Rachel Rubinstein│Rapid identification of bacterial contamination in an industrial fermenter

Large-scale fermentation is a critical process in the successful deployment of Ginkgo Bioworks' products such as fragrances, flavors, and specialty enzymes. As such, rapid identification of contamination that occurs at this scale is imperative to ensuring successful deployment of the product as well as maintaining high quality and industry standards. Often, the identification of contaminants using traditional methods such as next-generation Illumina sequencing and NCBI BLAST is too time consuming, with results being returned much too late for tangible action. However, the Oxford Nanopore MinION along with the WIMP (What's in my pot) real-time analysis workflow allows for sequencing and rapid identification of potential bacterial and fungal contaminants in less than one day. Using extracted DNA from an offsite fermentation sample, we at Ginkgo Bioworks were able to identify a bacterial contaminant in approximately eight hours from receipt of sample. This quick identification allowed for significant decisions to be made about the fermentation run before it was finished, in turn protecting the product, saving thousands of dollars, and influencing decisions for the post-processing of the sample.

Flongle, GridION, MinION, MinIT, PromethION, and VolTRAX are currently for research use only.