I am a modeler and the model that I ended up for FM/CFS/ME/IBS came out building “sub-models” that took collection of research findings and found a simple model that explains all of the research results.
Today, I chatted with a CFS person who has severe migraines and was wanting to try probiotics. She was wisely warned to delay starting them because some probiotics can give massive headaches — massive headaches on top of migraines will likely result in non-compliance to the approach.
Why would probiotics cause headaches? Probiotics produces antibiotics against other strains and species. These can kill off those bacteria — just like taking an antibiotic.
In this post I will describe the model that I use for the topics in the title. A model explains what is happening and thus can suggest things that could be tried.
The diagram below shows the model:
The root cause of all three symptoms is low oxygen delivered to the brain (or in the case of FM, to tissue).
- “Abnormal microcirculation and temperature in skin above tender points in patients with fibromyalgia.”
- “Fibromyalgia syndrome: overnight falls in arterial oxygen saturation. 
- “migraineurs are more vulnerable to Acute mountain sickness,”  … Acetazolamide is effective for both conditions.
Looking at what can cause low oxygen, hypoxemia, we actually have a significant list:
- Thick blood aka hyper-coagulation. Blood moves slower and thus the volume of blood (oxygen) that gets delivered is reduced.
- Low iron — hemoglobin in the blood is what transfers oxygen. It needs iron.
- Inflammation – swelling of tissue and blood vessels means that the volume of blood that gets thru is reduced. Instead of having a 1″ garden hose, you have a 1/4″ hose.
- Vascular constriction – this may be due to inflammation OR due to other causes.
- There are a few other causes:
- Living at altitude (i.e. one mile or 1.5 kilometer above sea level)
- Mild carbon monoxide poisoning, as well as a variety of other chemicals
A few diagnostic points:
- Oxygen saturation in the blood may be normal (except for iron deficiency). The problem is with oxygen delivery and not the oxygen level in the blood. It can also be localized to specific spots (the brain or tender spots in FM) This is why SPECT brain scans for CFS that show hypoperfusion (low oxygen delivery to brain tissue) is important. [Post with references to studies]
- “SPECT was performed on 5 patients with classical migraine and 18 patients with migraine accompagnée. At the time of investigation, all patients were symptom-free. Cerebral blood flow was decreased in all patients with migraine accompagnée, and often corresponded to the site of headache as well as to the topography of transient neurological symptoms. This reduction was most obvious in a patient with persisting neurological symptoms. Most patients with classical migraine, however, did not show any alteration of cerebral perfusion. It appears that migraine–and in particular migraine accompagnée–is characterized by a permanent alteration not only of cerebral blood flow but also of neuronal activity. Migraine attacks may occur in connection with exacerbations of preexisting metabolic alterations.” 
Our model above has multiple possible causes — someone with migraines can attempt to address one cause at a time to see if it reduces the severity of the migraine. My suggestions (to be discussed with a knowledgeable MD always) are:
- Hypercoagulation: also see this post also:
- Grape Seed Extract (as alternative to aspirin)
- Alpha Lipoic Acid
- Turmeric (with some black pepper mixed in)
- Low Iron – a good PubMed article is here. It can be associated with H. Pylori and Giardiasis infections.
- Iron supplements
- Inflammation – there are many herbs and supplements that are anti-inflammatory. Unfortunately there are no studies comparing their effectiveness in human patients.
- My own preferences are the gums such as boswellia, mastic and myrrh. Many of these can be chewed in the mouth.
- Vascular constriction
- Regular flushing niacin. This is also the cheapest niacin. You do NOT want no-flush niacin, nor time release. You want to turn red as a lobster!
- “We have found that when red blood cells are exposed to abnormally low oxygen for long periods, they become depleted of an essential substance that they normally release to relax blood vessels in the lung,” 
If any of the above does reduce the severity of migraines, then it points in a direction for further treatment. If you suffer from migraines, then a herx — dumping of toxins into the body will likely make the migraine very much worst.
Again, this is a model to provide a framework for experiments to deduce the cause. I believe strongly is systematic and progressive experiments. Almost all of the items above can be associated with microbiome shifts – which leads back to my model.