@B2trail, it looks like in that study that you linked above is saying that the immune system reaction is to precursors to B2 that are produced by bacteria and fungi, NOT to vitamin B2 taken as a supplement, or even to Vitamin B2 in any form, actually. Maybe someone else can read it and verify that.
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That looks like it, doesn't it Violeta? Vitamin B2 supps are absorbed in the small intestine (in the jejenum) and absorbed there without a problem but food with the precursors in it that are synthesised into Riboflavin may trigger these T-Cells in the colon. Maybe this is why people who end up with their colon removed don't get vitamin deficient, except perhaps B12 and vit K which are absorbed at the ileum - junction of small and large intestine.
Meanwhile, been reading very interesting stuff about Riboflavin being produced by the bacteria b. subtilis in the colon. This is often in Kefir. I cannot take kefir although lots of IBD people can.