arrow33 Comments
  1. Betsy
    Dec 10 - 5:22 pm

    I think it was this site where I recently read that Dr. Cheney sees a lot of folks with pain in their lower right quadrant to touch. I wonder if he’s looked into this or only noted it?

  2. katytweety
    Dec 10 - 6:14 pm

    So does this mean that a pro-biotic would help with this?

    • Marilyn B
      Dec 11 - 7:56 am

      As a nurse and a CFS/FM’s pt..and from my past nursing in research.. On totally convinced of this! While working in the emergency room from age 25 to 40.. I was “blessed” with the Shigella parasite. My GI system has never been the same even though I was treated with the correct medication and had follow up stool cultures. When you read about Shigella…and many other still parasites it does mention several complications on down the line from the parasite having been in your system ie arthritic conditions etc. when I turned 30 I began having a lot of thyroid issues and multiple other illnesses.. Then an acute Rhabdomralysis

      • Marilyn B
        Dec 11 - 8:32 am

        As a nurse and a CFS/FM’s pt..and from my past nursing in GI research..I’m totally convinced of this! While working in the emergency room from age 25 to 40.. I was “blessed” with the Shigella parasite. My GI system has never been the same even though I was treated with the correct medication and had follow up stool cultures. When you read about Shigella…and many other stool parasites it does mention several complications on down the line from the parasite having been in your system ie arthritic conditions etc. when I turned 30 I began having a lot of thyroid issues and multiple other illnesses.. Then an acute drug interaction resulting in Rhabdomyalysis,renal insufficiency, g e r d, pancreas titis,sleep apnea, and tripled liver enzymes along with liapse/amylase at 130,000!! I should have been fatality..but got very lucky.( I do not drink). I then began to have issues with arthritic origin. No DX of rheumatoid arthritis yet..but definitely osteoarthritis in spine..lower and upper, fingers and wonder if this is sequeli? I just retired from doing GI research and after working and that for several years put myself on a daily probiotic answer reviewing many patients charts and noticing that this seems to be a routine for patients who had Crohn’s or ulcerative colitis. I also noted the use of a certain newer antibiotic used and IBS. I have not been on any antibiotics, but I do use a daily probiotic called Align. I felt pretty good taking that and fiber with “Calm” at night for my IBS chronic constipation for several years. however this has changed recently and I am noticing more GI symptoms with GERD, abdominal tenderness And inconsistency in stools with bloating, food intolerances and because of the costly Probiotic have had to Chg to a different one. I so agree with the GI theory..just hope help comes sooner with this discovery than it did with diagnosing my fibromyalgia!I have noticed an increase in muscle pain that was missing for the last 8 years and also increasing fatigue and more stiffness in the mornings and it sucks to return to this state of being when life is getting easier now. I will continue on as I’m doing..and try to use less sugar,gluten(harder yet) and fatty foods that I allowed back into my diet after feeling well for the last 6 yrs but at smaller infrequent amounts…what else are we to do? I’ve had 3 colonoscopies in the last 8 trust it is a diet thing with a possible irritation of diverticulitis. So hard to eat a diet for all these intolerances . I think the one thing that always makes me hot as in seeking medical attention is that a lot of the doctors refer one back to their cfs/FM’s symptoms and will most likely tell me to live with it..sadly enough! Such a life,lol.

        One lives in hope that these studies will find answers!!

        • NancyS
          Jan 04 - 9:44 am

          Shigella is a bacterium, not a parasite.

    • Ivy
      Dec 17 - 12:11 pm

      What a fantastic site! Research has demonstrated that the probiotic in Yakult yogurt helps alleviate FM. It would be worth a shot for CFS. The Dummies Guide to Probiotics is a fascinating guide I can recommend.

      • Cort Johnson
        Dec 17 - 12:51 pm

        Thanks for the tips Ivy :)

  3. John L Whiting
    Dec 10 - 9:17 pm

    Bile salts inhibit the growth of Pevotella species in normal individuals, and the increase in Prevotella in the stools of many CFS/ME patients, as per studies by BioScreen in Melbourne Australia, can be reduced to normal by administering oral ox bile as a medication.

    It is the milieu in which bacteria in the bowel compete with each other, which determines the outcomes of such internal interspecies ‘germ warfare’. Oral ox bile changes this milieu and brings about a slow but sure clinical differences in many but not all CFS/ME patients of mine.

    The finding of oral streptococci in abundance, using Bioscreen’s technology, is a strong indicator that these bacteria evade the chemical defences of the upper gut e.g. stomach acid, and outcompete with the normal flora of the lower intestine.

  4. Just Saying
    Dec 11 - 2:02 am

    Isn’t it obvious to everyone. We eat collagen containing food, bacterial nasties start breaking it down, our gut immune system recognizes these particles as an antigen, our gut system makes the correct antibody (differentiated for the type collagen, think maybe kidney in sausage or muscle sheathes for fibro), these antibodies go in lymph to near the heart to be pumped throughout our system, find the correct collagen and attack it. It’s the way our immune system works. It is impossible to not have been found out previously.

  5. Philip Brown
    Dec 11 - 2:40 am

    Which specific strains of probiotic may help with ME/CFS and what might be the correct dose?

  6. Els Van Hoof
    Dec 11 - 4:02 am

    In june 2099 I had an extensive stooltest done.
    As expected (long term gastro-intestinal issues before I got ME (cfs) ) there was extreme dysbiosis.

    Prevotella (anaerobic) + streptococcus + enterococcus (aerobic) were high. Too high.

    Especially enterococcus were about 97 % of my aerobic bacteria, where it should be around 5%.

    Prevotella was about 28% (should be less than 10%),
    whereas bifidobacterium was only 0.5% and
    Lactobacillus were down to 0% (!)

    In 2010 a rotating treatment with ABx was started. One week per month AB and the rest of the month probiotics. This continued for about a year and a half.

    I found that, while it was not curing, since then I seem to have made it one step high on my ladder. Where before I was continuously sick (really sick – extreme flu feeling with enlarged lympnodes etc), I started to notice that sometimes I got some time off that terrible unbearable sick feeling.

    Now, after not being on the program anymore, I’m still standing on my first step of that ladder.
    The constant sick feeling has been replaced by a “coming and going”, which for me made a tremendous difference.

    I must add that I was on a strict diet too (esp. no sugars, of any kind! that includes most fruits and most processed foods, even mayonaise).

    That being said, there is a gut connection. I’m sure.
    It’s not the whole picture though and it doesn’t “cure” ME or CFS (the neuro-immune kind).
    But it was of great worth to have my gut flora screened and doing the ABx/probiotic regimen.

    • Marilyn B
      Dec 11 - 8:35 am

      I agree!

    • Marco
      Dec 11 - 10:04 am

      I’ve been doing a little reading up on how peripheral inflammation can become systemic and from there can induce neuroinflammation and came across some interesting stuff on leaky gut/bacterial translocation.

      It appears that when LPS (the major component of the outer membrane of gram negative bacteria) leaks into the bloodstream there are two pathways by which it can be deactivated and detoxed. One is via the portal vein to the liver and a secondary route is via the lymphatic system. Normally the liver deals with the vast majority of LPS and is able to clear it entirely.

      But – if the liver function is impaired, LPS clearance then falls to the lymph glands which aren’t very good at it and you end up with systemic inflammation and elevated pro-inflammatory cytokines which in turn activates and primes microglia in the brain which leads to many symptoms associated with ‘sickness behaviour’.

      Primed microglia is associated with aging and the elderly are prone to an exaggerated sickness response to common infections which can often hasten cognitive decline.

      Sounds plausible. I’m beginning to suspect that gut microbiota may be more of a key player than I’d previously thought.

  7. Gijs
    Dec 11 - 4:13 am

    In Belgium, is currently a large-scale research on intestinal bacteria. About 5,000 people will participate. Among these people are healthy and the sick. A large number of CFS / ME patients will participate. This group is large enough to show a connection. This study will take several years to complete. Let’s hope something will be found.

    • Cort Johnson
      Dec 11 - 3:22 pm

      Good news, Gijs – thanks for passing that on.

  8. Audrey Dorfman
    Dec 11 - 5:00 am

    I have suffered with intestinal issues for 30 yrs. This past year by adding Kombucha, cultured vegetables and kefir daily to my diet, all issues gone. It all has to do with adding good bacteria and good yeast that develops colonies in body. I took drug Xifaxan for a while and it did nothing.

    • Cort Johnson
      Dec 11 - 3:22 pm

      Wow….we need to talk…:)

    • Els Van Hoof
      Dec 13 - 5:13 am

      oddly enough Xifaxan made everything worse for me. My gut couldn’t tolerate it and cramped up. Major IBS return.
      Same for most probiotics and yeast and whey protein.

      I’m still looking for a probiotic I can tollerate. I think I tried about every kind there is. Except Kyodophilis … the only one left on my list I think …

      Since taking Lyrica my IBS episodes (which are very very severe and painful) went from about 70 on a scale of 100 to 20 (!).
      Yesterday all of a sudden I had a major episode again. Unbelievable painful. I’m putting my ABx regimen on a hold. It’s unbearable. Today I thought it was over but about an hour ago it started again. Can’t make any sense of it all …

      My gut issues +
      my autonomic nervous system (diminished HRV etc, alpha delta sleep, NMH, POTS, two day CPET test from bad to worse, …) +
      my immune system (low NK cell function, low RnaseL, high elastase, low cd57, active hhv6, reactivating herpes viruses, … all the “ME” markers)
      are the main focal points of my illness.

      That’s the only thing I know for sure.
      But how the puzzle fits or which is the chicken or the egg?
      Don’t have a clue.

      • Andy
        Dec 16 - 10:18 pm

        I’m curious what kind of gut tests did you run?
        I need to do some , but not sure which is good.

      • Cynthia
        Dec 30 - 2:18 pm

        I can’t find a probiotic I can tolerate either. I have both PANDAS & ME/CFS. Even lactobacillus strains trigger my pandas so I’m pretty hesitant to try them. I’m also highly allergic to yeast, including good nutritional yeasts. What do you when you’re too reactive to the good stuff? I do my best on doxycycline and diflucan together. I can’t take an antibiotic alone, but gut issues stay at bay most of the time on those two meds. I wonder if a transplant can counteract that super reactivity, like an immune system transplant?

    • Cindy Cirlincione
      Dec 14 - 9:40 pm

      We’re you on the body ecology diet – Donna Gates? Did you have pain and now don’t?

    • John Buettner
      Dec 22 - 4:40 pm


      Thanks for this. This Kombucha recipe looks Quite good. I’m going to give it a go.

  9. CateK
    Dec 11 - 8:23 am

    I’m glad to hear that a blog on ‘Healing the Gut’ from Niki Gratrix will be posted soon – I’ve been waiting and watching for it, after reading the other posts she’s written (as in, yup, my guts are screwed up, now what can I *do* about it!)

    • Cort Johnson
      Dec 11 - 3:25 pm


      I’ve cut out wheat (gluten) since then and my bloating which had reached record levels has subsided dramatically. I can also tolerate more sweets without bloating -a nice side benefit…

  10. Iquitos
    Dec 11 - 1:06 pm

    Homemade kefir seems to do it for me. I get the starter on Amazon and make it from powdered skim milk so it’s not so expensive. And it’s been found that lactose intolerant people (most of them) are not intolerant when the milk is fully fermented, the way one does it at home, instead of the commercial kind that is stopped early so it will taste sweet.

    I also make a ranch-style salad dressing from it, adding powdered garlic and dried Italian herbs.

  11. Cort Johnson
    Dec 11 - 3:12 pm

    Here’s another fascinating study on the gut and autism. Picked this up from a link on the WPI’s Facebook site. Giving autistic mice a probiotic reduced some of their autistic behaviors.

    Gut Microbes Linked to Autismlike Symptoms in Mice
    5 December 2013 12:45 pm
    Gut feeling. Scientists think this common microbe, Bacteroides fragilis, could help restore normal behavior in autism-mimicking mice.
    CNRI/Science Photo Library
    Gut feeling. Scientists think this common microbe, Bacteroides fragilis, could help restore normal behavior in autism-mimicking mice.

    Many physicians and parents report that their autistic children have unusually severe gastrointestinal problems, such as chronic constipation or diarrhea. These observations have led some researchers to speculate that an ailing gut contributes to the disorder in some cases, but scientific data has been lacking. Now, a provocative study claims that a probiotic treatment for gastrointestinal issues can reduce autismlike symptoms in mice and suggests that this treatment could work for humans, too.

    The reported incidence of gut maladies in people with autism varies wildly between published studies—from zero to more than 80%—making it difficult to establish just how commonly the two conditions go together, says principal investigator Sarkis Mazmanian, a microbiologist at the California Institute of Technology (Caltech) in Pasadena. Overall, however, the evidence seems to point toward a connection. Last year, for example, a Centers for Disease Control and Prevention study of thousands of children with developmental disabilities found that kids with autism were twice as likely as children with other types of disorders to have frequent diarrhea or colitis, an inflammation of the large intestine.

    For many years, Mazmanian and his and colleagues have been studying the effects of a nontoxic strain of the bacterium Bacteroides fragilis on diseases such as Crohn’s disease, which causes intestinal inflammation and allows potentially harmful substances that should pass out of the body to leak through junctions between cells that are normally tight. Although the researchers don’t understand the mechanism, the bacterium appears to restore the damaged gut, possibly by helping close these gaps.

    “The fact that we have an organism that repairs the gut makes it a very appealing” tool for testing whether gut abnormalities can contribute to autism, Mazmanian says. To explore that question, Mazmanian and colleagues at Caltech used a mouse model of autism that is thought to approximately recreate three of the disorder’s hallmark deficits: lack of social interaction, decreased communication (mice normally emit ultrasonic, birdsonglike chirps), and repetitive behaviors such as compulsive grooming or burying marbles.

    The first step of the experiment was to determine whether the mice showed signs of gastrointestinal inflammation or other gut abnormalities, says microbiologist Elaine Hsiao, a postdoctoral candidate at Caltech and lead author of the study. By the time the mice were 3 weeks old, the researchers found that their intestines were indeed as leaky as those of mice that had been treated with a chemical that induces colitis. Next, the researchers tested whether they could reverse the damage by feeding the mice applesauce laced with B. fragilis for a week. A second group of autism-mimicking mice as well as a group of healthy mice ate applesauce that did not contain the bacteria. Then the group waited to see what effect the bacteria would have on the rodents’ intestines. “We didn’t know what would happen—we were hoping the bacterium would survive in the gut,” Hsiao says.

    After 3 weeks, the team measured the levels of gut-derived molecules in the rodents’ bloodstream and found that the treatment had stopped up their intestinal leakage. Bacterial counts from rodents’ poop showed that although B. fragilis did not establish lasting colonies in the mice, they did “shake up the community,” of microorganisms, bringing it closer to that of the normal mice, Hsiao says. After the treatment, the autism-mimicking mice also resembled their normal peers in two behavioral tests, the authors report today in Cell. The animals no longer compulsively buried marbles in their cages and increased their ultrasonic squeaking to typical levels. They did not increase their social interactions, however, Hsiao says.

    “It’s really striking that any bacterial treatment—even a transient one—could have a lasting impact on behavior,” Hsiao says. The most interesting thing about the results, she says, was not the correction of the autistic symptoms in the mice, but the clues the study provided about how the gut’s microbial population may affect the brain and behavior. The researchers found that levels of a substance called 4-ethylphenylsulfate that is produced by gut bacteria increased 46-fold in the mice with autistic symptoms, but returned to normal after treatment with B. fragilis. When the team isolated that chemical and injected it into healthy mice, the rodents showed increased anxiety, another autismlike symptom, she says. Although the substance did not provoke the symptoms seen in the previous experiment, Hsiao says that the animals’ altered response suggests that the substance could play a role in the disorder. Hundreds of other metabolic byproducts also changed in quantity after B. fragilis was administered and could have an effect, she adds.

    By demonstrating that a widely used mouse model of autism does have gastrointestinal problems, and that these problems are associated with behavioral symptoms, the new research “shows us something fabulous,” says Betty Diamond, an immunologist at the Feinstein Institute for Medical Research in Manhasset, New York. She cautions, however, that it would be premature to use B. fragilis or another probiotic as a treatment in humans. “We don’t really understand” which bacterial species are important or how they colonize the gut, she says.

    Although the findings are interesting, the study does not establish that the changing levels of microbes and the chemicals they produce caused any of the behavioral changes seen in the mice, says Emanuel DiCicco-Bloom, a neuroscientist at Rutgers University in New Brunswick, New Jersey. “I’d want to know more about the mechanism” by which the bacteria altered behavior in the mice before beginning to translate the findings to humans, he says. The group also didn’t investigate how the bacteria affect a normal animal, because the microbes were administered only to autistic mice, he says. It’s possible that B. fragilis could have a deleterious effect that the study didn’t detect, he says. Combined with the inherent difficulty of extrapolating findings about human autism from a mouse, he says, “I think this is less well-established than it appears.”

    “We propose that after the repair of the leaky gut, neurotoxic molecules do not get into the system and cause behavioral abnormalities,” Mazmanian says. But he agrees with DiCicco-Bloom that there are alternative explanations for why the mice changed their behavior—for example, “maybe bacteria are activating nerves in the gut that are communicating with the brain,” he says. After resolving some of these questions, the group plans to initiate clinical trials in humans, Hsiao says. “We don’t want people to start applying this to humans” just yet, but “this opens the door to future research” in people.

  12. doctari
    Dec 13 - 11:42 am

    For me this illness is an evolutionary process with development of multiple symptoms over time with some seeming to resolve and always new ones cropping up. I had two phases-first was three systemic vax rxns that caused deep aching pain of the entire arm, numerous bruises coming up everywhere, then finally arm numbnes followed several weeks later with arm tremor. Left me with intermittent episodes of deep aching arm pain. Phase two started seven months Iater induced by thinking that exercise and getting fit would help me, so I started a treadmill regimen thinking of running a marathon. Six weeks in I could feel something was very wrong! I was doing 8 miles in ~72min. but it didn’t feel right! I wasn’t getting fit with the increased effort, I was exhausted at end of sessions and after them! Something was wrong! Then I had a relapse of the tremor and arm pain. First in the most affected arm, then in both arms. Exercise was of course stopped. Six weeks later while still having arm pain/tremors I developed a GI bug. Vomiting and diarrhea and then PROFOUND lethargy. Literally couchbound. Five days into this I forced myself to make a difficult drive into the doctors. He pulled blood but didn’t know what was going on. On driving home, I had this spontaneous gush of clear fluid come out of my right nostril and then it just kept dripping for several minutes. I remember thinking, I’m so tired because of an upper respiratory virus, but I didn’t have any other symptoms of one. I developed difficulty swallowing and hearing loss. Had great difficulty preparing meals. Never developed any runny nose or other signs of an upper resp virus. Never recovered from the fatigue, and this ended most of the high functioning I had prior to this. No more work. Great difficulty with focus, planning, and multitasking, all mandatory for the work I did.

    I developed diarrhea during this time in which the stool in the toilet was literally churning almost like the water was boiling but more of a slow simmer. I had my fiance look at this ~ 10 minutes later just for confirmation of the peculiar event and that I wasn’t crazy. She concurred it was real and very weird. Regular stool checks for pathogens were negative. I am curious if any of the acute onset group ever noticed this type of occurrence, and if anyone knows what kind of bug could cause gross visable churning like this?

    Prior to this trainwreck the only problems I had were with low thyroid and IBS.

    • Cort Johnson
      Dec 13 - 12:11 pm

      Amazing story, doctari!

      It all seems so viral to me..

      • doctari
        Dec 14 - 3:09 pm

        I agree with you. The first phase with identical 10-14 day post vax. onset of arm pain, multiple hemorrhages seems likely that it induced autoimmune or autoantibodies that are still at work now. Recent skin biopsy of leg showing decreased number of small nerve fibers(SNF) and poss. autonomic neuropathy. CRPS or RSD of R arm was a presumptive diagnosis of one CFS doc. It caused burning pain like radiation or severe sunburn. That presumed autonomic neuropathy has spread to both legs. It’s the shits!

        However, the acute onset after the physical stressor of exercise likely was viral . Further studies have shown high titers for EBV, HHV6 viral activation, and I developed shingles ~8/2010. Interestingly, with the GI symptoms, I tested negative for Parvo B-19. Enterovirus wasn’t tested for.

        Also from reading about Dr. Cheneys recommendations, I had nagalase tested twice and it was quite elevated both times. This can be associated with retrovirus, other viruses(Herpes?) and tumors. This causes a bit of a quandary when developing a treatment plan. To immune suppress or not to? Working on IVIG for decreasing immunoglobulins, and neuropathy, but getting insurance to pay is another matter.
        Thanks Cort for the most up to date info and help you give to all of us.

        One other thing that has me concerned is weird back pain that started ~ 13 months ago at L5S1. It reminded me of Corriene’s(sp) neck pain in that it feels like an electric shock is put right on my spinal cord at that level. It first started when I drove anywhere for more than 30 minutes. It seems to have progressed because now it can occur when I am in bed and there is no movement whatsoever. They had me do a sitting up MRI which showed stenosis at 3 levels that was mild but I’m not sure that what is causing the electrical shock sensation. I was wondering if that might be from a vasospasm or migraine like deal in the spinal cord?

    • Lee
      Dec 14 - 12:47 am

      The gush of clear fluid and subsequent functioning issues reminded me of a news story here in which a person had an Cerebral spinal fluid leak.

      • doctari
        Dec 14 - 3:33 pm


        Thanks for the link. Great info there! I was driving on the freeway at ~ 75 mph when this occured. Glad I didn’t herniate something in my brain! I wish I hadn’t been so dense back in 2008 when this happened, but now I think I had viral encephalitis that was never diagnosed. My neurologist was thinking MS with the swallowing issues and hearing loss and he ordered an MRI about 2 weeks later. It was read as normal, but I don’t know if they would see that lesion, or sella abnormality with an MRI with dye? It would be nice to find a radiologist with CFS experience for second opinions on some of these issues.

        I had the exact same study done in 7/2012 mostly because of cognitive decline. It had new lesions of 5mm diameter white matter lesion as well as global atrophy – somewhat more than expected for age. A different neurologist said it was a normal MRI. I was a pretty youthful 53 year old when all of this started, now I am 59 but feel like I’m 89 much of the time! Thanks again Lee!

  13. […] Study Suggests Gut Bacteria May Be Able to Trigger Autoimmune Disorders […]

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