The only thing IMHO that can be an issue is just eating too much carbs (because it's so damn good) or sensitivity to gluten. However, it is known that sourdough/pain-au-levain is more digestible than regular bread for folks with gluten intolerance. Sourdough is decidedly more acidic (that's why it's called "sour") than dough which has been risen with commercial yeast. This acid partially breaks down the gluten in the dough during fermentation.
People have been eating naturally fermented bread since the dawn of civilization. The bacteria and yeast in properly fermenting dough do an excellent job of keeping any nasty stuff out.