New publication: Minimizing caging effects in murine lung microbiome studies
Jezreel Pantaleón García
For several years, Robert Dickson has been working with medical student Jezreel Pantaleón García and his mentor Scott Evans (both at MD Anderson) to study the effects of immune modulation on lung microbiota. Last year, this team published the observation that augmenting lung immune tone (via an inhaled agonist of TLR2, TLR6, and TLR9) has no appreciable effect on the lung bacteria of healthy mice. This study suggests that the known correlation between lung microbiota and lung immunity is more likely due to the host responding to dynamic changes in lung microbiota (rather than vice versa).
As a follow-up to that work, and as a service to all of us who study respiratory microbiota in mice, Jezreel led the way in a newly published letter: “Minimizing caging effects in murine lung microbiome studies.” We know that mice that are cohoused together converge in their respiratory and gut microbiota, which can result in false clustering due to “batch effects” from cohousing. If you house your mice by intervention, you’ll inevitably find differences in their microbiota, but you won’t know if it’s due to your intervention or the fact that cohoused mice cluster together.
To tackle this problem, Jezreel proposes a thoughtful and coherent solution: stratified random cohousing. “In stratified random strategies, originally cohoused mice are randomly distributed for caging with mice from all experimental groups. Then, additional stratified randomization to new cages is performed following each intervention.”
Failure to consider batch effects due to cohousing is a recurring limitation of murine microbiome studies. We hope this simple (and free) strategy will be of use to the field.
