Protein—some proteins are difficult for humans to digest such as the gliadin proteins that make up the gluten molecules in wheat products. These are also the proteins that cause an immune response in people with Celiac Disease. Research is showing that the fungal and bacterial microbes in sourdough degrade gluten into smaller peptides, including these gliadin proteins, decreasing toxicity to people with Celiac Disease and perhaps decreasing exposure to the general public. This research is still quite young.
Phytic acid—the decrease in pH that occurs with sourdough ferment (due to production of lactic acid by bacteria in the sourdough) will activate wheat phytase enzymes (enzymes that break bonds in the phytic acid molecules and make micronutrients available to the human body) in the dough. I have seen reports of 70% reduction in phytic acid with a 4-hour ferment at pH of 5.2-5.6.
Glycemic index—sourdough fermentation has been shown to decrease the glycemic load of sourdough bread. The exact reason why, is not confirmed, but is likely to be due to a variety of reasons. One reason is again the production of lactic acid and other organic acids that decrease starch digestion in bread, making it take longer in our bodies to digest and therefore decreasing the glycemic index.
This valuable information comes from our friend, Bethany Econopouly, a doctorate student with Washington State University. She is studying wheat breeding and its affects on nutrition and baking quality.