There is an unfortunate general ignorance outside of genetics of what these mice really are and how to think about them. Institutions that have their own colonies with have qualified and knowledgeable people as maintainers, but they aren’t writing the papers. In a nutshell, they are the renewable testing grounds of a genome we know and control, making them a valid background for a) interventions in that genome and b) interventions among genetically identical cohorts.

Black-6 descendant strains (like B6J, which this study likely used) are not intended to ask questions of diet or drug effect and extrapolate across non-identical colonies or other species, but rather to have a controlled genetic background against which to test the effect of interventions and/or genes which we add or subtract, ie knockouts.

The way that Jackson maintains B6J is by periodically reintroducing frozen gametes from the original “Adam and Eve” B6J pair, and using them to refresh the source colony based on the reference genome, which for B6J is called GRCm38.p6.

However, the inevitable fact is that as soon as you take mice away from that colony and start breeding them, they immediately start diverging from the source genome, accumulating mutations which have the potential to alter their physiology and bias study results. This is why it’s so critically important that you always denote the exact substrain being used, but also more broadly that we take a huge grain of salt when we see some change in outcomes in a mouse population for which we don’t really have an precise background rate of that outcome. It’s not exactly the cohort that’s the problem, since if you’re using two groups of mice that are presumably nearly genetically identical to each other the deviation is null, but rather the comparison between studies.

eg, study 1 used “Black-6” mice and found diet A had 1.5 OR for some outcome compared to diet B, study 2 used “Black-6” mice and found diet A had 0.9 OR for the same outcome compared to diet B, but if we have no idea what the actual genetic differences between those two colonies were, the comparison is kinda fucked. We don’t know their distance from the reference genome, if the distance from each is symmetrical, if both have had cryorecovery done and at what points, etc. These mice are under intense selection pressure to breed large litters and survive a very unnatural laboratory environment, and we know there are substantial genetic differences accumulating among them, both from those environmental stimuli and from drift. And then you start bundling these things into meta-analysis and you have this growing source of invisible confounding.