There is a new frontier in medicine – the Human Microbiome, aka the gut, and the billions of micro bacteria in the human digestive tract.  Humans have long sensed that their gut is connected to their health.  “I have a pit in my stomach.”  “My gut is in a knot.”  It is early days, but now doctors are ‘decoding’ the human biome with new sequencing techniques, and researchers are beginning to understand what we each need in our biome to keep us healthy and to cure disease.  You can contribute data to this effort and the results may improve your life and the lives of others someday.

Many of us understand that we kill the ‘good’ bacteria along with the ‘bad’ when we take antibiotics.  We then eat yogurt and take probiotics to repopulate the good bacteria. However, it is believed that while the plant based probiotic formulae containing billions of bacteria like acidophilus are better than nothing, they are not very successful in repopulating the human digestive tract with a healthy microbiome.

The New York Times just published an extensive article about OpenBiome which has been one of their most shared articles.

(Stop reading if you are squeamish about human poop)

So if taking antibiotics is sometimes a necessary evil, how can we address this unhealthy change in our microbiome caused by the increasing use of antibiotics in medicine and in our food supply?  Doctors can take fecal matter (yes, poop) from healthy donors and transplant it into sick people.  Microbiota from the healthy gut multiply and repopulate in the recipient’s digestive tract.  Healthy human stool may be the ultimate probiotic!

A biotech start-up, OpenBiome, screens thousands of potential donors to identify those with clean family and personal health histories, and performs extensive infectious disease testing to yield a donor pool producing healthy, safe stool for transplantation.  OpenBiome processes the donated ‘poop’, which is rich in active microbiome, into dosages and sends it to doctors all over the world.  Yes, it is as basic as it sounds – fecal matter is transplanted ( Fecal Microbiota Transplantation, FMT) from exceptionally healthy donors to sick patients and they get better.

fmt, fecal transplant
From a Youtube description of FMT.

The FDA has tentatively approved FMT for patients suffering from recurrent Clostridium difficile (c. diff), a dangerous, sometimes deadly and debilitating gut infection increasingly found in hospital patients.  Nearly 7,000 patients have undergone FMT. Some of the most exciting results, those that could change medicine as we know it, have been discovered coincidentally as patients with c. diff were cured, and then reported improvement in other diseases and conditions.  After FMT, some Multiple Sclerosis (MS) patients, have seen significant reduction in MS symptoms.  A man with lifetime alopecia (no hair) began to grow hair. As a result of these findings, clinical trials are beginning to more rigorously explore FMT as a treatment or cure for many human diseases and conditions.

What if someone told you a single substance was currently being investigated as a treatment for such diverse diseases as Obesity, Liver Disease, Type II Diabetes , Alzheimer’s, Depression, Irritable Bowel Syndrome (IBS), ( Sclerosis (MS), allergies and potentially deadly infections? Believe it or not – just such a treatment may exist – and every single one of us produces it every day.

organs explaining human microbiomes path
From the National Cancer Center Singapore

This miracle drug is Fecal Microbiota – the bacteria present in all healthy human stool.  FMT is the process by which poop collected from a healthy donor is transplanted, by colonoscopy, Nasal-gastric tube, or capsules – into the colon of a patient. The healthy bacteria then repopulates in the recipient’s colon and restores order, either by killing the infection, or by changing the colon biology in such a way that myriad other diseases can benefit.“

What is the Human Microbiome?

 Microbes are tiny living organisms, such as bacterium, fungus, protozoan and viruses.

The Human Microbiome is the description of all of the microbes in the human body – the gut microbiome is the area specifically targeted in FMT.

OpenBiome’s mission:   “OpenBiome is dedicated to expanding safe access to fecal microbiota transplantation (FMT) and catalyzing research into the human microbiome.”

What If I want to have my Microbiome decoded?   OpenBiome’s new service, Personal Biome, includes both a report on your Biome and the option to ‘bank’ your stool (yes, your poop) –  in case you like your own biome and want to repopulate your own gut with it after treatment with antibiotics or chemo therapy.  More on OpenBiome’s Personal Biome Project.

American Gut, another young organization, is enlisting participants to gather data from skin, saliva and poop and link the composition of each donor biome to their diet and health. The more people who complete the seven-day food diary, answer health questions and send biome samples in the kit provided by American Gut; the more information scientists will have to discover links between diet, biome and health.

 Human Microbiome, gut

Join the American Gut Biome Study  

You pay $99, give information about what you eat and return samples in the kit they provide.  American Gut will analyze your biome, compare it to others and share information on the link between diet and biome.  You will be contributing to the effort to understand the powerful connection between diet-biome-health.

One powerful story of a young girl with c. diff saved by FMT in Georgia:  Three-year-old Avery Lee was given antibiotics for a sinus infection.  She developed c. difficile, opportunistic bacteria which took over her gut, replacing the healthy biome the antibiotics had destroyed.  Almost overnight she suffered from severe abdominal pain, bloody diarrhea, and stomach cramps.  Avery’s health deteriorated over the next six months despite repeated doses of strong antibiotics.  Desperate, her doctor treated her with FMT from OpenBiome and within days her gut was healthy – she got her life back.


If you want more detail on the work of OpenBiome, here is a more complete explanation.

So how did investigation into FMT begin? Perhaps with a blessing in disguise – Clostridium difficile. Clostridium difficile, or c. diff, is the most common hospital acquired infection in the United States. It is a nasty bug that causes symptoms of extreme stomach flu – so extreme that it kills as many as 30,000 patients a year. C. diff belongs to a class of infections that the entire healthcare community fears – Multi-Drug Resistant Organisms (MDROs) such as the infamous MRSA – that have been on the rise largely due to overuse of antibiotics. C. diff responds to our strongest antibiotics, about 25-30% of the time, whereas a single FMT treatment has a success rate of about 94%. These impressive numbers are even more remarkable when you take into account that FMT is typically only administered to those who have already failed treatment on antibiotics; in other words FMT has a better than 90% cure rate in the most difficult cases of c. diff. Because c. diff is typically acquired in a hospital setting, it has been analyzed in labs and has pushed the field of microbiology forward incredibly rapidly. Say a patient is hospitalized for MS and at the same time acquires c. diff, that patient then receives an FMT and may find that both the c. diff and MS have been treated. These sorts of ‘incidental’ or accidental findings have expanded our understanding of the microbiome in more diseases than we  possibly could have imagined.

Modern data supporting FMT has been available for more than two decades, however logistics and costs have prevented it from becoming mainstream until recently. Previously, doctors who wanted to pursue FMT for their patients would have to go through a lengthy process identifying and screening possible stool donors for infectious diseases and underlying health conditions, and then if they were lucky enough to find a suitable donor, they would need to collect and prepare the transplant material. Needless to say, few were willing to offer FMT to patients. However, a few organizations have worked diligently to provide safer and wider access by creating ‘stool banks’ with carefully screened universal donors.

OpenBiome is a non-profit start-up created by MIT researchers that rigorously screens donors for more than 200 medical history risk factors, and then performs blood and stool testing to find the healthiest possible microbiomes in the community. Once the donors are selected, as a result of a process that fewer than 3% of potential donors pass, they then donate their stool for $40 a donation and that stool is processed into hundreds of treatments for patients. As of September 2015, OpenBiome has shipped nearly 7,000 doses to 49 states and 6 countries, is actively supporting 15 clinical trials and was used in 25% of total worldwide FMT trials published this year.

OpenBiome’s success has been covered in many publications from the New Yorker to CNN – if you’d like to read more check out their press page here OpenBiome Press Page. Organizations like OpenBiome and its commercial counterparts like Seres Therapeutics, are allowing doctors to administer FMT without the vast time and monetary investment required for personal screening and thus thousands of patients are given access to this life-saving therapy. Though this field is newly emerging, it holds enormous promise, so keep an eye out for a whole new perspective on poop. A more recent article was published on 11/9/15 in the New York Times.

If you’d like to learn more there are many resources on-line. One particularly good one is the Harvard Microbiome Outreach website or, this informative YouTube video!

*Update July 2016 – The New York Times continues to follow breakthroughs in this field, and has a new article, Fecal Transplant Can Be LIfe-Saving, but How?