Celiac sprue is an auto immune disease. It has nothing to do with gut flora.
Except that autoimmune diseases, such as arthritis, Crohn’s, even psoriasis are very interactive with the gut flora and immune system. Celiac almost certainly.
For instance, one common drug used to treat some autoimmune diseases is a sulfa drug. They do not know its exact mechanism, other than it affects the gut bacteria.
http://www.ncbi.nlm.nih.gov/pubmed/16393236
Gut microflora associated characteristics in children with celiac disease.
http://www.celiac.com/articles/21685/1/More-Evidence-Links-Gut-Bacteria-to-Celiac-Disease/Page1.html
More Evidence Links Gut Bacteria to Celiac Disease