In experiments designed to test the effect of diet/drugs etc. on the mouse microbiome, one could assume that the initial microbial content of each mouse of one commercially-sourced set of mice is uniform. But how valid is this assumption? Presumably the mice and their parents were all grown in identical conditions, but to what extent does this guarantee similarity in microbial colonization and maintenance? Does anyone have any data to address this?
Some of the studies done so far with mice suggest that this assumption may be valid. Although, each individual mouse in a strain might have slight differences, overall, a strain of mice would be expected to have a similar microbiome. An interesting study that might help is the one done by Turnbaugh and colleagues where they looked at the distal gut microbiomes of ob/ob, ob/+, and +/+ littermates.
Although papers particularly describes mouse with some genetic modification, or background and its correlation with microbiota. In near future, we need to address the issue of microbiota composition in all commercially available mouse strains. Genetic backgound has significant contribution to microbiota as such.
The microbiome varies from source to source, in fact it can vary from housing facilities on the same site.
Unless they are co-housed the composition can vary a lot.
even if they are co-housed there are slight variations as pointed out.
My concern is that there may be minor differences in microbiota composition at the outset of a dietary/drug intervention, but that these differences may become amplified with the application of the selective pressure. So that two "identical" mice may, over the course of the treatment, show a quite different evolution of their microbial populations.
as long as the mice are derived from the single line from a same facility, and co-housed. The differences in microflora should not be profoundly different as a result of diet?drug intervention (diet would effect more though).
At the end as long as the experimental design has proper controls in pace you should be able to see statistically significant changes if any, the background noise should in principle not be amplified to distort the actual pattern.
Good luck.
There are substantial housing effects: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047416
This suggests that one should be cautious in presuming upon uniformity among batches of mice from the same strain and same commercial source.
It is also a question of which body site you are considering; it is almost axiomatic that the gut flora is more stable and more consistent than the skin flora, for example. It seems consistent with experiences at the NIH and elsewhere; that it is more difficult to create consistent experiments over time, even in the same facility with the same source of animals, for the skin or oral microbiomes than for the gut.
It depends in part on the study (as stated by other answers). It depends upon your facility (as well as the source facility). There will be variations between mice from the same facility if they were taken from different housing "barriers". So you should speak with the vender from which you want to order and make sure that the mice come from the same house (barrier).
In addition to the PLOS study link, you might also want to look at these two studies which address the problem in which you are interested:
Hildebrand, F. et al, Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biology 14.
Campbell, J H, et al, Host genetic and environmental effects on mouse intestinal microbiota, The ISME Journal (2012) 6, 2033–2044; doi:10.1038/ismej.2012.54; published online 14 June 2012
I have seen some cage effects in my own research as well.
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