2013: The Year of the Microbiome?

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fecal transplant


The role of the microbiome, the complement of bacterial passengers

carried around by every human being, gets more intriguing by the month.

The Economist, February 2013


There’s nothing more powerful than an idea whose time has come, and it seems that 2013 was the Year of the Microbiome.  Will 2014 be even bigger and blow our socks off?  Like an Alfred Hitchcock movie, I cling to my cyber-seat in anticipation of the next twist.

For biome-watchers, here’s a recap of the goodies delivered in 2013:

  • The year starts with a bang, with the publication of the Van Nood study in the New England Journal of Medicine showing a 94% success rate for treatment of C diff with Fecal Microbiota Transplant (FMT).  The results were so spectacular the control group were put out of their misery and offered the FMT. Although FMT had been used successfully outside of trials, this study gave FMT credibility in the medical community and has initiated subsequent trials around the world.  FMT is now becoming a standard treatment option for anti-biotic resistant cases of C diff.

  • The US FDA attempts a moratorium on FMT by declaring it an investigational new drug and requiring further research. Patient groups are not invited to a FDA workshop held in May to discuss the decision.  

    The moratorium leads to uproar in the C diff patient-doctor community, a doubling of visitors to the PoP site and the FDA backdown in July, which permitted use of FMT for C diff that has not responded to standard treatment, provided the patient signs an informed consent.

  • C diff survivor and sole patient present at the FDA workshop, Catherine Duff recruits doctors and others to establish the Fecal Transplant Foundation a non-profit dedicated to raising FMT awareness, supporting patients and funding research.

  • The New York Times publishes Why I Donated My Stool, a donor story.

  • The American Gastroenterology Association declares Fecal Microbiota Transplant a promising new treatment and launches a FMT Website for doctors and patients. 

  • Dr Ben Eisman is repeatedly heralded as the father of modern-day FMT with a nod to 4th and 16th century Chinese medicos Ge Hong and Li Shizen and 16th century Italian surgeon Fabricius Aquapendent. The Koreans aren’t quite sure what the fuss is about as they have been downing poop wine for centuries.

  • US-based OpenBiome takes a non-profit approach to FMT, streamlining the collection and testing process and commencing distribution of screened fecal microbiota to hospitals for treatment of patients with C diff. Canadian hospital North York General builds the world’s first fecal self-banking system, collecting and freezing patient stool to use as an antidote against possible infection with C. diff.

  • Cleveland Clinic lists FMT as No 6 on its list of Top 10 Medical Innovations for 2014. 

  • We learn that that the diversity and quantity of our microbiota differs, depending on our genes, our blood type, what we eat, where we live and our age. We discover that we inherit our mother’s microbiota before we are born, that caesareans inhibit development of microbiota, that breast milk is the ultimate pro-biotic for baby and that we share microbiota with those we live with, especially our dogs. 
  • Links are increasingly demonstrated between the microbiome and bowel cancer, lymphoma,  blood pressure, heart disease, immunity, arthritis, multiple sclerosis, HIV, autism, liver health, obesity, insulin resistance, diabetes, autism and inflammatory bowel disease. However correlation dose not signify causation and scientists urge caution in drawing conclusions. More research is needed.

  • FMT shows promise in the treatment of Ulcerative Colitis and Crohns, albeit not at the same level of effectiveness for C diff.  More research is needed.

  • The gut-brain connection migrates from naturopathic folklore into science journals, with the personalities of mice altered by fecal transplants. No it’s not demonic possession – it’s science.  Truth is indeed stranger than fiction and this research was extremely gratifying for those of us who have experienced gut-brain symptoms.  Hopefully this discovery will lead to treatment of root causes of biochemical mental dysfunction instead of the symptoms, and spare the long-suffering (usually female) patient the “is everything ok at home dear?” response from doctors.

  • UBiome and Amercian Gut invite citizen scientists to sequence their microbiomes. Ubiome founder Jessica Richman asks Why should science be limited to scientists?

  • Gut Microbiota conferences proliferate. The European based Gut Microbiota for Health bridges the gap between microbiologists and the media and becomes the leading plain-english resource for all things microbiota.  Their 2nd World Summit of Gut Microbiota for Health is held in Madrid, Spain in February and delivers much appreciated research to the online patient community.  Microbiome conferences are also held in the USA and China, with more scheduled for 2014 in UK and USA .  The Best of the Gut Microbiota for Health 2013 Summit and registration for the 2014 summit are available here.

  • Bio-tech companies and startups scramble on board the biome-bonanza. Whether it’s preventing premature birth, controlling diabetes or inventing fake poop, there’s a company trying to do it.  Even L’Oreal researches the skin microbiome for use in cosmetics.  In addition to these initiatives, it is increasingly recognized that the interplay between the microbiome and pharmaceuticals will impact how all new drugs are evaluated.

  • Respected biome-blogger and open-science advocate Professor Jonathan Eisen calls for a Noble Prize for microbiome research. 

Finally, let’s talk about ourselves.  The growth of the PoP FMT Facebook group, while not news is certainly newsworthy.  The group is a little over a year old with 1100 members, some of whom are in medical and scientific professions.  There is a tremendous amount of knowledge and experience in the group and the anecdotal evidence shows some recurring themes, including:

  • Some very heartening success stories, including one from a doctor with UC
  • Conditions treated include: C diff, diarrhea of indeterminate origin, constipation, UC, Crohns and CFS/ME type symptoms.
  • A clear link between the level of inflammation and success of FMT, with intestinal permeability and bacterial translocation identified as perpetuating factors in dysbiosis
  • The need for maintenance FMTs for a number of people
  • Some disappointing setbacks in those who have had impressive results from FMT, only to once again trigger the condition.
  • More similarity than you would think, between those with IBD and those with food intolerances, autoimmune conditions & CFS/ME symptoms, suggesting that while the outward symptoms are different, the genesis and pathology of the illnesses are similar.
  • Risk factors for dysbiosis are: genetic/family predisposition, environmental triggers (both one-off and repeated courses of anti-biotics, NSAIDs, food poisoning or traveler’s diarrhea), intestinal permeability, stressful life events and gender.
  • It is disturbing how many young people have been given anti-biotics throughout their childhood for non-gut conditions, only to end up with their guts in an absolute mess by the time they reach their ’20s.

Correlation does not equal causation and the big question is: does our microbiome determine or reflect our health? Do you have dysbiosis because you are sick or are you sick because you have dysbiosis? The truth probably lies somewhere in between.

I take this opportunity to put on record that we here at PoP do not claim that FMT can cure illnesses other than C diff. More research is required to prove this in a way that will satisfy, not only the medical-scientific community, but the patient community too. That said, we have seen some encouraging results that suggest FMT is worth exploring for conditions other than C diff.

Anecdotally, the experiences in 2013 in the FMT Facebook tell us three things. Firstly, FMT does work for conditions other than C diff, for some people. However, it is not a quick-fix or miracle cure for everyone. Secondly, people in our group are very sick. You don’t join a fecal transplant discussion group and experiment on yourself, if you have easier options. Strong and consistent results will always be problematic with a sample like this. Thirdly, there is evidently a complex relationship between the health of the gut wall, the immune system and colonization of new gut flora, which differs between individuals.  

Complex problems often have complex solutions.  In 2014 our brain-storming needs to focus on how to make a happy home for our new flora; how to stabilize the gut wall, reduce inflammation and maximize the results from FMT.  I suggest that future scientific research into FMT needs to do the same. The reliance of mainstream medicine on drugs alone, is frustrating, albeit understandable. The anecdotal experience of our group, is indicating that an integrated multi-factorial approach to healing is required.

Challenges ahead

Get ready for a DIY FMT backlash in 2014. It will only take one home FMT to go wrong and the media will have a feeding frenzy. I take this opportunity to repeat, as I always do, that NO ONE should do FMT without first testing their donor under supervision of a doctor. Outwardly healthy donors can carry blood and fecal-borne problems that are asymptomatic in them, but might wreak havoc in the fragile system of someone with chronic illness. Accordingly to the Van Nood study, two out of three donors tested were unsuitable.  Don’t risk it.  

In a recent interview Dr. Neil Stollman declared FMT the most patient-driven treatment he’s encountered in his twenty-plus years of practicing medicine, stating that three-quarters of his patients come to him due to their own initiative, and it often involves convincing their doctors.  He attributes the reluctance of doctors to offer FMT as due to the risks, amount of labor, and lack of compensation associated with fecal transplants. I would add to that, the ick factor. Most doctors are repulsed by FMT.

Clearly there is a great divide between the majority of doctors and patients on this issue. A compassionate harm minimization approach to FMT on the part of the medical profession is critical. If there are doctors reading, I urge you to show compassion toward your chronically ill patient if they ask you to test a FMT donor. Don’t put them in a position where they risk an untested donor.

As the founder of PoP, I wholeheartedly believe that chronically ill people, whom the mainstream cannot help, are entitled to explore experimental procedures like FMT and are entitled to as much information as possible about the possible risks and benefits of such a therapy. That’s the purpose of PoP until such time as the medical profession is willing and able to have these conversations with patients. I hasten to add that many patients are finding doctors who understand the situation they’re in, and support their right to try FMT.  However they are a minority.

The decision to keep fighting an illness, or to surrender to it, is a very personal one and should be respected by health practitioners, friends and family of the person afflicted. Patients who refuse to give up should be supported, not dismissed or ostracized for refusing to surrender to their illness. Walk a mile in our shoes.

Moving forward

A big thanks to those who have supported PoP in 2013.  If the finely tuned balance of the microbiome teaches us a lesson, it’s that collaboration beats competition.  Together we are stronger than alone.

I look forward to working with you all again in 2014 and to meeting other kindred spirits willing to fight to protect the human microbiome on which we depend so dearly for health.  I look forward to this site becoming redundant, once safe accessible FMT is available to all who need it. I look forward to the next generation of children who will be taught they have a microbiome and how to take care of it, so that they never have to end up begging a doctor to let them try fecal transplant.

As 2013 draws to a close, it’s apparent that notwithstanding 60 years of anti-bacterial propaganda culminating in the hand-sanitizer generation, we humans are evolutionarily wired to exchange microbiota. So if you’re looking for a New Year’s Resolution, try this one: embrace your microbiota, trash your hand sanitizer and get used to the fact that you’re not alone. 

Happy New Year ;-)

If the finely tuned balance of the microbiome teaches us a lesson,

It’s that collaboration beats competition. 

Together we are stronger than alone.

Tracy Mac

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