Do a search for 'ammonia breath' and you will see the causes.
The fecal odor is caused by proteolytic bacteria in the lower intestine metabolyzing proteins. In a healthy person much of the food proteins are broken down before the large intestine and only a small amount is available to the bacteria to produce the bad odor of feces. People can have more bad smelling feces if they eat a high protein diet.
When you were only eating bread you overloaded yourself with gluten and carbohydrates. Look at the Gluten Syndrome website, it may be helpful. To help get your body back in balance look at the acid forming and alkaline forming diets online. (Also called acid ash and alkaline foods)
The high concentration of hydrochloric acid kills almost all organisms eaten in food and the upper intestinal tract has no bacteria unless there is a problem with digestion. Although probiotics and taking other supplements and herbs may help you many of us have had better results if we follow a program, such as those featured on this forum, to improve digestive health.