Effect size of technical and biological variation in the murine fecal microbiome

Background: The gut microbiome (GM) affects host growth and development, behavior, and disease susceptibility. Biomedical research investigating the mechanisms by which the GM influences host phenotypes often involves collecting single fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice and while efforts are made to minimize these sources of variation, biological variation at the cage or individual mouse level and technical variation from 16S rRNA library preparation exist and may influence microbiome outcomes. Here we employed a hierarchical fecal sampling strategy to 1) quantify the effect size of biological and technical variation and 2) provide practical guidance for the development of microbiome studies involving laboratory mice.