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Stool test shows different bacterial/species shortages, help!

Discussion in 'The Gut: De Meirleir & Maes; H2S; Leaky Gut' started by jason30, Dec 27, 2015.

  1. jason30

    jason30 Senior Member

    The Netherlands
    Hi all,

    A stool test revealed that some bifidobacterial species and other species are reduced. A stool test from 2014 showed these reduced levels as well.

    I wonder if I can solve these shortages by simply taking a probiotics or prebiotics?

    I would like to hear your tips / advice, thanks in advance.

    The results (the shortages are in red)

  2. Richard7

    Richard7 Senior Member


    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.







    If you get into fermentation I recommend looking for Sandor Katz's videos on youtube (and elsewhere) and or read his books.
  3. Richard7

    Richard7 Senior Member


    Overnight it occured to me that the vegetable farm list of fibre filled foods is a bit limited.

    This isn't

    you can go down the list and choose fibre, and then choose to search in all foods, which will come up with a whole lot of processed stuff, or you can go to the last field and choose to only search within fruits or vegetables or legumes or nuts and seeds.

    There are also apps that you can use to follow what you eat and calculate the total fibre etc.

    also on betaine hcl



    You can obviously search for more information, I suspect the reason I have been able to reduce my betain hcl consumption a bit may because I am using bitters, kind of. I am not using a commercial preparation, they look expensive, but you have probably had the experience of chewing on dandelion leaves and feeling changes in your stomach. Well I tend to chew on a bit of whatever I am going to eat, say a piece of raw carrot that did not go into the pot, and to take a bit of olive leaf extract (that I would take at some point in the day anyway) and swirl it around in my mouth.

    I try to do the things that make my tummy not quiet grumble but certainly stir, I want it to be well and truly ready for the food.

    hope this helps.
    jason30 likes this.
  4. jason30

    jason30 Senior Member

    The Netherlands
    Sorry for the late reply.

    Thank you so much for the comprehensive and useful reaction Richard! It’s more clearly now about the stomach acid, enzymes and bile.

    I think I take enough fibre on a day. Though I will count them to make it sure (will look into your app and site suggestion).

    I have came across the important role of stomach acid before (weston price forum). I am deficient in Vitamine B12 and have other symptoms of low stomach acid.
    6 months ago I have tested NOW Betaine HCL. I took 1 capsule 30 minutes after dinner (with chicken). It gave me too much stomach acid I guess because it gave me heartburn (pain on the chest ). The day after taking Betaine HCL even the smallest food or coffee, which raises stomach acid, gave me heartburn.
    So I stopped taking it because I thought I have enough stomach acid. Or maybe 1 capsule was too much? 1 NOW Betaine HCL capsule contains: Betaine HCL 648 mg + Pepsin Enzyme 150 mg.

    Did you also took the Betaine HCL 30 minutes after dinner?

    Or could I have enough stomach acid but less bile maybe? Then OX bile would help. I do have problems with digesting fats so I wanted to test OX bile for that purpose. I wonder if it’s wise to combine the intake of OX bile together with fat soluble supplements like vitamin d or vitamin e for better absorption?

    Thanks for the suggestions. I eat a lot of cooked vegetables. Mostly those which don’t give a reaction such as Brussels sprouts, cauliflower and green beans.
    I have tried bone broth (because of leaky gut) but I get a lot of complaints (gas, SIBO) = poor fat digestion. For now I focus on better fat digestion before I introduce fermented foods again. Meanwhile I am searching for a good probiotic to support the digestion.

    Thanks for the Mutaflor suggestion, I found a site that delivers to my country. It's pretty expensive though (€90).
    Do you know if Mutaflor can be taken together with another probiotic and prebiotic?

    So if I understand you correctly then you chew on a bit of food and that gives you more stomach acid (so you can lower the Betain HCL consumption)?

    I also don’t handle diary as well. I will look into that Indian yoghurt recipe, that looks promising.
    I have read about kombucha before, I will look into it. I also don’t tolerate kefir.
    And thanks for the links and Sandor Katz's videos on youtube, I will look into them.

    Again, thanks a lot!
  5. Richard7

    Richard7 Senior Member

    Chewing is one of those important signals to the stomach to wake up and start working it also releases amylase (which breaks down carbohydrates) in your saliva and the protein that will coat and protect b12 when acid and pepsin release it from the meat you consume.

    Digestion is really complex.

    About 5 minutes before I start eating (I don't time it) I take something bitter and usually chew a bit of the food I am preparing to try to wake my stomach up. From what I have read, and felt, bitter things like olive leaf extract and dandelion leaves trigger the release of bile and generation of acid.

    I have not read any research papers on this though.

    I take the acid just before I eat the meal.

    When taking fat soluble things like CoQ10 I always take ox bile or lecithin and some fat. I cannot remember where, but I read a summary of japanese research on the absorption of vitamins a, k and d which showed that the near 100% absorption of a and d was possible with moderate fat 10g or something while K kept going up as the fat increased up to 40 something grams (which was where the experiment ended, they did not identify some plateaux).

    So when I don't know (CoQ10) I just make sure that I have it with a meal or coffee with coconut cream or something of the sort.

    I still don't handel dairy well. I tried a yoghurt in December and it seemed to make my pots worse for the afternoon. I will probably keep trying it every 6 months or so because I miss it. The chili yoghurt was the best of the yoghurts I made but I would not advise it for someone with dairy issues.

    Art Ayres (cooling inflammation) reckons that these food intolerances should dissapear once our guts are completely sorted. I hope he is right.

    you may also find this podcast useful http://www.latestinpaleo.com/paleo-podcast/2015/11/30/latest-in-paleo-148-derailing-evolution.html

    or you might just want to skip to the articles he links to under the heading diet and microbiome. (Which I am about to read)

    I just listened to this podcast yesterday, and was rather taken by the way one of the researchers angelo coppala quoted described bacteria in a fibre rich gut behaving like shoals of fish.
  6. Richard7

    Richard7 Senior Member

    re e.coli. My doctor had me eat an alkaline diet high in galactose and fructooligosacharides.

    Well we tried with the Mutaflor, which was very expensive and failed, then we tried this massive change to diet in the hope it would increase the amount of e. coli.

    I don't know if he was worried about urine pH or anything like that, he may have jusst wanted to ensure I was eating a lot of vegetables. Anyway I spent a year working of PRAL tables and ensuring that I always had enough of the right kinds of fibre.

    Which was maddening as i could barely understand what I was doing much of the time and got lots of things wrong. I can remember having to add vast amounts adzuki beans of sweet potato with skin to balance out curries that would have otherwise been to acid-causing.

    It worked isn the sense that I got the right bacterial populations, but I got the galactose from dairy. Mostly as milk. The bacteria in your gut or yoghurt break lactose into galactose and glucose.

    My gut got the right balance of bacteria but my health declined. And N=1.

    At the time (late 2009) I was just desparate to follow my doctor's advice, but had little money and looking at the tables he gave me I could afford the recommended amount of milk but not the recommended number of dried figs.

    The tables were quite detailed but these were the two things with large concentrations of galactose/lactose, and I could not think well enough to be adding everything up.

    Looking at the tables I think I misinterpreted them. My memory is that I needed to have at least a large raw onion or 1.5 cups of legumes a day for the fructooligosaccharides and 7g galactose. Rereading the tables 7 g galactose would have been about 175 dried figs or 300ml milk. But I seem to have misread/understood the 3x 100ml of milk as 3 cups (750ml) of milk.

    Prior to this I used to but 3 or 4 blocks of cheese, maybe 4 or 5 kilos of yoghurt, a kilo of sour cream and about 2 - 4 litres of milk as milk a year.

    If I was doing it again I would do my own research, or just take lactose as a supplement if I was not well enough to do the research. Indeed I still do take a little bit of lactose most days in the hope that I will maintain populations of lactose consuming bacteria and be able to to have the dairy I like (cheese and yoghurt) without negative side effects one day in the future.

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