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“The Subset Maker”: Lipkin Chronic Fatigue Syndrome Study Highlights Energy Issues In Gut Subset

Looking for clues to the cause of chronic fatigue syndrome (ME/CFS), Ian Lipkin has, over the years, poked his fingers into a number of different areas. His 2012 XMRV study showed that the virus was not infecting people with ME/CFS. (It was a contaminant). His pathogen studies (unpublished) found no evidence of a viral infection in ME/CFS.

Subsets

Lipkin may have uncovered more potential subsets than any other researcher and has long emphasized the need to break ME/CFS up into its constituent parts.

lipkin subsets ME/CFS

Lipkin believes identifying subsets is critical to the progress in this field

Lipkin and Mady Hornig’s 2015 cytokine study  which found the immune system going gangbusters early in ME/CFS but then pooping out, exhausted, later identified two possible subsets (early and long duration patients.) Lipkin then teamed with the Simmaron Research Institute to document similar findings in chronic fatigue syndrome (ME/CFS) patients’ spinal fluid.  Dr. Peterson, Lipkin and the Simmaron Research Institute then uncovered an atypical ME/CFS subset (the “Peterson subset”.)

In an email Lipkin emphasized the critical need to identify the subsets he believes must be present in this disease.

ME/CFS is not a single disorder and is unlikely to have  single cause or a single treatment. As we learn more about ME/CFS, we are beginning to define subtypes. This is critical to understanding how people become ill and developing practical solutions for management. The challenge is not unique to ME/CFS. It is representative of the Precision Medicine initiative that is sweeping clinical medicine and public health. Just as there is no one cause or cure for all cancers, all forms of heart disease, or all infections, there will be more than one path to ME/CFS and more than one treatment strategy.

Over the past couple of years Lipkin – who has been intensely interested in the role that gut bacteria plays in this illness – has been digging into an ME/CFS plus irritable bowel subset. We’ve learned in the past ten years just how influential the gut is. Gut bacteria and the metabolites they produce don’t stop at the gut. If they leak out of the gut they can directly affect the immune and central nervous system functioning. Some of the metabolites showing up in ME/CFS metabolomic studies originate in the gut.

Last year Lipkin’s group published the most comprehensive gut bacteria study in ME/CFS yet done, which incorporated immune and clinical findings. This year he repeated the gut bacterial analysis and added metabolomics  and clinical findings to the mix. The man clearly likes large, complex studies.

The 2017 Gut Study

The large 2017 Nagy-Szakal/Lipkin gut study was notable for it’s size (n=100) and it’s breadth – it included patients from no less than six ME/CFS practitioners including Dr. Peterson. It found, amongst other things, increased levels of bacteria from a family (Clostridiaceae) known for its abundance of toxic and disease causing bacteria.

One of the few gut studies that’s actually been able to identify individual bacterial species, the study found increased abundances of several bacterial species (Faecalibacterium & Coprococcus spp.) that have been associated in other studies with IBS-like symptoms, including colonic pain, bloating, and GI discomfort.

Using a type of data analysis called topological data analysis (TDA) which is able to incorporate metagenomic, metabolic pathway, immune and clinical data, the Lipkin group found that the presence of irritable bowel syndrome (IBS) was having a major effect on disease severity, gut microbiota, and immune profiles.

That finding led the Lipkin group to split the ME/CFS patient cohort into ME/CFS with IBS and ME/CFS without IBS subsets and examine the differences in microbiota (gut bacteria).

gut bacteria ME/CFS

The gut bacteria in the ME/CFS plus IBS subset was different from the ME/CFS only group and the healthy controls

The results were astonishing. A dissimilarity measure found that gut bacteria differed as much between the ME/CFS + IBS patients and the ME/CFS – IBS patients as between the ME/CFS group as a whole and the healthy controls. That analysis suggested that the guts of the ME/CFS patients with and without IBS featured significantly different bacteria.

The cytokine data in the study did not add to the analysis but the microbiome analysis revealed a number of interesting possibilities,

Metabolic pathway analyses revealed the ME/CFS + IBS and the ME/CFS – IBS groups differed in some important ways. Both groups featured enriched metabolic pathways that produced Vit. B6, but an important part of the energy production process (the pyrimidine ribonucleoside degradation pathway) was enriched in the ME/CFS only group. That same pathway was hit hard in the ME/CFS plus IBS group.

Plus, the abnormalities found in the urea cycle, which is closely linked to aerobic energy production (Krebs or TCA cycle)  occurred mostly in the ME/CFS + IBS group.

The data suggested that people with ME/CFS and IBS group had different bacterial gut makeups and might have more problems with energy production than people with ME/CFS, and it set the stage for Lipkin’s next effort.

The 2018 Gut and Metabolomics Study

Sci Rep. 2018 Jul 3;8(1):10056. doi: 10.1038/s41598-018-28477-9.Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics.  Nagy-Szakal D1, Barupal DK2, Lee B1, Che X1, Williams BL1, Kahn EJR1, Ukaigwe JE1, Bateman L3, Klimas NG4,5, Komaroff AL6, Levine S7, Montoya JG8, Peterson DL9, Levin B10, Hornig M1, Fiehn O11, Lipkin WI12.

After striking that rich vein, the Lipkin group expanded their research effort – incorporating metabolomics for the first time into their studies. (Lipkin and the Simmaron Research Foundation are also currently engaged in the first metabolomics spinal fluid study.) Once again incorporating a wide variety of doctors from different locations (Peterson, Bateman, Klimas, Levine, Montoya) and using a fairly large sample set (n=100) Nagy-Szakal/Lipkin, the Lipkin group fused together blood metabolomic, fecal bacterial metagenomic, and clinical data to paint a new picture of ME/CFS.

The study represented the first attempt to meld two potentially important fields in ME/CFS – metabolomics and gut microbiome findings- together.  Lipkin and Hornig have proposed that the gut issues play an important role in ME/CFS, and several studies have found evidence of dysbiosis (pro-inflammatory gut bacteria) in ME/CFS.  Unutmaz is chasing down a T-cell gut connection, and past studies have suggested that bacterial leakage from the gut could help explain at least some of the post-exertional malaise present.

Given the group’s past gut findings – that significant differences in gut bacteria, immune profiles and possibly energy production exist between ME/CFS + IBS patients and ME/CFS patients without IBS, it made sense for the Lipkin group to once again split the ME/CFS group into subsets with and without IBS and analyze the heck out of them.

Study Results

Energy Production Problems Highlighted

The study confirmed past general findings of decreased levels of phospholipids and sphingomyelins – two important findings by Naviaux- and increased levels of triglycerides (TG’s). (Triglycerides have been associated with metabolic problems and hypothyroidism.)

That both the ME/CFS + IBS group and the ME/CFS without IBS group had reduced levels of metabolites associated with the choline-carnitine energy pathway suggested that both groups had similar core metabolic problems.  (Carnitine participates in the TCA cycle, ATP production and energy metabolism).

More Was Better

The Lipkin group’s decision to integrate metabolomics, microbiome and clinical data worked. Not only did incorporating all this data together illuminate a possibly important subset – the ME/CFS IBS subset – but it also allowed the group to better differentiate ME/CFS patients from controls. It suggested that studies which combine multisystemic data together will do a better job in describing this multisystemic disease.

As with the 2017 study, having or not having IBS was the biggest driver in determining the kind of bacterial profile (and bacterial metabolic pathways) present. This time the study found that the metabolomics of the ME/CFS + IBS group were significantly different from the ME/CFS only group as well. That suggested these two subsets of ME/CFS patients might be quite different indeed.

In contrast to Naviaux, the study did not find a “consistent decrease” in ceramide metabolites – the most commonly disrupted metabolite Naviaux found in his ME/CFS group.  When Lipkin controlled for IBS, he found increased levels of ceramides in the ME/CFS plus IBS group but decreased levels of ceramides in the ME/CFS only group. That suggested that key metabolites in ME/CFS might be different in these two ME/CFS subsets.

The Core Problem in Chronic Fatigue Syndrome Identified? Naviaux’s Metabolomics Study Breaks Fresh Ground

Bacterial Toxins Highlighted

Nagy/Lipkin suggested that increased levels of bacterial toxins (IBS connection) in ME/CFS may be triggering an enzyme called sphingomyelinase to produce the ceramides which then may damage the gut lining and possibly interfere with energy production.

gut metabolomics ME/CFS

The metabolomic analysis suggest unique metabolic problems may be present in the ME/CFS plus IBS group

Ceramides are waxy fats that figure in a number of processes that may be important in ME/CFS. Not only can they produce many free radicals (reactive oxygen species) that can damage the gut lining (the IBS connection), they can also interfere with electron transport (the energy connection) as well as contribute to insulin and leptin resistance (metabolism issues).

The authors also proposed that the higher mannitol levels found in the ME/CFS could reflect the breakdown of two important barriers in the body: the gut barrier and the blood-brain barrier.

Several studies suggest a breach in the gut barrier could be contributing to systemic inflammation in ME/CFS, and one suggests that exercise may further widen that breach. Several researchers, including Jarred Younger and Avindra Nath, have also postulated that the suspected neuroinflammation in ME/CFS results from immune cells entering the brain through a weakened blood-brain barrier.

The Gut Shines in Distinguishing ME/CFS Patients From Healthy Controls

Interestingly, for all the focus on metabolomics, a network analysis using differences in gut bacterial abundance was better able to distinguish ME/CFS patients from healthy controls than did metabolomic results.

That suggested that gut bacterial differences may be more prominent than metabolomics differences in ME/CFS patients. That was a surprise, and we’ll see how this all turns out. It stands to reason that the closer we get to the core of the problem, the more striking the differences we’ll see between healthy people and people with ME/CFS.  (Will the gut play a bigger role than we thought?)

Possible Treatment Options

The group suggested that their findings, if validated, could present some possible treatment options. They included using SMAse blockers to reduce ceramide levels and giving carnitine supplementation to increase the low levels of metabolites in the choline-carnitine pathway.  One open-label study found that carnitine supplementation helped over half of ME/CFS patients.

Given the unrevealing cytokine data from Lipkin’s cytokine data and his recent turn to metabolomics I asked Lipkin how important a role cytokines were likely to play in future ME/CFS research and treatment. Lipkin felt they may yet play an important role in ME/CFS indeed:

“Cytokine disturbances can result in fatigue, cognitive and other disturbances. The observation that other biomarkers such as metagenomic or metabolomic profiles are highly associated with disease does not diminish their (cytokines) importance. There may be people who would benefit from drugs, including antibody therapies, that modulate cytokine responses.”

Scheibenbogen is pursuing antibody therapies in ME/CFS, and Nancy Klimas is reportedly using Enbrel (etanercept) – a cytokine (TNF) blocker – plus mifepristone in her Gulf War Illness trial. Other biologics are available and more are coming on the market.  Recent findings in POTS suggest that antibody drugs will probably play an important role in that disease as well.

Since the study also found that taking Vit. B supplements was associated with higher levels of pantothenic acid and lower fatigue scores, taking Vit. B supplements may be a good idea.

The 5-MT Question

Decreased levels of 5-MT, a metabolite associated with tryptophan, serotonin and melatonin metabolism could reflect problems with serotonin/melatonin conversion. This finding, however, was confounded by the high use of antidepressants (50% of the ME/CFS group) which could have produced the decrease.

Correlation studies do suggest, though, that low 5-MT levels could contribute to problems with cognition, sleep and fatigue. Larger studies are needed to determine if the low 5-MT levels are associated with those symptoms in ME/CFS – and if they are – if it might be beneficial to modulate that pathway using drugs in ME/CFS.

Next Up for the Simmaron Research Foundation and Ian Lipkin

The next phase in the Simmaron Research Foundation’s ongoing collaboration with Ian Lipkin is an expanded study which will, for the first time in ME/CFS, analyze the metabolomics of ME/CFS patients cerebral spinal fluid. The study, which will also include immune analyses is the third Simmaron/Lipkin CSF study to date. The first two studies found dramatic evidence of immune activation and the presence of a potential new subset.

Simmaron’s Spinal Fluid Study Finds Dramatic Differences in Chronic Fatigue Syndrome

Lipkin also reported rapid progress from his new NIH research center and a new collaborative effort with ME/CFS researcher and NIH ME/CFS research center leader Derya Unutmaz. The idea of two top labs in the country collaborating in a complementary fashion is an exciting one – one we will hopefully see much more of in this field.

Lipkin and Unutmaz are merging their respective strengths in a collaboration – something we could use much more of in ME/CFS.

We are completing analysis of saliva, blood, and feces for bacteria, viruses and fungi from ME/CFS and control subjects using powerful new sequencing methods. This will be the largest and most comprehensive study to date on the microbiome in ME/CFS. We will soon begin metabolomic, proteomic, and transcriptomic analyses of ME/CFS and control subjects before and after exercise. We are deeply grateful to the patients who are contributing to this work despite the implications for their health. They are true heroes.

We have begun a new collaboration with Derya Unutmaz and Jackson Laboratories that builds on the complementary expertise of our teams in cellular immunology and molecular microbiology and biochemistry.

Dana March and Tony Komaroff are building an app to help ME/CFS subjects and their caregivers track their status. We have had great support in this effort from people in the community.

Conclusions

In the past three years Lipkin’s identified three potential subsets (early/late duration patients, the “Peterson subset”, ME/CFS + IBS subset) and his explorations into the ME/CFS IBS subset continues to reap dividends.

Lipkin has been a vocal advocate for ME/CFS

Dr. Ian Lipkin, Center for Infection and Immunity, Columbia University

His metabolomic study found signs of energy production problems in all ME/CFS patients, but when Lipkin separated out the ME/CFS + IBS patients, he found altered, even at times opposite metabolic findings that could suggest a different source of fatigue was present in the ME/CFS + IBS patients. His earlier study suggested more severe energy production problems may be present in ME/CFS patients with IBS.

The importance of the gut bacteria in ME/CFS perhaps rose to a new level of significance when a network analysis found larger differences in gut bacteria than metabolites. Lipkin’s ability to better differentiate ME/CFS patients from healthy controls using gut bacteria, metabolomic and clinical data suggests that large studies which tie together multiple systems will be the most helpful.

In short, the latest study from the Lipkin group indicates that the gut does matter in ME/CFS and that in those with gut problems it may matter more than we think.

The Simmaron Research Foundation and Lipkin are employing metabolomics in the study of cerebral spinal fluid for the first time, and Lipkin has launched a new collaborative ME/CFS effort with fellow NIH ME/CFS Research Center leader Derya Unutmaz.

 

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.

precision-gut-data-me-cfs

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”.

IBS-ME/CFS-GUT

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

 Symptoms

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

good-bacteria-reduced-me-cfs

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.

Conclusion

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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