The 12th Invest in ME Conference, Part 1
OverTheHills presents the first article in a series of three about the recent 12th Invest In ME international Conference (IIMEC12) in London.
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Fecal metagenomic profiles in subgroups of patients with ME/CFS

Discussion in 'Latest ME/CFS Research' started by Kati, Apr 26, 2017.

  1. quasar

    quasar

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    Hi Helen, you know I took course of antibiotics and brufen. My CFS started after taking these drugs. I am not sure maybe there are also other factors, such as poor diet, stress, trauma, other drugs, or exercise that alter gut microbiome.


    Same for me. I believe if we fix gut and altered microbiome ,all of us will get rid of this disease.
     
    Last edited: May 3, 2017
  2. alicec

    alicec Senior Member

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    I've just caught up with this thread.

    I have a series of uBiome tests of my gut microbiome - 18 in total starting in December 2014. I have been through these and compared them with the analysis in this paper where appropriate and thought others might find this interesting.

    First a few general comments.

    The techniques used are different and so are not directly comparable. uBiome (and previous studies on the gut microbiome in ME/CFS) sequences the 16S rRNA gene. This gene is restricted to bacteria and archaea and has well characterised constant and variable regions which, respectively, enable PCR amplification of the target DNA of all organisms and then assignment of the generated sequences to specific organisms down to the genus level.

    The limitations are that the initial PCR amplification may slightly favour some and slightly discriminate against others so the complexity of the starting mixture of organisms may be distorted a little.

    Also species level identification is not entirely reliable because of the short lengths of DNA generated - sometimes these don't contain enough information to discriminate between some closely related species. For this reason uBiome reports results to the genus level though by downloading raw taxonomy data, it is possible to see which species they have reliably identified.

    The technique is rapid and relatively cheap and lends itself well to surveys of many different environments and to automated testing of many patients.

    Lipkin et al have used shotgun metagenomic sequencing - ie they have randomly fragmented the DNA and sequenced all fragments of genomic DNA. Overlapping sequences mean that relatively long pieces of DNA can be reconstructed. This increases reliability in general and means that species can be identified with precision. The technique is more difficult, time-consuming and more expensive since much more sequencing is involved and is more suited to research.

    Data bases for identification are not as extensive as for the 16S technique so there may be discrepancies in identification.

    I should comment also on my own circumstances, particularly in light of Lipkin's findings that the presence or absence of IBS has a strong influence on microbiome balance.

    When I first became ill around the year 2000, IBS was definitely an issue, not drastic but consistently noticeable. While initially I had an alternating constipation/diarrhoea pattern eventually this settled into IBSD.

    I had a partial remission and relapsed again towards the end of 2012. In the intervening time long term treatment with digestive enzymes, bile salts, betaineHCl, dietary interventions etc had greatly improved my digestion, virtually eliminated food intolerances etc and left me with virtually no IBS symptoms apart from consistently very loose BMs.

    I became interested in microbiome studies, particularly of the gut very early on and decided to get a uBiome test soon after it became available, out of curiosity as much as anything. It quickly became obvious to me that there was a great deal of changeability in my gut so I decided to follow this over time to see if changes corresponded to symptoms or environmental changes. In the early days uBiome offered a lot of 3 for 1 then 2 for 1 specials so this wasn't such an expensive exercise.

    I made a special effort to greatly increase dietary fibre to see how this influenced my gut and can report that it has had a very favourable effect. I no longer have any digestive problems, dont take any digestive enzymes etc and for the first time I can remember have consistently good BMs. I have gone from Bristol 6-7 with occasional 5 at the beginning of the uBiome series to Bristol 3-4 occasional 5 towards the end.

    In other words, perhaps there was a slight element of IBS at the beginning but now I definitley fit into the category of no IBS. My gut microflora balance has also improved considerably.

    Improving my gut however, has had no effect on my ME/CFS. Actually this has steadily gotten worse.

    So against this background I have considered Lipkin's results only to the genus level and tried to see if I can discern any similar patterns among my own results.

    I can't.

    Sorry I inadvertently posted this before I finished. Will continue in another post.
     
    Last edited: May 6, 2017
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  3. alicec

    alicec Senior Member

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    So a brief comparison of results.

    Overall they concluded that for the ME/CFS +IBS group, decreased Faecalibacterium and increased Alistipes was the best indicator while for ME/CFS -IBS, increased unclassified Bacteroides and decreased B. vulgatus was the best marker.

    Interestingly, at my very first test, when possibly IBS might be considered a slight issue, I did fit the low Faecalibaterium high Alistipes category, though I'm not convinced this was not just chance. Both these genera have varied widely over time, soetimes high sometimes low and not in any relationship to each other.

    Unfortunately it is impossible to consider the marker for the -IBS category. B vulgatus is a species reliably detected by uBiome but I have no way of knowing what is contained in Lipkin's unclassified Bacteroides category so have no way of comparing.

    I mention this because that first test with low F and high A is the only concordance I can find but I don't think it really means much.

    If I look at other patterns discerned by the different analytical techiques used I don't find much agreement.

    TDA analysis finds at the family level decreased Lachospiraceae and Porphyromonadaceae and increased Clostridiaceae. In every test I have had, I have the exact opposite pattern.

    At the genus level, this analysis found decreases in Dorea, Faecalibacterium, Coprococcus, Rosburia and Odoribacter and increases in Clostridium and Coprobacillus.

    In my gut Dorea and Clostridium are consistently low and Coprococcus and Coprobacillus are virtually non-existent. Faecalibacterium, Roseburia and Odoribacter are very variable - sometimes high sometimes low - and as far as I can tell there is no reason for the variability. So the pattern of my test would depend on when the test was done but this doesn't seem to bear any relationship to the state of my disease. It seems to be more random.

    Similarly with conclusions from the linear analyses. While a few of the genera found to be low are also low in my gut, others of the low category are very variable for me while those of the high category are not in me.

    I have looked at the analysis of metabolic pathways. I can't find much accord here either.

    I can find only a few categories reported by uBiome that seem to exactly coincide with those of Lipkin. These are vitamin B6 metabolism, atrazine degradation (both of which were increased) and biosynthesis of unsaturated fatty acids (decreased)

    My unsaturated fatty acid synthesis is slightly decreased (around 0.9 average), B6 metabolism is average to slightly below average and atrazine degradation is a bit lower (around 0.7).

    What are we to make of all this?

    Well first I suspect that Lipkin's average is very different from that of uBiome. His control group consisted of 50 people. uBiome's database is very much larger - many, many thousands of people. Because of the enormous individual variability of microbiome composition, the size of the group could have an enormous influence on average composition.

    This may be reflected in Lipkin's reporting of the break-up of the two main phyla which together constitute more than 90% of gut inhabitants. He find 63.4% Bacteroidetes, 29.7% Firmicutes in controls (patients are very similar). This was very surprising to me in light of the many gut studies I have looked at.

    The relatively high fat, high simple sugar Western diet greatly favours Firmicutes. Bacteroidetes thrives on high fibre unprocessed plant foods and high levels are typically found in traditional, agrarian societies. In Western societies, the ratio is almost always the other way around and often Firmicutes greatly exceeds Bacteroidetes.

    The uBiome average is about 60%Firmicutes, 31% Bacteroidetes.

    Whether the discrepancy is just related to this particular group of controls or whether it has something to do with the different technology used is impossible to say.

    Potentially big differences in averages could completely negate the kind of comparison I have tried to do.

    In any case, I don't think it is particularly helpful to focus on the list of organisms. Yes it is necessary to accumulate this info to understand if there are differences in overall composition but that is as far as it goes.

    The significance doesn't lie in the actual organisms present. There is no single ideal pattern, there are many possible combinations, all of which work because of the considerable redundancy in the microbiome. Many different organisms can fulfill the same function.

    So all of the studies showing differences in composition in various disease states are just the first step. Working out the meaning of the difference will be far more important and will be much harder to do.
     
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  4. arewenearlythereyet

    arewenearlythereyet Senior Member

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    Amazing detailed review @alicec I can't imagine how much work this has been for you.

    One thing that may be in play is interaction between species of microbe in terms of metabolites used and produced etc, so as well as balance of genus/type there is also the symbiosis of species?

    I just can't get my head around the massive scale of the work to do. Studies so far seem to be looking at genus rather than species. There are potentially 300-1000 species at play with a combined genome much greater than our own. When you add strain on top of this plus the unknown symbiotic factors, the maths of mapping healthy gut flora without even looking at diet and other variables just seems immense.

    I'm wondering how long this will take ...but my maths is pretty poor at the best of times......just seems really really big.
     
  5. msf

    msf Senior Member

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    That is IBS, it´s just that she has managed to treat it through diet, as I have also managed to do through adopting the FODMAP diet. I also pay attention to Paleo ideas about leaky gut - four out of those five foods you mentioned are supposed to make the gut leakier, and I have noticed this effect from peppers in particular. I also try to limit insoluble fibre, alcohol and caffeine.

    I don´t believe that treating the IBS cures the dybiosis though - at least it hasn´t done in my case. I think it just limits the effect of the dysbiosis on the body as a whole.
     
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  6. rosie26

    rosie26 Senior Member

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    @Tunguska :) After reading that you sip on orange juice throughout the day I thought I would try it. Bought some crushed orange juice and sip on 1/4 - 1/2 glass each day. I find I have to do this in the late morning through afternoon and stop before evening because I found it started to repeat on me at night. I needed to take some baking soda in milk one night because the orange juice cause some reflux.

    But I just wanted to say that I actually feel more resilient since starting this a few weeks ago. It might also be that I have been having half a banana and grated apple with yoghurt each day. I think both have been good. Thanks for mentioning about the orange juice I want to keep up with this.
     
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  7. Tunguska

    Tunguska Senior Member

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    Glad to hear Rosie, can't remember who but another poster was doing it before (can't claim this one). Though I mix baking soda right into the orange juice - can't tolerate it otherwise - and I sip with a straw almost down the throat to avoid hitting front teeth too much over time (it needs these disclaimers if you're gonna use it a lot)
     
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  8. bertiedog

    bertiedog Senior Member

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    I had an American Gut Stool test this year and it broadly matches the findings mentioned. I had all of the above present but only in small amounts compared with the overabundance of Bacteriodetes which were 87% of the total. A very unhealthy micro biome which I have been trying to improve with some success since early September.

    Edit to say that I have eaten a very healthy diet for the past 12 years and have taken lots of good probiotics and home made Kefir for a year which actually made me worse. I now know that I was taking the wrong yoghurt, wrong Kefir and wrong probiotics cos they all contained L Acidophilus and that feeds the bad bacteria I need to get rid of.

    Pam
     
  9. bertiedog

    bertiedog Senior Member

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    Do you remember the dose of Berberine and Oregano that made you bad. I have just started this combo having been on Neem for a month which did make me herx and also quite high dose Oregano which doesn't obviously cause me symptoms. So far just taken 400 mg berberine once daily but my migraines have come back which might be connected. I had severe muscle aches on the Neem and the probiotics on some days especially when I had a massage. The glands have been up in my neck and underarms too from time to time so I think Lipkin et al is definitely onto something.

    I do think there could still be something else that will need correcting too but haven't a clue what that will be. I guess it all depends if we can successfully clear this overgrowth permanently and I have my doubts about that.

    Thanks
    Pam
     
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  10. ljimbo423

    ljimbo423 Senior Member

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    Hi Pam- Before I took a course of Rifaximin, even small doses of Berberine or oil of oregano would make me very sick, like maybe 50-100mg. After the Rifaximin, I went up on the Berberine 100mg at a time and the only real side effect was a big increase in energy.

    Which was nice until I tried to sleep, it gave me insomnia. 400mg Berberine I think is a big dose for many with cfs to start with. I wouldn't at all be surprised if that is what's causing your migraines and swollen glands.

    You might be right about having to address other issues besides dysbiosis and leaky gut. Although I do believe those are the core issues for many or most even. I also think mito dysfunction plays a huge role in cfs, so I am also treating that as well.

    I think once sibo/dysbiosis is well established, then cleared. It's a lifelong process to maintain it. It's my understanding that it's a chronic condition, so one will always be at risk for it returning without low carb diet etc. Lately, I have been having doubts about beating my dysbiosis too.

    However, I won't give up and if I need to, I'm seriously thinking about taking a short course of a systemic anti-biotic like doxycycline and see if that helps. Whatever it takes!:) As long as it don't kill me.;)

    Are you doing a low carb diet with the herbs and probiotics?

    Jim
     
  11. ljimbo423

    ljimbo423 Senior Member

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    One other thing I forgot to mention is about the immune system. My immune system is very weak and I catch a lot of colds and flu's. I wonder how big a role that might play in ongoing dysbiosis and if boosting the immune system could help, if done aggressively enough for long enough.

    Whenever I take herbs to boost my immune system though, I feel much worse. If that's die off from gut bacteria, that's a good thing. Maybe if I get my dysbiosis a little better under control I can take the immune boosters without getting sick and they could help me to beat it completely.

    Does it sound like I might have given this dysbiosis a little thought?:rofl:;)

    Jim
     
  12. bertiedog

    bertiedog Senior Member

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    Jim I used to be very similar to you in regard to catching many viruses especially through the winter. Last winter was dreadful for me, I was always ill.

    However, since starting the probiotics I have mentioned and taking the herbals I have had many episodes of sore throat but haven't really felt ill and I have managed to knock the virus out after a couple of days with dropping tincture of Echinacea Augustafolia down my throat every couple of hours. Tastes foul but it works.

    I am sure there is published evidence of how probiotics are almost like an antibiotic to bad bacteria and that they can really boost the immune system. I think it might be the Bifido ones but not 100% sure on that. So it might help you if you switched to specific probiotics, not the normal ones. Soil based ones have helped to calm my gut very quickly and introduce many unusual type of bacteria which apparently do seed into the micro biome. Symbioflor 1 is also designed to boost the immune system especially if suffering with repeatedly upper respiratory infections.

    Yoghurts like Activa were also recommended for me and I take this 3 times daily but I make it myself with organic whole milk and use the Activa as the starter. I add fibre like Acacia to feed the good bugs and can also tolerate china seeds and psyllium. Good for my immune system and tastes good too.

    Pam
     
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  13. bertiedog

    bertiedog Senior Member

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    Yes I have been low carb for a long time. The only grain I have is in the form of Sorghum thins taken with butter and some mild cheese. I don't eat rice or pulses and watch out for anything that feels like it might ferment in my gut. Basically I would say I eat low Fodmap vegetables and fruits. Luckily I am ok with dairy but try and stick with organic versions. There have been big improvements in my gut since September since starting the protocol.

    Pam
     
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  14. ljimbo423

    ljimbo423 Senior Member

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    Dr David Perlmutter thinks Acacia is the best prebiotic going.
    I am going to buy some Acaicia fiber in the next week or so. Can you tell me anything you might have noticed about taking it? Side effects? Benefits?

    I just started taking some inulin a week or so ago and I feel like there have been some improvements.

    Happy to hear you are noticing improvements in your gut. Sounds like you are going at this dysbiosis thing "guns a blazing"!:D

    Jim
     
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  15. bertiedog

    bertiedog Senior Member

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    Just to mention that I was told not to take inulin as in my case it was feeding the bad stuff. I did use to "blow up" after taking it and could feel fermentation which isn't great!

    This doesn't happen at all with Acacia. I started at 1/2 teaspoon twice daily but only take about 1 large heaped teaspoon now three times daily. Have had no issues with it but I do think along with the Active/probiotics' it is really helping me to have more normal bowel movements. Have suffered with years with bad constipation and this is hugely improved but some days comes back to remind me of its problems. This doesn't happen very often now thankfully.

    Good luck with your "journey" too I believe a lot of this is trial and error because we are all different. Flax seeds weren't good either with regard to fermentation and feeding the bad stuff and everything is much calmer without them. Chia seeds are fine though. I did leave them off for a month and then restarted without any negative effects.

    Pam
     
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  16. ljimbo423

    ljimbo423 Senior Member

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    I noticed some minor bloating for a day or so from the inulin. The fact that it was gone in a day or so, I'm taking as a good sign. It's like you say though, each of us are unique in what we need to get healthy. It's mostly trial and error.

    I read a bunch of reviews at iherb and amazon. Most people there said they had no side effects from the acacia either. Fingers crossed, when I get mine, I won't either.

    Good luck to you as well!:)

    Jim
     
  17. aimossy

    aimossy Senior Member

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    I had that exact same experience!
     
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