Hashimoto's is an autoimmune condition often due to leaky gut. Low or high cortisol can cause gut infections and therefore the stomach may not be able to produce enough acid to digest our food. High cortisol shuts down the valves in the gut. If the food doesn't move through the small intestine well, you end up with SIBO. During sleep the migrating motor complex performs a cleansing process but it can't if you have SIBO. This is where bacteria back up and overgrow, hence the term, small intestine bacterial overgrowth.
Breath testing for hydrogen and methane may reveal SIBO which tells them what treatment you need. Others do antibody testing.
This is probably not a do it yourself project although there are things you can do. If you find someone who can treat you they may use these types of therapeutics.
Rifaximin is the antibiotic which stays in the small intestine and does not become resistant but sold for $800. This may kill the bacteria but not go into the bloodstream and cause resistance. It doesn't work for everyone.
You can go on the Elemental Diet which is the nourishment given through feeding tubes and tastes terrible because of the amino acids. The object is to get food through the stomach quickly so any bacteria cannot keep replicating. Usual a 2-week treatment.
A biofilm destroyer like Interfase by Klaire seemed popular. To heal nerves in the digestive tract supplements like acetyl l carnitine and water extracted Lion's Mane and alpha lipoic acid. Also fish oil as an anti inflammatory.
"When the lining of the gut is impaired a variety of genetic and acquired factors can disrupt the small intestine brush border, which may result in low activity of brush border enzymes. SIBB-Zymes™ supplies a blend of enzymes normally found in the small intestinal brush border that are critical for the final steps of carbohydrate and protein digestion."
Unfortunately SIBO can coexist with Hashimoto's which makes treating one without the other incomplete and why IBS,, Crohn's and anemia symptoms remain.