Look into sourdough, that's really good for the gut, and it is really good once you get into it.
Avoid wheat if it is not organic. For the past 2 decades, they have been using glyphosate to kill ("conventional") wheat plants before harvesting, and i think that may be contributing to the correlated rise in celiac disease. best to avoid that stuff.
also try experimenting with adding alternative grains to the flour. Maybe try sorghum grain, millet, amaranth, quinoa, oats, or treenuts.
maybe try sprouting some of them first.
careful sprouting US grown treenuts as the usda requires even "raw" treenuts to be pasteurized, so you either have to get them from a farmer, a co-op, your own tree, or europe. (Thanks, big brother) ::rolls eyes::