Reduced housing density improves statistical power of murine gut microbiota studies

The gut microbiome of humans and animals is critical to host health. Mice are used to investigate the microbiome and its influences; however, the predictive value of such studies is hindered by cage effects due to coprophagy. Our objectives were to evaluate the influence of cage density on the statistical power to detect treatment-dependent effects of a selective pressure on microbiome composition. C57BL/6 mice were separated into groups of 2 or 4 mice per cage and then assigned to groups receiving enrofloxacin, broad-spectrum antibiotics, or control. Fecal samples were collected at weeks 0, 1, and 4, along with contents of the jejunum and cecum. Bacterial DNA analysis examined microbiome richness, diversity, and variability within and between cages. Statistical analyses reveal that reduced housing density consistently results in comparable susceptibility to antibiotics, reduced cage effects, and increased statistical power to detect treatment-associated effects, justifying the practice of reduced housing density.