Detection of Lactococcus lactis contamination in standard and ethanol-washed casein used in mouse diets for microbiome studies

Casein is a common source of dietary protein in defined diets used to investigate the effect of diet on the gut microbiota. Previously it has been shown that the metagenomes of mice fed with a diet containing casein were contaminated with DNA from the bacterium Lactococcus lactis and that washing the casein with ethanol removed this contamination (https://doi.org/10.1016/j.chom.2019.06.013). We have identified the same phenomenon when identifying proteins from mouse diets with casein However, in contrast to DNA sequencing we did not see a reduction in L. lactis contamination in proteomes. Two lots each of standard casein and ethanol-washed casein were analyzed using proteomics.