Histamine is one of the things i plan to ask my functional medicine doc about on my next appointment and see if she can order a blood test for. I had a plasma amino acid analysis done two years ago that lists ammonia levels as normal and urea levels as yellow range low if that means anything.

The body has to clear ammonia and it depends upon what you eat and when so the result might not reveal much about what is happening. I would not take it as accurate. Urea is naturally produced in the body and present in many fluids so that also would not mean much.

A digestive permeability test aka Leaky Gut test might be worth having if you can get one done. Chances are that that will show an above normal level of digestive permeability. The simplest test is lactulose/mannitol and a urine collection and testing.

also, since i posted this thread ive set up an appointment with an allergist, any ideas on specific things to ask the allergist about would be welcome.

Allergies are a difficult thing to test for unfortunately. It depends largely on how a person reacts to those allergens. People react with different types of antibodies. Some, including me react strongly with IgE antibodies, the primary allergic antibody. Other people react to food which is incorrectly absorbed into the bloodstream before it is completely digested with some of the other antibodies. I cannot predict which you would react with. Allergies are primarily IgE and the runny nose could be an IgE antibody reaction.

The most basic test is IgE skin prick test using allergens such as foods, house dust mite, pollens etc. If the skin reacts with a red weal then the reaction to the allergen is positive. It's not the most accurate of tests.

There are more advanced blood tests which can test a range of antibodies. I do not know the test names, you would need to research that.

i have some cladosporium mold in my house that i can't get rid of but im not sure that it's related, been considering staying somewhere else for a few weeks to see what comes of it.

You could be reacting to the mold, it's certainly a possibility.

How do you know it is that specific mold? A guess? Have you had it tested?

Why have you been unable to eliminate it? Did you try spraying with a fine borax mist? Borax is cheap and works on most types of mold and fungi. Did you try colloidal silver? Another one that could be tried is potassium iodide. This is clear and not brown staining like lugols iodine.

what you say about the pump inhibitors interests me, at one time i had really bad chronic constipation and when i started on betaine hcl and digestive enzymes my bowels returned entirely to normal, i mean it could have been just the enzymes but I doubt it since there was no stomach burning from the hcl, so I agree, the stomach is definitely important to health.

Constipation is common with CFS. Choline is in short supply to produce acetylcholine which is used to stimulate the bowel. The liver uses up the supply of choline leaving not enough to stimulate the bowel. That is my thoughts and ideas on the matter. I cannot say it is 100% correct but it certainly fits. I have supplemented with lecithin which improved my bowel function. Lecithin is a source of choline.

I am not convinced that supplementing HCl works, certainly not when a urease bacterial infection is present. In such cases it is more likely to make things worse by producing even more ammonia to neutralise the acid.

A burning is no indication of sufficient stomach acid. It's a false idea IMO. I managed to reach a state of stomach burning with about 12 HCl capsules but wind and burping followed and the burning subsided. Around 12 more capsules reached a burning, followed by more burping/wind and the burning subsided. Not swallowing saliva stopped this and allowed my stomach acid to rise. It's difficult swallowing HCl capsules and not swallowing saliva, washing the mouth out with water and then swallowing capsules as quickly as possible. Salt water helps too as sodium hydrochloride provides hydrochloride to produce stomach acid.

anymore when I take the betaine hcl, even small amounts, I get gut burning. I've tried a lot of things to heal the gut tissue but it hasn't changed. It could also be something to do with the way I was ramping up hcl doses right before I got my current run of chronic fatigue, maybe for once my stomach acid is too high

I used to get burning in my stomach about 20 years ago. It usually means insufficient stomach acid rather than too much acid. I used to take anti acids not realising that they were not needed. More stomach acid was required.

I've had several stool tests done and have had antimicrobials targeted at the specific bacteria found several times but with no good result

I have doubts about these tests and their value.

Would an Esophigo Gastro Duodenoscopy help? I hear physicians can use them to take biopsies of the stomach tissue, lets, what methods would you recommend using to detect the stomach bacteria?

No test will detect any bacteria other than helicobacter pylori which is not the cause of CFS. The bacteria is far more resistant than pylori. I have thrown a lot at it and only got a minor indication that it had any effect. I did manage to destroy a biofilm in my stomach which gave quite a strong feeling in my stomach, greater than the effect I have had against the bacteria which causes CFS. The effect I got against that bacteria was much more than I have ever had before but not enough to destroy it. I have tried many different antimicrobials including essential oils - no effect whatsoever, lauricidin - no effect, lots of different herbs - no effect or sensation, Olive leaf extract - no effect. The essential oils which I took on many occasions did cause a slight feeling in my stomach in the same location where I destroyed the biofilm with reduced colloidal silver. The reduced CS did produce a far greater and intense feeling than the essential oils ever managed but this only happened in one area of my stomach, the other areas with biofilms were totally unaffected by the reduced CS. Ionic silver had zero effect in any way, not the one I purchased or any that I have made. I do not waste time with ionic silver. It is unsafe to use internally but I did give it a shot on multiple occasions and it failed.

I did try many enzymes to degrade the biofilm and antibiofilm and antimicrobial substances, such as interfase+, serrapeptase which is also present in interfase+, nattokinase, N-Acetyl-Cysteine a known antibiofilm compound, Xylitol plus extra EDTA which interfase+ contains a little but not enough, lauricidin, oregano e.o., clove e.o. EDTA binds to minerals such as calcium, magnesium and iron which are used in biofilms to bind together the biofilm. When these are disolved with enzymes they need to be bound up so that the bacteria cannot reuse them to reinforce the biofilm.  I took whole capsules of interfase+, serrapeptase, nattokinase and I also took interfase+ emptied into a cup with water to eliminate the capsule. All of this followed some time later with reduced CS did produce a fairly significant sensation in my stomach which was not quite as strong as the effect on the other biofilm which was destroyed but it was much more significant than any effect that I have had against it.

All that did not beat it. I did have another go and added licorice root powder which is meant to have efflux pump inhibiting effects against some gram negative bacteria but it did not help. I did also add DMSO to the mix which I dislike using internally or even externally but it had zero effect. Less than the earlier effect but I think I know why that failed and will not make that mistake next time. I have also used black cumin oil which is claimed to cure everything but death - it failed. Mixed with lauricidin and essential oils emulsified with lecithin with zero effect.

The moral of the story is that these bacteria are extremely quick to adapt and will counter everything thrown at them.

I doubt that any biopsy will detect anything because they do not know where to take it. The location is important. Only one location results in CFS, other locations produce other autoimmune illnesses and not the fatigue. A tiny distance further away can cause rheumatoid arthritis or asthma or eczema etc depending upon the state of the nervous system and immune system control.

The best idea would be to do a test for stomach acid first. That is probably low but it cost virtually nothing to do at home. It gives an indication of hypochlorhydria.

http://www.livingfoods.co.uk/pages/articles/the-acid-test.php

If that indicates low stomach acid then do an acid challenge. Get some lemon juice or vinegar and mix it about 50:50 in some warm water. Get another glass of warm water and mix some sodium bicarb. Then one more glass and fill with warm water. Then drink the acid mix and then suck as much saliva as you can and swallow it. Wash that down with the warm water.

Then wash the sodium bicarb mix around the mouth and SPIT OUT! Do not swallow any of this! It is only to deactivate any of the acid on your teeth. Wash you mouth out with the remaining warm water.

Then wait. If there are any urease bacteria present they will use the saliva to produce ammonia to neutralize the acidity. This will produce carbon dioxide which will produce wind/burping. I have a lot of biofilms of a substantial size which means the activity is high and the amount of ammonia and resulting carbon dioxide is quite large which makes it very noticeable. I do not know whether this would be the same with a smaller infection. The fact that some people do not notice it suggest that it could be a lot less noticeable in some people. In many people just low stomach acid results whereas in people like me with a big area of infection burping and wind is much higher and unmistakeable. Therefore it might not be reliable relying on this effect because it could still be increasing the stomach ph and lowering the stomach acid level.

It's not as accurate as a urea breath test but it can give an indication of the presence of urease bacteria. You could get a urea breath test which would be more accurate. It is meant for helicobacter pylori but it would work with other urease positive bacteria. An ELISA blood test should eliminate the presence of h. plyori so you would know that a positive urea breath test was not caused by h. pylori.

If you do have a urease bacterial infection then I would recommend that you try consuming liquid protein such as 80% pea protein, 50% hemp protein or 80% rice protein. Urease bacteria use urea from saliva therefore denying them this helps stomach acid levels to rise. I use Pea and hemp as I dislike the texture of rice protein and I add l-cysteine, l-methionine, glycine and maybe a little l-glutamine. It's the cysteine or cystine and methionine which are very low in pea and hemp protein and these are needed for glutathione production.

Taking sea salt with HCl and not swallowing any saliva allows stomach acid to rise and the protein to be digested quickly.

Also high dose B12 can be helpful against IgE antibodies as it raises t-suppressor cell activity. This stops all joint and muscle pain for me. I found it on wikipedia before someone edited it out. This research is very difficult to find, it is supressed and unavailable.