Elimination of pathogens by laboratory rodent commercial vendors has substantially improved standardized conditions as well as laboratory animal welfare. However, pathogens are also important for basic activation and functioning of the immune system with consequential influences on the symbiotic bacteria composition in the individual microbiota. One of the reasons for failures of translating results from preclinical research to the clinical phase in some studies could be due to unintentional selection processes. Some recommendations are provided to increase researchers' awareness on this point, together with a practical checklist to optimize information from microbiota knowledge.