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Columbia & Simmaron Gut Study Uncovers Another Chronic Fatigue Syndrome (ME/CFS) Subset

With their second myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) study published this month, Ian Lipkin and Mady Hornig’s Center for Infection and Immunity (CII) and collaborator Simmaron Research are on an ME/CFS roll.  As with all CII studies, this one combined unusual rigor and the latest technological advances to cast new light on ME/CFS – and possibly  produce yet another subset.  Longtime CII collaborators, the Simmaron Research Foundation and Dr. Daniel Peterson provided samples for both studies.


This study used the latest technology to dig deeper into ME/CFS patients guts than ever before.

Published this week, the new study combined microflora, metabolic and immune analyses in fifty chronic fatigue syndrome (ME/CFS) and healthy controls from four clinical sites (Dr. Peterson, Dr. Lucinda Bateman, Dr. Nancy Klimas and Dr. Susan Levine). A typically rigorous study  from the Center, it matched ME/CFS and healthy controls in numerous ways (age, sex, race, geographic site and season of sampling). The goal was to take the deepest look yet at gut bacteria and their effects on metabolic pathways and the immune system.

Species, Species, Species….

This was a gut study with a twist.  All chronic fatigue syndrome (ME/CFS) gut studies to date have used a process called 16 S rRNA sequencing to characterize the gut microbiome. Unfortunately this process, which focuses on one section of the bacterial genome, is unable to differentiate approximately 40% of the species within each bacteria genera.  Because different primers can also produce discordant results, results of 16 S rRNA studies can also vary from study to study.

These studies have been valuable; they’ve have indicated that something is off in the ME/CFS patients guts, and have given us some idea about the bacterial species involved, but because they can’t differentiate between some of the helpful or harmful species in a genera, they lack specificity.

Lipkin has changed the ways researchers identify pathogens

Dr. Ian Lipkin, Columbia Center for Infection & Immunity

Enter Ian Lipkin. It’s perhaps no surprise that technological ace Ian Lipkin would be the first to produce a study that really gets at gut species in ME/CFS.  (Lipkin has invented several viral identification tools). Lipkin used a more expensive tool called metagenomic sequencing which analyses the entire genome. It has even been used to identify species new to science.

Lipkin’s ME/CFS study identified more than 350 bacterial species.  How cutting-edge Lipkin’s approach was showed up when I asked him if finding 350 species was unusual. He said he couldn’t say; the technique hasn’t been used enough in other diseases to tell. He was confident, though, that the species the study identified were correct.

The study indicated that the guts of people with chronic fatigue syndrome (ME/CFS) were harboring  a significantly different flora than the healthy controls.  As in other studies, the relative abundance of species from one phylum (Firmicutes) chiefly defined the ME/CFS.

Moving from the top down, topological  analyses and prediction models found that the relative abundances of seven bacterial genera (Faecalibacterium, Roseburia, Dorea, Coprococcus, Clostridium , Ruminococcus, and Coprobacillus) differentiated ME/CFS patients from healthy controls as well.

Getting into the species level, four gut species in particular (C. catus, P. capillosus, D. formicigenerans , and F. prausnitzii) and four others (C. asparigiforme, Sutterella wadsworthensis, A. putredinis, and Anaerotruncus colihominis) mainly differentiated the ME/CFS patients from the healthy controls.

Thankfully, the study’s general conclusions jived with the results of past ME/CFS studies which also found reductions in Faecalbacterium and increases in Alistepes bacteria.

Another Study – Another Subset

Ian Lipkin and Mady Hornig are beginning to specialize in uncovering subsets in ME/CFS. Their studies are bringing scientific definition to Dr. Peterson’s and other clinicians’ long experience of clinical subsets. First they identified a short/long duration subset, then they uncovered Dr. Peterson’s atypical patient subset and now they’ve illuminated an ME/CFS-irritable bowel syndrome (IBS) subset.

Whether they had IBS or not, chronic fatigue syndrome patients had a different microbiome than the healthy controls. Topological analyses, however, indicated that having IBS, changed a great deal.

The relative abundance of four bacteria (Faecalibacterium species, R. obeum, E. hallii, and C. comes) were lower in the ME/CFS + IBS group than the ME/CFS – IBS group. One bacteria (D. Longicatena) that was increased in ME/CFS patients – IBS, was actually decreased in the ME/CFS + IBS patients. This appears to suggest that ME/CFS patients with IBS specialized in having lower abundances of “good bacteria”.


Irritable bowel syndrome (IBS) added another overlay to the ME/CFS gut picture

Encouragingly some of those same bacteria are low in IBS studies. Low levels of these protective bacteria have been associated with gut hypersensitivity, bloating and discomfort in both animal and human studies.

That suggests that having inadequate levels of these bacteria may result in inflammation which attacks the gut lining and allows bacteria to escape to the blood.  Once in the blood the bacteria are believed to trigger a systemic immune response that may be able to affect the central nervous system.  Evidence of leaky gut has shown up in several ME/CFS studies.

Gut Triggers

Lipkin drew a possible connection between the flu-like onset in ME/CFS that many people experience and gastrointestinal infections that can precede irritable bowel syndrome. Studies indicate that gastroenteritis or the stomach flu increases one’s chances of coming down with IBS six fold – but does it also increase the risk of getting ME/CFS?

Lipkin asked if the same gut infection could trigger both diseases. Studies suggest yes. Even when treated, giardia infections can produce long lasting cases of ME/CFS. (Three years after being treated for Giardia, 50% of those affected still suffered from chronic fatigue and/or Giardia.) Tests indicated that their illness persisted long after they’d cleared the bug from their system. Dr. John Chia, of course, has long associated ME/CFS with enteroviral gut infections.

Several well-known ME/CFS patients (author John Falk, Tom Hennessey, Whitney Dafoe) experienced some sort of stomach flu before becoming ill. (I contracted Giardia about three years before becoming ill. Tests years later indicated it was still present.)

Metabolic Tweaks

We know that the bacteria in our gut affect our metabolism.  It’s in the gut, after all, where many of the metabolites that our bodies use get manufactured.  Next the researchers used a pathway analysis to try and determine what effects those differences might have on metabolic functioning.

Differences, Differences – Their metabolic pathway analysis indicated different metabolic pathways were accentuated in the different groups.  Vitamin B6 biosynthesis and salvage, pyrimidine ribonucleoside degradation, and atrazine degradation all appeared to be going gangbusters in the ME/CFS patients at large while the production of arginine, polyamine, unsaturated fatty acid (FA), and mycolate appeared to be significantly reduced relative to the healthy controls.

gut bacteria-IBS-ME-CFS

Are gut bacteria in contributing to the energy problems in ME/CFS patients with IBS?

The ME/CFS with IBS group looked far different from the ME/CFS group overall with projected increases in the production of fucose, rhamnose, atrazine degradation and L-threonine biosynthesis, reduced heme, AA and polyamine biosynthesis, and reduced purine, pyrimidine, and unsaturated FA metabolism compared to the controls. Of those pathways only the atrazine degradation and decreased unsaturated FA metabolism were similar to the ME/CFS patients without IBS.

Energy production has become a key area of study in ME/CFS but no study until this one has implicated IBS in that problem.  A mitochondrial pathway affecting the Krebs cycle was upregulated in the ME/CFS – IBS group and downregulated in the ME/CFS + IBS group.  The pathways affecting metabolites associated with the urea cycle (another metabolomic finding) also only effected the ME/CFS + IBS group.

Throughout the paper the authors cautioned that they didn’t know if bacterial issues in the gut might be causing problems with energy production or other factors.  The findings, though, lead the authors to speculate that some metabolomic findings could be caused by the inclusion of high numbers of  ME/CFS + IBS patients in their studies. That’s an intriguing question given that up to 90% of ME/CFS patients may have IBS.

Similarities – Problems with fatty acid metabolism proved to be one of the ties that bind: the reduced activation of those pathways in ME/CFS patients with and without IBS suggested that problems with fatty acid metabolism could be producing inflammation in both groups.

Enhanced vitamin B-6 synthesis was also a hallmark of  both the ME/CFS + and – IBS groups. Dr. Wessely, of all people, suggested way back in 1999 that poor Vit. B6 synthesis in ME/CFS could be causing central nervous system issues. A further analysis nailed increased atrazine  (a pesticide) degradation as a key factor in both the ME/CFS and ME/CFS + IBS groups compared to the controls.

Conclusion – Some important similarities in bacteria activated metabolic pathways are present in both ME/CFS patients with and without IBS, but important differences were found as well.

 Immune Study

Mady Hornig sits on the Simmaron Research Foundations Board. She and the Simmaron Research Foundation are frequent collaborators.

Dr. Mady Hornig, Columbia Center for Infection & Immunity

In a recent blog, Dr. Hornig pointed out that it’s clear that the bacterial communities in our gut shape our immune response. For all the bacterial differences found in this study, though, none were linked to changes in cytokine levels – a somewhat surprising finding since bacterial alterations are believed to produce their effects via immune activation.

Dr. Lipkin, however, suggested that too few short duration ME/CFS patients with upregulated immune systems were present in the study to pick up immune differences. It could also be that a bigger patient sample would have detected them as well.

Some important immune differences were found, however. One of the master pro-inflammatory immune factors in the body – TNF-a – was increased in the ME/CFS group.  Plus Jarred Younger’s big finding – leptin – plus another CXCL immune factor showed up in the ME/CFS + IBS group.  CXCL-8 has not been found in ME/CFS before but another chemokine CXCL-9 was significantly reduced in Dr. Peterson’s atypical subset, and in Houghton’s cytokine study


The differences in gut makeup didn’t show up in immune system changes but they did appear to effect symptoms. Increased levels of  several species (R. gnavus, C. bacterium, C. bolteae, and C. asparagiforme) were associated with better vitality, health change, and motivation scores. Decreased relative levels of F. prausnitzii and C. catus were associated with worse emotional well-being scores, while levels of R. inulinivorans and D. formicigenerans were associated with improved motivation scores.

 A Focus on Faecalibacterium prausnitzii


A good bacteria that was reduced in ME/CFS is also reduced in IBS, IBD, asthma, depression and other diseases.

F prausnitzii is not your ordinary gut bacteria. Making up about 5% of our gut bacteria, F. prausnitzii is one of the most abundant and consequential bacterium found in our guts. Unlike many other gut bacteria, F prausnitzii hangs out in and around our gut lining.    It mainly  produces short-chain fatty acids such as butyrate (remember the fatty-acid synthesis problem?) through its fermentation of dietary fiber. It also appears to have anti-inflammatory effects including  the induction of IL-10 and TGFB-1.

F. prausnitzii is considered a “clostridial microbe” – a bacteria that’s distantly related to the dangerous Clostridium difficile. While C. difficile causes inflammation, bleeding and sometimes death by diarrhea, other clostridial microbes such as F. prausnitzii work to soothe our immune systems and strengthen our gut lining. F. prausnitzii was recently highlighted in a Scientific American article “Among Trillions of Microbes in the Gut, a Few Are Special“.

Reduced levels of F. prausnitzii have been associated with both gut diseases  (irritable bowel syndrome (IBS), Crohn’s Disease, inflammatory bowel disease, ulcerative colitis) and others including asthma, psoriasis, and depression, of course, now chronic fatigue syndrome.   It’s considered a potential prime candidate in the treatment of inflammatory bowel disease.  It was the only gut species that showed up in a meta-analysis of irritable bowel syndrome gut studies.  It appears to be an indicator of general gut health.

Reduced levels of F. prausnitzii (and one other bacteria) were the strongest predictors of having ME/CFS in this study.

Treatment (Treatment?)

“Much like IBS, ME/CFS may involve a breakdown in the bidirectional communication between the brain and the gut mediated by bacteria, their metabolites, and the molecules they influence. By identifying the specific bacteria involved, we are one step closer to more accurate diagnosis and targeted therapies.” Ian Lipkin

One of this study’s strengths was it’s ability to identify specific bacterial species. A targeted prebiotic-probiotic approach could presumably use findings such as these to jack up the levels of beneficial bacteria in hopes of producing a healthier gut. In a U.K Times interview, Lipkin speculated that given the dire need for effective ME/CFS treatments, some people were going to try to do just that.

“The ME/CFS community is very eager to find solutions. I expect there will be people immediately trying to modify their microbiota. In the end we think all this needs to be done in a full clinical trial but there will be people acting on this.”

I asked Dr. Lipkin if we were ready for a focused pre and probiotic treatment for ME/CFS.  As always he warned against one-size fits all prescriptions for ME/CFS but stated that we were getting there….

 Getting there. Treatment for ME/CFS won’t be a one size fits all. We anticipate that some people will benefit from pre and probiotics.

He also provided an interesting teaser: some upcoming studies from his group will suggest that different types of ME/CFS patients will benefit from immune or neuro-modulating drugs.

 In work we are preparing now for publication we see clues that that some people will also benefit from drugs that modulate immune responses whereas others will benefit from drugs that modulate neurotransmission.  

A Growing Field

ME/CFS may not be ready yet for a targeted probiotic treatment but the probiotic drug field is growing. Like any new field it’s going through its growing pains. A startup named Seres, valued at $130 million when it went public last year, failed at a clinical trial aimed to treat C. difficile infections with drug derived  from human feces.

Theoretically it should have worked. OpenBiome says it’s successfully treated 15,000 cases of C. difficile infection  since 2012 using raw poop donated by volunteers. Seres simply provided a well characterized mixture of what it thought were the right bacteria species.

The NIH is helping to move things along, so to speak, by funding a fecal transplant registry that sequences the microbiomes of fecal transplant patients pre and post-transplant in an attempt to uncover which bacterial strains work best.

A recent small autism fecal transplant clinical trial, on the other hand, went swimmingly well. Like ME/CFS, altered gut microbiomes and irritable bowel symptoms are common in autism. (Bob Naviaux finds similar patterns of metabolites in both diseases.)

First the kids got an antibiotic, and a gut cleanse to clear the gut of bacteria. Then they got a dose of “standardized human gut microbiotia” (either orally or rectally) in combination with a stomach acid suppressant (Prilosec) for 8 weeks to repopulate it. According to a Medscape article “Fecal Transplants May Yield Lasting Benefits in Autism“, autism scores went down significantly.

Autism and gut tests eight weeks later indicated the improvements had persisted and that many of the new bacteria had permanently colonized the gut. A much larger placebo-controlled, double-blinded trial is being planned.

It’s clear that Dr. Lipkin believes that targeted pre and probiotic treatments will be able to help some people with ME/CFS. He’s certainly not alone in believing the probiotics are going to help with disease. Money is being pumped into several companies aiming to produce probiotic drugs. Here are some examples.

After a Japanese researcher identified 17 clostridial species  including F. prausnitzii that were able to halt runaway pro-inflammatory activity in mice, Vedanta Biosciences, a Massachusett’s company, pulled in $50 million in venture capital to produce live bacterial drugs to treat inflammation, infections or cancer. Vedanta asserts that the “here today, gone tomorrow” bugs found in yogurt are too transient to do much good.

Synlogic brought in $70 million over a couple of years to develop a “smart” bacterial based drug that responds to different conditions in the gut.  A San Francisco company, Second Genome, recently scored $43 million to develop a bacterial-based drug for inflammatory bowel disorder. The military gave Gingko Bioworks almost $2 million last year to produce a “probiotic vaccine” to protect U.S. troops against the bad bacteria they encounter overseas.

 Intellect and Compassion

Ian Lipkin has a reputation as a hard-nosed scientist but he has a strikingly compassionate side as well. He was one of the few doctors willing to treat AIDS patients early in the epidemic. While everyone who could left China during the SARS epidemic, Lipkin flew on an empty plane bringing medicines to China. In a Times UK article titled “Gut bacteria linked to chronic fatigue” Lipkin made a direct appeal to ME/CFS patients to hang on.

“We don’t think this could be a panacea. It is a complex disorder. But we do think there are a group of people who may be helped. It is our fervent hope to find real solutions. People become despondent and even suicidal. I want them to realize that we are working on this. Please hang on.”

Next Up for the Lipkin/Hornig Team

I asked Lipkin what was next for his group. After laying out his desire for a comprehensive and integrated approach to ME/CFS, he noted that despite the NIH’s increased funding, a thicker shoestring is still a shoestring and once again called for a much more funding.

We are currently putting the finishing touches on our NIH Collaborative Research Center proposal. And, we are integrating clinical, microbiome, metabolomic and gene expression data using mathematical programs with the goal of achieving precision medicine for the ME/CFS community. What we need is a moonshot akin to what will be done for cancer. Our challenge is to do it on a shoestring.

lab testing

The CII is one of probably 7 or more sites vying to become an NIH funded research center

Lipkin has the samples to do this. He and Hornig gathered samples at different time points over a year in many ME/CFS patients but inexplicably weren’t given the funding to analyze them. Had he finally gotten that funding yet?  It turned out that even with a successful research center application he will still need more money. (With the heavy administrative reporting needs baked into the research centers and the need to bring in outside researchers, $1.2 million is not going to go a long way).

 Wish we did.  In the event we are successful with our Center application—and that is by no means certain because many excellent teams are putting in applications—we will still be significantly short because there is so much to do. Continued community support is critical!

The competition will be intense indeed for those three NIH funded ME/CFS research centers. Applications are believed to be going in this week from at least seven groups: Ron Davis, Nancy Klimas, Ian Lipkin/Mady Hornig, Jarred Younger, The Nevada Center for Biomedical Research (formerly WPI), Dr. Montoya and Maureen Hanson. Others may be applying as well.


The Center for Infection and Immunity was able to distinguish ME/CFS patients with and without IBS from healthy controls using  analyses of their gut flora. Underlying alterations in gut flora were common to all ME/CFS patients but having IBS as well had a  major effect on the gut flora and possibly on ME/CFS patients’ metabolism.

Using a technique that was better able to identify more gut species than past studies, the group found marked differences not just in the gut flora of ME/CFS patients with IBS but in the metabolic pathways those differences are believed to effect. Problems with ATP production and the urea cycle might be more associated with ME/CFS + IBS patients while problems with fatty acid metabolism appear to be common to all ME/CFS patients. The study suggested that infectious gut illnesses might be common triggers of  both ME/CFS and IBS.

The Simmaron Research Foundation

Three studies – three subsets identified using clinical expertise, cutting-edge technologies, and precision medicine. With your support the Simmaron Research Foundation is  redefining how ME/CFS is understood and treated.


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  • Issie

    April 28, 2017 at 4:44 am - Reply

    Makes me think of Ken Lassesen – he has been saying there is an issue with our gut ecology forever. Getting that sorted should improve things.

    I know with me, at a young age my gut ecology got messed up by over medicating by doctors with antibiotics – long story short – ruptured appendix, no insurance. No surgery till 2 years later. Had pneumonia at same time. Because of antibiotics, severe colitis – doc said worse he had ever seen and most die in 2 days of having it that bad. Had to do chemo, 2 separate rounds, to kill all bacteria both good and bad. But — I LIVED. I’m sure, especially with so much of the immune system being in the intestines…this didn’t help anything. IBS, after affect. But lots of probiotics and diet change- pretty good now. If I can come back from all this…..others can too.


  • PamC

    April 28, 2017 at 9:09 am - Reply

    I also fit the model presented by this great study. Although I suffered severely with vestibular migraine which was triggered by a bad dose of influenza which severely affected my life from 1979, I still had normal, good energy between attacks.

    However this all changed in 1998 when I was very ill for 2 weeks with confirmed Campylabactor poisoning. After this I had severe IBS and attacks of severe fatigue plus pain throughout my body which at one time I thought might be Rheumatoid Arthritis.

    In 2000 I was so unwell that I had to give up my part-time teaching job because I was almost permanently dizzy/exhausted and spent most of my time on the sofa. After a lot of interventions the IBS is improved but I still have a bowel which can change from one day to the next.

    My last G I Effects Stool Test by Genova at the end of 2015 confirmed that I have low numbers of these protective bacteria. Therefore I cannot wait for Dr Lipkin’s next study which might suggest a way forward.

    As always Cort thanks for the write-up and explanations.

    • Cort Johnson

      April 28, 2017 at 6:35 pm - Reply

      You are definitely in this subset Pam..I’m beginning to wonder if food poisoning and the like can lead to more severe cases of ME/CFS.

  • AndyPR

    April 28, 2017 at 12:17 pm - Reply

    Thanks for the write-up Cort.

    Towards the end you talk of how difficult Lipkin and Hornig are finding it in obtaining appropriate levels of funding, and Ian Lipkin himself says that “continued community support is critical.”. The Microbe Discovery Project are the patient team who fund raise to support Lipkin and Hornig’s work, their website is and they can be found on Facebook here,, donations can be made direct to Columbia University here,

  • Johannes

    April 28, 2017 at 1:25 pm - Reply

    Very interesting. I appreciate that you also summarized the FMT studies in other conditions.

    I am seriously considering a fecal microbial transplant for my IBS that set in a few months after ME/CFS and has gotten only worse over time. While illegal in the U.S. at this time for conditions other than C. Difficile, I could have the FMT done by a doctor in Germany for a reasonable cost when I visit my family in Germany this summer. Btw, FMT can also be done at home (check out the power of poop website and youtube).

    However, given that I am doing pretty good right now, I am not sure the benefit/risk profile is quite right for FMT for IBS and ME/CFS quite yet. While early studies show that FMT is pretty safe, there is so little evidence that it works. The study described in this article doesn’t show any causative connection between gut bacteria and IBS or ME/CFS.

    I just read Valerie Free’s book “Lighting up a Hidden World…” and am shocked by the type of experimental treatments she tried that just ended up making her worse. I don’t want to try this in a rush and then think in two years, “What the h*** was I thinking?”

    It might be too early. Right now my sense is that I might not try FMT until there has been a phase 3 study for at least a large phase 2 study for how it works in IBS and/or CFS.

  • Stephanie Stultz

    April 28, 2017 at 1:46 pm - Reply

    Interesting about the connection to having Giardia. In the early 80’s I spent a year in Ecuador with HCJB (World Radio Missionary Fellowship, The Voice of the Andes) and contracted Giardia, as well as Shigella and was hospitalized. I also came back to the states with numerous bacteria and pathogens in my gut, as identified by a Tropical Disease specialist. I was never the same health wise after that. And add to it that I had Mononucleosis in my teens as well as over use of antibiotics over the years. Eventually, after I developed ME/CFS, I had comprehensive gut analysis tests done and went through a 2 year natural protocol for Candida and Fungus and Bacteria and Parasites and Protozoas, with rotating herbs and such as well as Oil of Oregano which is amazing stuff. It’s THE best cure for a Protozoa called Blastosystis Hominis, which apparently is very common. While my digestive issues have improved considerably over the last few years it doesn’t seem to have made any difference in the severe ME/CFS symptoms nor it’s eventual progression. Still, I have to believe that being healthier ‘inside’ is better than not!

  • Grace Burke

    April 28, 2017 at 2:17 pm - Reply

    I had no luck treating parasites with oil or oregano. I had blastocystis, Giardia and E histolytica and what eradicated them were combinations of anti-parasitic drugs. There was one herbal preparation from an African doctor that eradicated E histolytica but I travelled again (long story) and reinfected with it. The second time it responded to a combination of Albendazole and I think secnidazole which has a high rate of success with E Hitsolytica. I am immune compromised so it took a lot of meds to cure me of the parasites.

  • Audrey Brimson

    April 28, 2017 at 2:36 pm - Reply

    Agree, many gastro attacks when living close to a refinery, (chemicals or bugs?), no lab tests ever done for pathogens, always treated with anti-biotics, then severe candidiasis, low grade temp, drenching night sweats etc. etc. 7 years treatment with anti-fungals, then 3 mths treatment for giardia. Severe ME/CFS 1980, more energy now but lifestyle still considerably curtailed by food and chemical sensitivity and obvious oxygen limitation to periferal blood vessels. Yoghurt and probiotics tried with no obvious help. Chemicals in food and general surroundings reduce me to days of collapse and severe abdominal pain. Mesenteric adenitis?? But even so I am much better than in the 80s and 90s. Bonus!

    • Cort Johnson

      April 29, 2017 at 2:30 am - Reply

      Did the Giardia resolve? I wish I had stayed on the treatment for Giardia but I stopped it when I got some side-effects. I was, however, experiencing some unusual erections of all things. My gut was always a bit messy as a child and then there was the Giardia….I recovered but a decade later it was apparently still there I wonder if that set things in motion…

  • Chris Pfeiffer

    April 28, 2017 at 2:44 pm - Reply


    My gut issues started before my GI issues after bouts of food poisoning and giardia when travelling the world. I wish I had known about pro-biotics 30 years ago. Whenever, I can get my gut stable, I am usually fairing better with my overall condition. The problem is that when it goes out of whack like it is now, it is not an easy feat. Also, now my gut is like the canary in the coal mine, any thing that affects it currently, affects my ME/CFS symptoms. For example, when i got gastroenteritis last year, the following days/weeks, my brain fog became extremely severe and energy levels plummeted. When I take a probiotic or anti-biotic now, I immediately feel awful and that was not the case before 4 years ago. That is why I am focusing on learning all I Can about FMT (fecal microbiota treatments) at the moment since that seems the way to get a better range of healthy bacteria. The main problem is finding the right donor.

  • Carole Rushing

    April 28, 2017 at 2:54 pm - Reply

    Most interesting comments. I did not start out with Gut issues. I started with Mono , CMV and Pesticide poisening . Also worked in a dental office ( Dental Hygienist before we wore protective gear. The one thing that brought me back 28 years ago was Immune Globulin IM shots. Watched my diet but was not that educated about what I Needed to eat. Last 6 years have learned and am on Gluten free, no fried foods, No sugar and many many Probiotics. Immune Globulin is gone as the one that worked for me sold out to another company and the generic form did not work at all.Still take Hydroxy b-12. IM. We have no doctors I have found in the Atlanta area that are knowledgeable about ME/or CFIDS. Sad. Now I have more Vestibular issues with ME. I do maintain that Diet is everything and just came through 2 surgeries in 10 days for Sissile Adenoma Bowel Polyps. Thank all of the Researchers for keeping on-Keeping on. Starting back with my Yoga now.

    • Cort Johnson

      April 29, 2017 at 2:27 am - Reply

      I wonder if Jarred Younger in Birmingham would have any ideas about doctors? (Not sure how far that is from Atlanta).

      • Issie

        April 29, 2017 at 2:33 am - Reply

        He is in Birmingham, AL. About 2 – 2 1/2 hours from Atlanta. I have family up there.


  • Carole Rushing

    April 28, 2017 at 2:59 pm - Reply

    Forgot to thank Cort for his ongoing passion on this subject. The best info and comments on any of the Health sites for us.

    Best to you Cort. Looking still for someone in the Atlanta Area????

    • Cort Johnson

      April 28, 2017 at 5:46 pm - Reply

      Thanks Carole!

  • elvira

    April 28, 2017 at 3:40 pm - Reply

    From my experience, the gut-brain connection has to be important. I suffered from IBS for years. After the energy treatment for the vagus nerve, it simply disappeared, along with the severe tiredness and constant exhaustion. The rest of the symptoms are still present. I am tempted to start taking some serious amounts of probiotics and see what happens. It can’t be worse than it is.

    • sharon

      April 28, 2017 at 9:55 pm - Reply

      What do you mean by “energy treatment” for the vagus nerve?

    • Tammie

      April 28, 2017 at 10:47 pm - Reply

      Can you say more about the specifics of the vagus nerve treatments you had? I’m always looking for more to help mine work properly.

      • judy wickert

        April 30, 2017 at 7:27 pm - Reply

        check out: VIE LITE 810 re vegus nerve

  • kate

    April 28, 2017 at 3:49 pm - Reply

    I have taken many probiotics over the years but have repeatedly been stopped by the warning labels on the side. Do not take if you have any immune system problems (which it sure feels like I have, since I am constantly sick with some virus or other). Now I feel like trying some serious ones again. Any suggestions?

    • Cort Johnson

      April 29, 2017 at 2:21 am - Reply

      Hi Kate! You might want to check out this blog – She took an unusual approach – she just took large quantities of several different probiotics – but she does have some good suggestions.

      I seem to tolerate most probiotics pretty well. I have had trouble recently with the Garden of Eaten (?) brand. For the most part I’m focusing on Gut Shots/kefir and fermented vegies right now.

      • kate

        May 7, 2017 at 3:51 pm - Reply

        Gosh Cort, I missed your reply. Thanks a million….or a billion. 🙂 I’m going to have another go at trying an abundance and variety of probiotics. This research is making me take probiotics more seriously and I need to learn more. I’m currently reading Jo A. Panyko’s book.

  • Tonya

    April 28, 2017 at 7:37 pm - Reply

    As always, Cort, thank you for your layman’s version of the latest research. Have you heard of improvements from anyone traveling overseas for fecal transplants?

    • Cort Johnson

      April 29, 2017 at 2:17 am - Reply

      Thank you. I haven’t heard one way or the other but I think with enough research we will targeted probiotic/fecal transplants for at least some of us.

  • Christine Knott

    April 28, 2017 at 9:47 pm - Reply

    I had six episodes in a year of what my doc called ‘gastric flu’ before finally coming down with ME/CFS in 1988. I read the story of one guy who had recovered twice from ME by taking mutaflor. He said he felt really rough while taking it but recovered totally after completing the course. I am really considering it.

  • Troy

    April 28, 2017 at 10:07 pm - Reply

    This makes me wonder how those of us with MCAS, IBS and ME/CFS would be sub-typed given that MCAS can cause IBS. It would be interesting to know how MCAS fits in to this picture.

    • Cort Johnson

      April 29, 2017 at 2:16 am - Reply

      It would indeed. I suspect that it has to for a significant number of us…There’s MCAS induced IBS, orthostatic intolerance and I’m sure other issues.

  • Tammie

    April 28, 2017 at 10:51 pm - Reply

    very interesting research, but I am wondering where that leaves those of us who can’t take probiotics….I suspect the reason we can’t is due to the by products that they make like H2S, so if there were some way to mitigate those, then perhaps we could all be helped by probiotics…otherwise, it’s yet another avenue that I know I can’t go down….probiotics made me severely worse

    • Issie

      April 28, 2017 at 10:58 pm - Reply

      You have to rotate strains. You don’t want to overdo and cause more gut issues. It’s all about balance. You can imbalance the bacteria in another way by adding to much or weaken what is there that should be. You need to rotate them. There is also foods that can be used and may be a better option. Jicama is a prebiotic and very tasty. But, for some – fermented with vinegar isn’t the best route. For others it is good. You have to pay attention to what your body is saying. I rotate between about 3 kinds of supplements of probiotics.


    • Cort Johnson

      April 29, 2017 at 2:14 am - Reply

      Dr. Lipkin said there are subsets and referred to upcoming papers that will provide clues suggesting that some people with ME/CFS will benefit from immune modulators and others from neuromodulating (if I got that right). I am so happy that some subsets are being revealed. I think we’re only looking at the tip of the iceberg and over time some fascinating ones are going to show up…including yours. H2S is a fascinating subject.

  • Lala

    April 28, 2017 at 10:59 pm - Reply

    Consider the blog by Ken Lassesen, many have improved, not all probiotics are valid for ME / CFS, some will make them worse.

    Consideren el blog de Ken Lassesen, muchos hemos mejorado, no todos los probióticos son validos para ME/CFS, algunos haran que empeoren.

    • Matthias

      April 29, 2017 at 11:07 pm - Reply

      I agree Lala.
      This is an excellent and hopeful study, but we need to hone in on what probiotics will help CFS, and what may make it worse. It’s not so black and white as to say ‘start taking probiotics, they are all good’. And it seems to me that we will need more targetted and advance forms of delivery, which is where some R+D is going.
      By the way, I think this study is potentially quite relevant to CFS:

  • Denise

    April 29, 2017 at 5:13 pm - Reply

    Dr. Lipkin was referenced as saying some people will be trying new probiotic treatments even before more is known… Yep, I’m one of them. Desperate, although my symptoms of gas and bloating are worse when on them, so I’ve avoided all, but yogurt (which is said not to have much effect 🙁 .) I’ve had only minor IBS, yet after reading this, I remember I did have Giardia while living overseas in the 90s, several years before the beginnings of slow onset ME/CFS. (And who knows what else?) Always assumed it was the years of very high stress that triggered ME, so haven’t paid much attention to info on these “gut” subsets. I did not improve after my intiial treatment with anti-biotics for the common parasites my dr found, and probiotics 10 years ago. But now, I’m reconsidering. What I would like to know is, for those of you that have been taking a good variety of probiotic bacteria, and fermented veggies, Kefir, the like, how long before you noticed any improvement brainwise or energy wise? Or did you only notice improvement with the IBS? I am most debilitated by brainfog, cognitive impairment and sensory overload the past few years. And, thanks, Cort.

    • Cort Johnson

      April 30, 2017 at 1:15 am - Reply

      I know someone who’s brain fog cleared up on home-made kefir and kombucha. That hasn’t happened for you but I do notice some mild but pleasing increases in mental clarity and energy.

      • Drew

        May 3, 2017 at 2:58 pm - Reply

        Hi Cort. Excellent summary as always. Would you be willing to do a post on this person’s homemade kefir and kombucha process? Or maybe connect me with him/her? I have been able to improve my fatigue and pain but brain fog continues to be a debilitating symptom for me.

    • Troy

      April 30, 2017 at 1:21 am - Reply

      It’s my understanding that basically none of the identified low bacterial strains are available as probiotics, so I don’t know how people are going to go about self-treating.

  • Denise

    April 30, 2017 at 1:25 am - Reply


  • Esther

    April 30, 2017 at 7:11 am - Reply

    Very interesting. My severe IBS was helped by excluding wheat bran, but recently I have been having Kefir (Turkish probiotic) which has helped my bowel. The greatest results have, however, been since I added sauerkraut or kimchi a couple of months ago – I definitely have more energy and a desire to keep living. The gut is the centre of health – of that I am sure! I have had ME/CFS for 33 years. I was given a 12 month course of antibiotics for acne in my teens – I have often thought they could have been responsible for the beginning of my problems.

    • Cort Johnson

      May 21, 2017 at 2:56 pm - Reply

      Congratulations and thanks for passing that on :). I’ve been trying “Gut Shots” – I really like them.

  • Aidan

    April 30, 2017 at 2:47 pm - Reply

    Can anyone on here help Please with 2 email direct links to Ian Lipkin & also Dr. Ron Davis Please? thanks so much I have someone who needs to send some Research info to both of

    their attention thanks so much I am also on Facebook under Aidan Walsh the Golden Angel is my profile there in Southampton, UK thanks & appreciated lots :)’s blesses be well soon

  • Aidan

    April 30, 2017 at 3:11 pm - Reply

    I know one Woman from Spain on Facebook a Nurse who got Sick after getting Cipro Antibiotics I have lost touch with her now trying to find again her Facebook Friend link but she

    told me with her Fatigue Brain Fog Pain issues she fully recovered on 3 things now was she went completely Organic on Foods lots of Chicken fruits vegs Fish a total clean diet & she did

    say that Baking Soda daily mixed in water work best & she also used a Probiotic she bought online which I have now bookmarked it on Amazon she said also within days her Health

    turned around she is now back to working full time as a Nurse & told me her Health has more energy than she has had in her entire life & she fully exercises by lifting weights & other

    Sports to keep fit…She did say Diet was a plus with her total clean diet & she does take some other Natural supplements as well…I will try to see if I can still find her link on my Friend list

    which is quite long on Facebook to try get in touch with her again & Post here exactly what she is taking…She did swear by baking soda as really helping her Recover

  • Dee

    May 1, 2017 at 6:04 pm - Reply

    I was exposed to a great deal of mold and then developed ME/CFS and leaky gut. Symptoms included food sensitivity/allergy, asthma, digestive issues, chemical sensitivity, brain fog etc. I am grateful that research is being done in this area. I know some of you have been exposed to giardia. My question is has there been any studies focusing on fungi and its relationship to the gut? Thanks, Cort, for all that you do.

    • Cort Johnson

      May 21, 2017 at 2:54 pm - Reply

      Giardia is a known trigger for ME/CFS but I’m not aware of any research in ME/CFS anyway – relating it to gut flora.

  • laurajnyc

    July 25, 2017 at 11:06 pm - Reply

    I heard Dr. Lipkin mention using prebiotin or prebiotics instead of probiotics.