Fig. 1. Version control and barcoding of engineered cells.

a Graphical description of CellRepo. A repository contains all the information of the project. Several ideas can be tested using the branching mechanism. The users can decide what to document at each stage in the project through commits. At user-defined steps, a physical DNA barcode can be generated to be inserted in the genome of the strain. b Workflow for barcoding any microorganism or strain of interest. The roadmap can be applied to basically any biological system amenable to genomic insertions of short DNA sequences. Once a specific barcode is committed, it is synthesized and delivered to a stable region of the genome of the target organism. The different approaches followed in this study to select appropriate barcoding locations are described in the Supplementary Material. This can be made with a whole collection of genetic tools available to this end in a fashion dependent or independent on homologous recombination. As the resulting insertion is expected not to generate a conspicuous phenotype, proper delivery of the barcode to the expected genomic site is secured and selected with CRISPR/Cas9 technology or via the more traditional antibiotic resistance or auxotrophic marker approach depending on the laboratory carrying out the barcoding.