We learned of my son's gluten intolerance after he had unrelenting nausea following treatment for Lyme (he had the classic rash). Now, years later, I think he had gluten intolerance (or possibly CD) for a very long time (i.e. pre-Lyme) as he had chronic sinus infections and asthma as a young child. So I doubt Lyme triggered the intolerance but it seems to have triggered more classic GI symptoms which made us learn of the intolerance.
I am sure that is as clear as mud
--Judy