Jason,
I had some of these issues.
taking probiotics alone will do little. One also has to create the right environment for them with fibre/prebiotics so lots of fruit, vegetables and pulses.
If you are eating a low fibre diet, suddenly going high fibre will be an issue, you will produce a lot of gas and that can be painful, very painful, and disturb your sleep if the smooth muscle of your gut is not working well.
If I was back in 2010, when I had pathology showing undetectable e. coli, or 2003 starting all over again I would start with looking at stomach acid and bile. As I understand it most people with CFS/ME will have low stomach acid. A lot of people have low stomach acid, but people with CFS/ME are more likely too because creating acid is an energy intensive process.
It is important because without stomach acid you do not protect yourself against pathogens, and do not fully digest your food. It is necessary to absorb b12 from your meals. It is necessary to trigger the release of bile and digestive enzymes.
I take betaine HCL. The advice I followed was to start with one tablet and increase by 1 every meal until I felt some heat in my stomach about half an hour into the meal. I then stepped back 1 tablet. This took me to 7 back in April, I think, and I have dropped down to 4/5 for most meals as my own production of acid seems to have increased.
The amount you need will vary with the amount you are eating of course. People generally say it is only the amount of protein you are eating that matters, but I will also take a small amount with low protein meals in the hope that it will enable me to absorb the minerals etc properly.
I also took and take ox bile. The idea with this is that you take a fairly large dose (500mg) for a while and then drop back to a lower dose. Your body is meant to recycle bile, releasing it from the gall bladder and reabsorbing it from the terminal ileum (the next to last part of the small intestine). It is necessary to properly absorb fat soluble vitamins and things like CoQ10, it also helps kill of bacteria in your small intestine.
This reabsorption also means that you need a fair amount to get things started, but then find that you can tail back on the ox bile and hopefully stop once everything is working properly.
Your small intestine is meant to be pretty sterile. Food goes into an acid stomach, and then an alkali small intestine filled with enzymes and bile. When this system does not work the food and probiotics you add to seed and feed your lower intestine grow in the wrong spot, the small intestine, and you get SIBO (small intestine bacterial (and fungal) overgrowth) which is no fun at all.
In an interview with Terry Wahls, I came across the suggestion that people with poor digestion should start with cooked blended vegetables. They are the easiest to digest and then work their way up to fermented and then raw vegetables. So with that time machine, back in 2010 I would blend some of the vegetables I was eating in soups and stews.
I wouldn't blend all of them. I have tried that and do not like the lack of texture. If you like green smoothies I would have those too. (I do like them).
I would increase my fibre slowly, to avoid intestinal pain, and at the very least get up to the RDA which is a little under 40g for men. I would also make sure that it was from a wide range of sources. Because different fibres serve as food for different bacteria and one wants a diverse ecosystem down there.
At the same time taking probiotics makes sense. You can take them as commercial enterically coated probiotics. Or you can have fermented foods, or both. I would do both.
You can take mutaflor, probiotic ecoli. I don't know where you are in the world but If you can get access to the liquid form you can grow it as a probiotic yoghurt.
http://drmyhill.co.uk/wiki/Growing_Mutaflor , or you can just take the pills. Or both.
I have found that I do not handle dairy well, but the best youghurt I ever made was following an indian recipe. I just about followed the usual technique
http://biology.clc.uc.edu/Fankhauser/Cheese/yogurt_making/YOGURT2000.htm but used a dried chilli as the source of lactic acid bacteria.
The current yoghurt we eat is a bit of a joke. The traditional yoghurt of the Balkans, the stuff that made it famous as a health food, was just made from clabbered milk. You milk your cow or sheep or goat. leave the milk in a jug and let it go sour. If the bacteria is particularly good, and you get a really nice fermented milk, you keep some back and use it to seed the next batch of milk. If not you start again. think of it as fishing for the right bacteria.
To make commercial yoghurt people (Danone for example) studied traditional yoghurt and found individual strains of bacteria that could make something that looked and tasted much like yoghurt. I always think of this as a kind of placebo yoghurt – or maybe we should see it as cargo cult nutrition.
Anyway to extend the fishing metaphor, the chilli works as never-fail-bait, there may be a way to make it fail, but it always worked form me. And you can just keep back some of the chilli infused yoghurt to act as a culture for making yoghurt according to the above instructions. You are not condemned to chilli flavoured (and heated) yoghurt.
I eat home fermented veges, and probiotic drinks (kombucha and beet kvass) they seem to work for me. I buy unpasteurised bean pastes (miso and korean bean paste, mostly korean of late)
I have tried kefir, and coconut kefir, and tibicos but they were not for me.
Useful sites.
http://drmyhill.co.uk/wiki/Fermentation_in_the_gut_and_CFS
http://drbganimalpharm.blogspot.nl/2013/11/how-to-cure-sibo-small-intestinal-bowel.html
http://www.vegetablepharm.blogspot.com.au/p/dietary-fiber-info.html
http://coolinginflammation.blogspot.com.au/2015/01/gut-microbiome-2014-diet-inflammation.html
http://www.wildfermentation.com/forum/
http://www.nourishingtreasures.com/...ge-free-ferment-with-no-brine-cover-find-out/
If you get into fermentation I recommend looking for Sandor Katz's videos on youtube (and elsewhere) and or read his books.
