization of large-scale fermentations to rational protein engineering.
NGS sequencing technologies have become mainstream due to a dramatic reduction in costs and an increase in sequence read lengths and read quality and an essential tool for many novel applications beyond the assembly of single genomes: entire strain collections, lineages and even populations can be effectively sequenced and characterized at the whole-genome level. Currently, we experience the emergence of cost-effective long-read sequencing techniques. These enable faster and complete assembly of microbial genomes, relevant for studying genomic rearrangements, copy number variations, plasmids, aneu/polyploidy, repetitive regions, telomers, and centromers.
BaseClear has written an exciting review about topic together with principle investigators from DSM and DuPont, in which we provide a short history on sequencing and describe novel sequencing technologies and their applications in the field of industrial biotechnology. An update is given on microbial genome analysis with a focus on applications to strain development, enzyme discovery and microbial community analysis. The review was published by Oxford University press on April 23rd, 2018 in FEMS Microbiology Letters. For the abstract and access to the full article visit https://academic.oup.com/femsle/advance-article-abstract/doi/10.1093/femsle/fny103/4982775.