No, it is considered to be one theory which has not been proved conclusively
you are correct, my apologies for being unclear. To restate, it is NOT been proven beyond all reasonable doubt or yet to a largest degree of probable certainty. But there is lots of evidence which supports the idea that missing bacteria which regulate inflammation, could be the prime cause of all features of IBD, so there is good support for this idea being founded in reality.
It is a FACT that IBD patients have reduced diversity in bacteria known to be beneficial and regulate inflammation, it is a "theory" that is not yet proven, that replacing these missing bacteria can reverse all features of the disease. But supporting evidence does exist that suggests this is the case, and this would be the current human trials of fecal transplants.
I would also like to add, some things are very difficult, but not impossible to be proven conclusively. We then resort to, the most probable explanation given all the current evidence that exists. Or we generate as much evidence(data) that is possible, then choose the most probable explanation. lets just say things are looking really good for the theory of missing commensal bacteria so far, it's a highly probable and worthy explanation. But we do need lots more evidence to prove it with a higher degree of certainty.