All of us, including dogs, have beneficial flora in our digestive tracts. Think lactobacteria, for example. There's also opportunistic flora (think clostridia to start) residing in the gut, and plenty of them. In a healthy dog, this opportunistic flora is kept in check by the beneficial bacteria. Lastly, there are microbes that are swallowed via food, eating dirt, grass, etc. It's the good-guy bacteria that protects the gut and keeps things under control. Gut epithelium (thin tissue that for the purpose of this discussion, forms the lining of the alimentary tract) gets at least half (some estimate it to be about 60%) of its energy from bacterial activity. So, when gut flora is damaged, lack of nourishment occurs and can damage the digestive wall. How? We need to look a bit closer at the gut lining in order to answer that.
Villi are finger-like structures. Cells called enterocytes are also called absorptive cells because that's exactly what they do - absorb water and nutrients. These cells coat the villi. If you spread your fingers, you'll see the valley or crypts between them, so imagine that your fingers are villi and the crypt is where enterocytes are born. As they grow, they travel towards the top of the finger/villi and are doing their jobs very well, but then they're shed when they reach the top. So, a constant supply of enterocytes is produced and this is how the epithelium of intestines is renewed and kept healthy.
Experiments on the sterilized gut of animals shows that when beneficial bacteria is removed, cell renewal goes haywire. Degenerated villi translates to an inability to digest food and absorb nutrients properly which leads to nutritional deficiencies.
The immune system needs proper nutrition and it can't function well if the very things (lymphocytes to protect mucus membranes by destroying bacteria, fungi, etc., macrophages to swallow the debris left by cells that gather round invading foreign and dangerous substances) that are supposed to keep the bacterial population in check end up going haywire. The gut flora is the foundation of a healthy immune system. #healthygut