Shared and distinctive features of the gut microbiome of C57BL/6 mice from different vendors and production sites, and in response to a new vivarium.

Document Type


Publication Date


Publication Title

Lab animal


JGM, JMG, Sacramento, Animals, Bacteria, Feces, Gastrointestinal Microbiome, Mice, Mice, Inbred C57BL, Reproducibility of Results

JAX Source

Lab Anim (NY) 2021 Jul; 50(7):185-195





First Page


Last Page









Animal models play a critical role in establishing causal relationships between gut microbiota and disease. The laboratory mouse is widely used to study the role of microbes in various disorders; however, differences between mouse vendors, genetic lineages and husbandry protocols have been shown to contribute to variation in phenotypes and to non-reproducibility of experimental results. We sought to understand how gut microbiome profiles of mice vary by vendor, vendor production facility and health status upon receipt into an academic facility and how they change over 12 weeks in the new environment. C57BL/6 mice were sourced from two different production sites for each of three different vendors. Mice were shipped to an academic research vivarium, and fresh-catch stool samples were collected from mice immediately from the shipping box upon receipt, and again after 2, 6 and 12 weeks in the new facility. Substantial variation in bacterial proportional abundance was observed among mice from each vendor at the time of receipt, but shared microbes accounted for most sequence reads. Vendor-specific microbes were generally of low abundance. Microbial profiles of mice from all vendors exhibited shifts over time, highlighting the importance of environmental conditions on microbial dynamics. Our results emphasize the need for continued efforts to account for sources of variation in animal models and understand how they contribute to experimental reproducibility.


We thank Tina Bishop, Paul Phillips and Justin Brouty of JAX for skillful and coordinated sample collection. We gratefully acknowledge Joseph S. Brown, Daniel Phillips and Purva Vats of the Microbial Genomics Scientific Service at JAX for expert assistance with DNA extraction and library preparation and the Genome Technologies Scientific Service for sequencing. We thank Benjamin Leopold and Sai Lek of the Microbial Genomic Scientific Service for processing and quality control of sequencing data. We acknowledge Adam SanMiguel of JAX for his insight and input on the data and organization of this manuscript. All funding was provided by JAX.

Please contact the Joan Staats Library for information regarding this document.