Cort Johnson has done some serious homework on the recent gut microbiome study from Columbia University Center for Infection and Immunity (CII) researchers. He delves more deeply into the study and spoke with Dr. Ian Lipkin about their work. This article was originally published on the Simmaron Research website and Cort kindly gave us permission to publish the article in full for the Microbe Discovery Project.
Columbia & Simmaron Gut Study Uncovers Another Chronic Fatigue Syndrome (ME/CFS) Subset
by Cort Johnson
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.
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.
This study used the latest technology to dig deeper into ME/CFS patients guts than ever before.
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.
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”.
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.
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.)
- The Giardia ‘Syndrome’ Strikes: Norwegian Studies Suggest ‘Minor Bugs’ May Commonly Trigger Chronic Fatigue Syndrome As Well
Are gut bacteria in contributing to the energy problems in ME/CFS patients with IBS?
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.
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.
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
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.
“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.”
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.
Huge thanks to Cort for such a thorough and brilliant read about this study.
Drs Lipkin and Hornig at the Center for Infection and Immunity need our support with donations. Check out the study they need donations for here. All links for donating including the donate button at the top of this page allow people to donate directly through Columbia CII’s secure site.