Likely a chronic overgrowth of pathogens (eg E. Coli), enabled by the disturbance in the microbiome via antibiotics, that got reduced by the phages. Pathogens (or imbalances) in the internal biomes can start autoimmune processes: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300652/
There has been absolutely no legitimate, scientifically proven study that can completely eliminate confounding factors and prove that gluten alone is the source of all these people's problems.
You'd think this community alone would be able to accept that until such a study is done you simply cannot draw such a dramatic conclusion.
Wrecking your microbiome with antibiotic overuse, and alcohol, is where my money is at. Every single person I know who swears gluten destroys their gut, also has a past of abusing antibiotics and or alcohol and utterly destroying their natural microbiome.
