Give me good digestion, Lord, And also something to digest; but where and how that something comes I leave to Thee, who knoweth best.                                                      Mary Webb

The major parts of the digestive system:

7 Autoimmune Disorders that Affect the Digestive Tract

Systemic Lupus Erythematosus The digestive system is responsible for extracting nutrients from the food you eat and ridding your body of waste products. Lupus can affect the entire digestive system, beginning with the mouth. People with lupus are prone to lesions on the inside of the cheeks, the lower lip, or the roof of the mouth. Certain medications prescribed to treat lupus can increase your risk for oral lesions. When the esophagus is inflamed, stomach acid can be forced back into the esophagus (acid reflux), causing heartburn and gas. It can also make swallowing difficult (dysphagia).

Some people with lupus take nonsteroidal anti-inflammatory drugs (NSAIDs). This can increase risk of bleeding ulcers in the stomach lining or where the stomach meets the bile duct, pancreatic duct, and small intestine (duodenum). Helicobacter pylori bacterium also can cause ulcers, a common problem for people with lupus.

Inflammation can cause fluids to build up in the lining on the inside of the abdomen (peritoneum). Symptoms include abdominal pain, nausea, fever, and constipation. Lupus patients are at increased risk for inflammation of the pancreas (pancreatitis). Use of diuretics, immunosuppressants, or corticosteroids increases this risk.

Digestive symptoms include constipation, diarrhea, and nausea. These problems can be aggravated by the use of corticosteroids or NSAIDs. Ulcers that form in the colon and rectum may cause bloody diarrhea.

Polyarteritis Nodosa PAN is a multisystem disease that may present with fever, sweats, weight loss, and severe muscle and joint aches/pains. The disease can affect nearly any site in the body, but it has a predisposition for organs such as the skin, kidney, nerves, and gastrointestinal tract.

Celiac disease Affects about 1 person in 200, occurs when a person becomes intolerant to gluten, a protein found in wheat, rye, and barley products. In people with celiac disease, the ingestion of gluten causes the immune system to attack villi, the tiny structures lining the small intestine.

Crohn’s Disease This condition occurs when the immune system attacks parts of the digestive tract, causing inflammation, swelling, and even scarring.

Ulcerative Colitis the “cousin” of Crohn’s disease, and explains that it happens when the immune system attacks the lining of the rectum and colon, causing ulcers. The ulcers can then bleed and produce pus.

Autoimmune Hepatitis Unlike most types of hepatitis, which are caused by viruses, autoimmune hepatitis happens when the body’s immune system attacks liver cells, causing inflammation.

Diabetes The partial paralysis of the stomach, which causes delayed gastric emptying. This delayed emptying is most often associated with poorly controlled diabetes.

Source: 

• http://www.resources.lupus.org/entry/antiphospholipid-antibody-syndrome
• http://www.myasthenia.org/
• https://www.betterhealth.vic.gov.au/health/conditionsandtreatments/autoimmune-disorders
• http://www.colgate.com/en/us/oc/oral-health/conditions/immune-disorders/article/autoimmune-diseases-effect-on-oral-health-0114