Improvement of industrially important microbial strains by genome shuffling: Current status and future prospects

•Genome shuffling (GS) is a rapid technology for phenotypic improvement of strains.•GS recombines genomes of multi-parental strains through recursive protoplast fusion.•GS is a breakthrough in the expression of complex phenotypes in a single strain.•GS has been widely used for improving substrate uptake, yield and tolerance of strains. The growing demand for biotechnological products against limited metabolic capacity of industrially used microorganisms has led to an increased interest on strain-improvement over the last several decades, which aimed to enhance metabolite yield, substrate uptake and tolerance of the strains. Among a few techniques of strain-improvement, genome shuffling is the most recent and promising approach used for rapid strain-improvement that can yield a new strain by combining whole genomes of multi-parental microorganisms using the principles of protoplast fusion. Genome shuffling has brought a major breakthrough in the strain-improvement concept as it is found to be effective and reliable for expressing complex phenotypes. This review will discuss the technical aspects and applications of genome shuffling for various industrial strains to present its current status and recent progress. In the concluding remarks, a summary will be presented focusing on the major challenges and future outlooks of this technology.