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.

Lauren L Long, The Jackson Laboratory
Karen L. Svenson, The Jackson Laboratory
Anthony J Mourino, The Jackson Laboratory
Michael Michaud, The Jackson Laboratory
James R Fahey, The Jackson Laboratory
Linda L Waterman, The Jackson Laboratory
Kathy L Vandegrift, The Jackson Laboratory
Mark D Adams, The Jackson Laboratory

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.


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.