Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies

L. lactis contamination in mouse gut microbiomes from casein based diets has been previously reported in DNA based metagenomics studies. In this study, we wanted to determine if there was bacterial contamination in the DNA of other common dietary protein sources used in mouse studies. We also wanted to determine if this bacterial contamination extended to metaproteomes. For this study we shotgun sequenced three purified casein and three purified soy protein sources to quantify how much of the protein source was bacterial. We also shotgun sequenced 3 fecal samples from mice and mice with a conventional microbiota both fed a casein protein based diet, as well as 3 fecal samples from each germ-free mice and mice with a conventional microbiota fed a soy based diet. Finally, we included one pure culture control from the bacterium T. mobilis in order to control for within Illumina lane cross contamination due to index hopping. Companion metaproteomes where submitted to pride: PXD041586 and PXD040649.