By Aaron Logan via Wikipedia

Very very interesting paper came out recent from some colleagues at UC Davis: PLOS ONE: Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice

Abstract: The mammalian intestine harbors a vast, complex and dynamic microbial population, which has profound effects on host nutrition, intestinal function and immune response, as well as influence on physiology outside of the alimentary tract. Imbalance in the composition of the dense colonizing bacterial population can increase susceptibility to various acute and chronic diseases. Valuable insights on the association of the microbiota with disease critically depend on investigation of mouse models. Like in humans, the microbial community in the mouse intestine is relatively stable and resilient, yet can be influenced by environmental factors. An often-overlooked variable in research is basic animal husbandry, which can potentially alter mouse physiology and experimental outcomes. This study examined the effects of common husbandry practices, including food and bedding alterations, as well as facility and cage changes, on the gut microbiota over a short time course of five days using three culture-independent techniques, quantitative PCR, terminal restriction fragment length polymorphism (TRFLP) and next generation sequencing (NGS). This study detected a substantial transient alteration in microbiota after the common practice of a short cross-campus facility transfer, but found no comparable alterations in microbiota within 5 days of switches in common laboratory food or bedding, or following an isolated cage change in mice acclimated to their housing facility. Our results highlight the importance of an acclimation period following even simple transfer of mice between campus facilities, and highlights that occult changes in microbiota should be considered when imposing husbandry variables on laboratory animals.

I personally think that we as a community are going to have to come to grips with the fact that the microbial communities in / on research organisms (of all kinds) may have a profound effect on experimental results.  This may explain many of the differences seen in experiments between facilities or over time within a facility.  In general, I think either controlling the microbes more carefully in lab experiments (e.g., using defined flora) or at least monitoring them is going to be very important to best interpret studies of plants and animals in the lab (or for that matter – in the field too).  Anyway -this paper is a tiny window into one of the ways that controlling for microbiomes may be important in lab studies.

Citation: Ma BW, Bokulich NA, Castillo PA, Kananurak A, Underwood MA, et al. (2012) Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice. PLoS ONE 7(10): e47416. doi:10.1371/journal.pone.0047416