Correcting the level of thyroid in the body is one of the most effective means of treating fibromyalgia. Dr. John Lowe estimates that about 90% of the people with fibromyalgia have a problem with low thyroid. About 10% of the patients have primary hypothyroidism (high TSH), about 34% have thyroid hormone resistance (thyroid isn’t getting into the cells) and about 45% have central hypothyroidism (poor response to thyrotropin releasing hormone, TRH).
Why do almost half of the people with fibromyalgia have central hypothyroidism? There are a few well-known possibilities.
1. Lack of Sleep. Simply not getting enough sleep will cause central hypothyroidism. 
2. Chronic Pain or Stress. This elevates free serotonin in the brain, and induces central hypothyroidism. 
3. Infection. Immune system cytokines IL-1, IL-6 and TNF, when present in the brain, can cause central hypothyroidism.  Elevation of these cytokines could be caused by an infection in the brain.  Or the infection could be elsewhere in the body, and the cytokines could cross the blood-brain barrier.
4. Bacteria Lipopolysaccharide (LPS). A toxin called (LPS) from gram-negative intestinal bacteria can cause central hypothyroidism. 
If your doctor relies only on the usual thyroid blood tests, he may miss your hypothyroidism. You need a doctor who will investigate this problem thoroughly and perhaps authorize a trial of thyroid hormone based on your symptoms. I suggest that you seek an alternative practitioner who is familiar with fibromyalgia.
What type of thyroid treatment is needed? People with fibromyalgia often (not always) need a special type of thyroid replacement therapy. Dr. Lowe’s patients are sometimes placed on a lot of T3 thyroid combined with a nominal amount of T4 thyroid or a nominal amount of desiccated thyroid. The patients are slowly worked up to relatively high doses of T3 thyroid. Effective dosages of T3 range from 75 μg to 150 μg, whereas normal replacement dosages are from 25 to 75 μg. This much thyroid can be TSHsuppressive. Yet the amount of thyroid is kept below that which would cause thyrotoxicity and muscle weakness. (Both too much and too little thyroid will cause muscle weakness.) This is Dr. Lowe’s website: http://www.DrLowe.com Dr. Lowe is the author of the book Speeding Up to Normal: Metabolic Solutions to Fibromyalgia. Besides using thyroid to improve metabolism, he advocates nutrients, diet modification, exercise and the elimination of narcotic pain medications. These also affect metabolism.
Please be aware that everyone will not need the same thyroid treatment. The ratio of T4 to T3 thyroid must be adjusted for each patient. Also, don’t forget to ask your doctor about trying a desiccated thyroid supplement like Armour, Westhroid or Bio-throid. I read where one lady and her sister were both suffering from fibromyalgia. They didn’t recover until they tried a combination of desiccated thyroid and T3. A combination of just T4 and T3 didn’t work for either of them.
LPS From Viral Infected E. Coli
Theophil Hey, MD and colleagues found that 80% or more of those with fibromyalgia are harboring a virus. It isn’t a human virus, but it is a virus that infects the E coli bacteria that is living in their intestines. His testing showed that only 12% of the people without fibromyalgia had this infection. When a group of fibromyalgia patients were tested during a flair of symptoms, 62 out of 63, or 98% tested positive for this problem.
When the infected E coli die, they burst and produce fragments of the E coli shell. Gramnegative bacteria, like E. coli, have a layer in their shell of a fatty substance called lipopolysaccharide (LPS). LPS is highly toxic to humans.
To eliminate the E coli, avoid undercooked food that may contain E coli and perhaps take supplements to inhibit viruses. These are some herbs that can help rid the body of E. coli: oregano, peppermint, grapefruit seed extract, bitter melon (Momordica charantica), Ophiopogon tuber, oak gall, Pau d’Arco, St. John’s Wort, garlic, Cassia obtusifolia (coffeeweed) and Cinnamonum cassia (a common source of the spice cinnamon). Carica papaya fruits and manuka honey also inhibit E. coli. Colloidal Silver will kill E. coli. A strain of probiotic bacteria called TH10 will lower the E. coli population too. (TH10 is in the LB12 probiotic made by Osumex.) Be careful with any herb or substance. Learn about it before using it. For instance, bitter melon may induce infertility in males or abortion in females.
Another consideration. When rats are exposed to LPS, they are able to survive the onslaught with much less damage to their intestines and organs if they are on a diet that excludes polyunsaturated omega-3 and omega-6 oils. Much fewer deaths result.  This is another reason to avoid corn, soy, safflower, canola, peanut, flax and cottonseed oils.