We had eliminated the use of antibiotics in our lab, but after a recent contamination, our new lab manager recommended we start using antibiotics for some of our more long term cultures. Do you think this is a good idea?

Answer

Antibiotics are extensively used preventive measures to avoid bacterial contamination within in vitro culture. Studies, however, have shown that antibiotics may induce changes in cell gene expression and regulation. For this reason, it is important to understand, test, and evaluate the effect of antibiotics within the specific cell culture outcome. You may also want to evaluate the use of antibiotics if you are doing any compound testing as drugs may interact with antibiotics in unknown ways.

An opportunity for a first testing and evaluation of the effect of antibiotics on the cell gene expression is offered by techniques such as RNA-seq and ChIP-seq. We suggest therefore to evaluate on a case by case basis the use of the antibiotics in short and long term cell cultures. The reference below may offer some guidance on this topic:

Ryu, A.H., Eckalbar, W.L., Kreimer, A. et al. Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Sci Rep 7, 7533 (2017).