Optimal Reference Strain selector
The choice of which bacterial strain should be used in laboratory experiments is a critical phase, as it is essential for both the reproducibility of the obtained data and the generalization of the results to the entire species. However, despite the common practice of employing strains historically defined as the first isolate of a species, the selection of a reference strain should take into consideration how it efficiently represents the ecological, genetic, and functional features of the whole species in a specific ecological niche.
Therefore, this study proposes the Optimal Reference Strain (ORS) selector tool, an innovative bioinformatic pipeline capable of evaluating how a strain represents its whole species from a genetic and functional perspective in addition to taking into account its ecological distribution in a particular ecological niche. Based on publicly available genomes, the strain that best fits all these three microbiological aspects is designed as ORS. Moreover, a user-friendly software called LAORS-selector was developed to allow researchers to screen their local library of bacterial strains for an optimal available alternative based on the reference ORS.
Five different bacterial species, i.e. Lacticaseibacillus paracasei, Lactobacillus delbrueckii, Streptococcus thermophilus, Bacteroides thetaiotaomicron, and Lactococcus lactis were tested in three different environments, dairy food, human gut and infant gut, to assess the performance of the bioinformatic pipeline.
