My lab has been working on gut microbiota using mouse models for quite a few years and I read quite some gut microbiota papers using mono-association of germ-free mice with certain bacteria isolates. I've been wondering what's the most appropriate bacteria controls for these kind of causality experiments and probiotics experiments to prove their beneficial effects in mouse models. Some papers only use vehicle control and I don't think it is enough in animal studies. Some use common gut flora bacteria such as E. coli as controls. Say if one wants to prove that L. bulgaricus is beneficial (at species level) , isn't the most appropriate control another bacteria (in the same genus) which is already known to have no effects? What if we find a novel bacteria species under a very new genus and not much information is known?
Some experiments are more complicated. Say people use probiotics cocktail that contains a few different bacteria (some could belong to different genera). What kind of bacterial control is the most convincing? I asked a probiotics company once in a conference and they only told me that they have came up a group of control bacteria that the company knew that they have no effects.
Isn't this kind of the chicken or the egg thing ? What did they compare these "control bacteria" to so that they could say that these bacteria have no effects in the first beginning ?
Am I thinking too much? What's your opinions?
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