My FMT (Fecal Microbiota Transplant) Experience
I have had inflammatory bowel disease for about 9 years now, and over the past two months, I have been in the hospital with a severe flare AND concurrent C. difficile infection. I had failed multiple treatments, and as a last-ditch resort I did a unique treatment called FMT (fecal microbiota transplant), sometimes referred to as a stool transplant. This is still a fairly new treatment that is not yet FDA approved, but studies have shown that it is extremely effective and even superior to antibiotic treatment. Before getting my FMT, I tried researching more about the actual process (from a patient perspective), but I had difficulty finding more than a few anecdotal stories. By sharing my experience, I hope to give others an idea of what to expect using the capsule method.
A little background on me:
In 2010, I was diagnosed with ulcerative colitis. This is a form of inflammatory bowel disease, which is a broad term that includes both Crohn’s disease and ulcerative colitis. Both of these conditions are autoimmune disorders in which the body views the gut as a foreign invader and attacks itself, leading to severe abdominal cramping, diarrhea, bloody stools, ulcers, fistulas, and a wealth of other problems. I talk more about my ulcerative colitis diagnosis here if you would like to learn more. My ulcerative colitis makes this story unique because there is very limited data on using FMT in patients who have both inflammatory bowel disease and C. diff. For anyone who is reading this who just has C. diff (without inflammatory bowel disease), remember that my FMT experience will likely be different than yours. If you do have inflammatory bowel disease and C. diff, I hope my FMT story can help you in your journey.
A little background on my current situation:
Ulcerative colitis has periods of flares (active disease) and remissions (symptom-free). In August 2019, I developed what I thought was a flare of my ulcerative colitis, and after waiting a few weeks to see if it would go away on its own, I eventually called my doctor to get a prescription for steroids (the treatment for acute flares). My doctor knows me well and was willing to do this, but first he wanted to check some stool tests to rule out infection. Surprisingly, I tested positive for C. difficile (also referred to as C. diff which is an abbreviation for the bacteria Clostridium difficile). I was shocked. C. diff is traditionally caused by antibiotic use, although it can also be contracted by exposure to the tough spore-forming bacteria in healthcare settings and infected patients. When you take an antibiotic, you are killing both good and bad bacteria, and if you kill too many good bacteria, it allows the bad bacteria to grow out of control. C. diff is a bad bacteria, and when this takes over your GI tract, it causes diarrhea, abdominal pain, fever, decreased appetite, and inflammation of your colon. Ironically, it is treated with antibiotics, but there is a very high recurrence rate, and about 1 in 5 people with C. diff will develop C. diff again in their lifetime. The only antibiotic I had taken prior to this diagnosis was a few months prior in June when I took a SINGLE 200mg dose of doxycycline for a tick bite (to prevent Lyme Disease). I still don’t know if that was the culprit, but if it was, I hope it serves as a warning to how powerful and detrimental antibiotics can be. When I got diagnosed with C. diff, I was treated with an antibiotic called vancomycin. Seven days into the ten-day treatment course, I had 0% improvement in my symptoms. I was having 20-30 watery bowel movements a day, blood in my stool, intense abdominal cramping, and weight loss. Since I was not responding to treatment, I was switched to the second-line antibiotic, fidaxomicin (Dificid). This did not help at all either. While on this treatment, I told myself that I would go to the hospital when I hit 100 pounds (I’m 5’ 3” and normally weigh 120 pounds). About 4 days into the fidaxomicin treatment, I hit 100 pounds and made my way to the hospital, where I was admitted.
While in the hospital, they re-tested my stool and it came negative for C. diff. This is very unusual, because even after treatment, the test for C. diff usually stays positive for several weeks. However, because of the negative result, they felt that my continued symptoms were actually due to an ulcerative colitis flare, which was not being treated. The treatment for ulcerative colitis flares (steroids) has the side effect of weakening your immune system, so they did not want to put me on this while I had an active C. diff infection. Unfortunately, the infection and untreated flare put my colon in a very vulnerable state, making my flare even more severe than when I started. In addition to the steroids, I also began treatment with Remicade which is an infusion of an immunosuppressant used to treat Crohn’s Disease and ulcerative colitis.
To avoid a long story, I spent the next six weeks in my local hospital (in Maine) going back and forth between treating my ulcerative colitis and getting diagnosed with recurrent C. diff infections. Each disease (and treatment) was worsening the other disease, and I could not get either under full control. By week 6, I was transferred to Mass General Hospital, four hours away in Boston. When I was there, I was diagnosed with my third bout of C. diff. I had multiple images and procedures which confirmed I also had an ongoing flare of my ulcerative colitis. Since I was already on max treatment for my flare (Remicade and IV steroids) and C. diff (failed treatments with vancomycin, fidaxomicin, and IV metronidazole), it was time to move on to plan B for treating the C. diff. This is where the FMT comes in.
What is FMT?
FMT, or fecal microbiotia transplant, is a novel treatment that involves re-colonizing a sick patient’s colon with “good” bacteria. It’s a fairly simple concept: Take poop from a healthy donor, inoculate it into the patient’s colon, and let it out-compete the C. diff. The process of becoming a stool donor is very strict, and only 2% of people who apply to be a stool donor will actually get approved. The process involves getting screened for infectious diseases, surveying the donor’s diet, checking a medical history, measuring BMI, and much more. There is so much we don’t know about the gut microbiome, and the stool donors will even get denied if they have a history of mental illness like depression/anxiety, because even that is thought to be linked to the gut microbiome (see NPR article here which discusses this interesting concept in more detail). On a different subject, I read a story about how a woman got a fecal transplant from an overweight donor, and after the transplant she became overweight. I find that so fascinating, and I encourage you to do your own research on the amazing world of the gut microbiome and how it affects more than just your gut.
There are several methods of performing FMT:
Colonoscopy - This is the traditional way that brings you right to the source. Getting a colonoscopy is a procedure that involves inserting a flexible tube into your rectum, passing it up through the colon until it reaches the small intestine, and then “depositing'“ the donor stool into the colon.
Nasogastric tube - If for some reason you are unable to get a colonoscopy, you can approach things from the other end. Using a thin, flexible feeding tube, doctors insert donor stool through a patient’s nostril, down the throat and into the stomach.
Capsules (“poop pills”) - A newer method that does not require any fancy preps, anesthesia, or equipment is to simply swallow capsules that contain frozen poop. I have seen studies that say this method is equally effective as a colonoscopy, while other studies say it is slightly inferior, but still very effective.
Because my colon was so inflamed from the ulcerative colitis and C. diff infection, I was unable to get a colonoscopy because of the high risk of perforation. Therefore, I took the capsules, or “poop pills”. My doctors were a bit hesitant to do FMT at all since there is little data on using this in patients with inflammatory bowel disease, but because I failed all other treatments, we all felt that the benefits outweighed the risks. There was the potential that the microbial burden could actually worsen my ulcerative colitis, but I was willing to take the chance. Below I will outline my day-by-day journey with my FMT.
Day 1: After being NPO (nothing by mouth, no food or water) since midnight, I was greeted by my infectious disease doctor at around noon. He had in his hand a big Styrofoam container (similar to the one pictured). I was confused as to what could be in there, but it was simply a bunch of ice and a prescription bottle that contained 15 large capsules, each about the size of a large multivitamin. After washing my hands, he said “Take as quick or as long as you need to swallow these, and then you’re done!” The capsules were frozen, so I was glad to have some room temperature water to get them down, and in less than two minutes, I had swallowed all 15 capsules. The capsules did not taste like poop, and I did not feel queasy at all after taking them. The doctor told me that the capsule shells used to be clear (as opposed to white), and the patients had a difficult time because they could visually see the poop inside the capsules. Luckily, I did not have to worry about that. The doctor told me that I may develop some abdominal cramping which is normal, but that never happened (other than my normal cramping that I had already been experiencing). I had my first bowel movement about 8 hours after taking the capsules. I noticed there were some funny white/yellow things within my stool, and I later figured out that I was looking at the capsule shells that had made it through my gut. My next bowel movement was about 1.5 hours after that, and it also contained some capsule shells. This stool was actually a bit softer than my previous one.
Day 2: Today, I got a second round of FMT at 10:15 a.m., again after being NPO since midnight (I was able to begin eating again 1 hour after taking the capsules). It was the same process as yesterday, simply swallowing my 15 frozen capsules. Today, I only had 4 bowel movements total, when I had been averaging 5-7 bowel movements a day prior to this. My stool was still soft in consistency, but nothing was getting worse. I was a little crampy this night, but I have been crampy for my entire hospital stay, and it was about the same intensity/frequency.
Day 3: I did not have any overnight bowel movements last night, and I only had two bowel movements for the entire 24 hour day! Bowel movements are still soft.
Day 4: The cramping has finally improved slightly, both in intensity and frequency. I continue to have a decreased appetite (which I have had since being hospitalized). Although I have not had any miracle 100% resolution in my symptoms, I certainly have noticed many positive changes, particularly in the number of bowel movements I have been having. Today I had 3 bowel movements, and they varied between soft and formed. One interesting thing I noticed is that both my poop and my farts smell different now. I read one lady’s story about how her husband was her donor for her FMT, and her farts now smell like his. How interesting!
Day 5: At this point, things have stabilized. I am having 2-3 soft/formed bowel movements a day with on-and-off cramping throughout the day. This is certainly an improvement from the 5-7 bowel movements I have been having during my hospital stay. While many people will notice a near-complete resolution in their symptoms after FMT, I suspect my ulcerative colitis is responsible for the residual symptoms I am experiencing at day 5.
Day 6 onwards: My symptoms were stable from days 6-9, and on day 10 I had what I could only describe as an amazing day. My cramping was nearly 100% gone, my appetite was through the roof, and my energy was great. Up until this point, I would describe my hospital days as “a little better” or “a little worse”, but day 10 (nine days after my first FMT dose, which I received 54 days into my hospital stay) was night-and-day exponentially better to a whole new level. The next day (day 11), this trend continued and my stool started to become noticeably more firm and large. At this point I was averaging 2-3 bowel movements a day. My overnight bowel movements decreased significantly as well. Since this point, I have continued to feel amazing, and my weight has finally started to go up. I think it’s safe to say the fecal transplant was a success!
Final thoughts:
As I write this, I am still in the process of evaluating my body’s response to my FMT procedure. After 72 days in the hospital, I can say with confidence that this is the one and only treatment I received that correlated with a SIGNIFICANT improvement in my symptoms. When I read articles on fecal transplants, I had the expectation that I would have a complete response in a day or two, but in my case, it was about 10 days before I went from noticing a little improvement to a lot of improvement. My bowel movements are now more solid than when I was “healthy” before my hospitalization, and I am still amazed at how my cramping went away nearly overnight and my appetite jumped through the roof on day 10. I truly wish this treatment was FDA approved and wasn’t as hard to obtain, because I was ready to do this the first day I was in the hospital, and I can’t even imagine how much pain and suffering (and financial strain) I could have avoided by doing this from the get-go. I am a firm believer that the gut microbiome is the link to many diseases (not just diseases of the gut), and I am so happy that I had the opportunity to do a trial of this treatment, even though it took 54 days in the hospital to get it. For anyone who is suffering from C. diff, I would highly recommend trying FMT if given the option. While you may experience the initial “ick” factor about the process, it truly can be a miracle treatment and life changer. Feel free to comment below with any questions or personal experiences to help spread the word on this wonderful treatment.
86 pounds...
I spent a total of 91 days in the hospital. This is what ulcerative colitis, C. diff, malnutrition, and sitting in a hospital bed will do to you. This stuff is no joke!
*UPDATE (08/17/2020)
It took a few weeks after my FMT treatment to get discharged from the hospital because my body was dependent on IV steroids, and the doctors were having a hard time switching me over to oral steroids. Eventually, my body started accepting the oral steroids (which I was taking for my ulcerative colitis), and I went home where I would taper off them over the course of 6 weeks. About 3 weeks into my taper, I started developing symptoms again of abdominal cramping, diarrhea, decreased appetite, and bowel incontinence. It turns out my ulcerative colitis came back with a vengeance , and I was so sick that I was admitted to the hospital on Christmas Eve. The doctors tested me for antibodies to Remicade, and they were positive. What this means is that my body created antibodies (soldier cells) that attacked the Remicade, rendering the drug useless. At this point, it was decided that I needed to get surgery to remove my colon. This was due to my ulcerative colitis, not the C. diff. I am feeling great now and finally living my life again, so I certainly don’t regret getting this done!
In regards to the FMT, I would still 100% recommend it to people who have C. diff. Like I said above, it was the only treatment that gave me significant improvement in my symptoms, and it made my stool firmer than before I was even sick. The reason I had my colon removed was because of my ulcerative colitis, but I do wonder if things would have been different if I had the FMT sooner, as opposed to getting it when I was 86 pounds and very sick/weak.
Supplement recommendations:
I’m generally not a fan of supplements because I prefer to meet all my body’s needs through a healthy diet. However, in times of desperation, I feel they do have their place. Below is a list of the supplements I am have used for both my ulcerative colitis and C. diff. The only one I have actually noticed a distinct correlation with symptom improvement is L-glutamine, but that doesn’t mean the other ones aren’t making an impact.
L-glutamine: I have been using L-glutamine on-an-off for several years for my ulcerative colitis. Glutamine is considered to be a conditionally essential amino acid, which means under certain circumstances (like chronic illness and stress), the body may require more glutamine than it can produce. It acts as the primary fuel for the rapidly growing cells of the immune system and GI tract, and it is thought to play a role in treating leaky gut syndrome, a condition where your gut allows toxins and other unwanted particles to cross into your bloodstream. This in turn is thought be a huge contributor to autoimmune diseases (and not just autoimmune diseases of the GI tract like Crohn’s/colitis). When I take glutamine, my bowel movements will go from soft to formed in a matter of days. If I am having a mild flare of my colitis, I can sometimes stop the bleeding and get my symptoms under control with glutamine as well. I typically use 1 rounded teaspoon in water once a day, but if my symptoms are more severe I will do this 2-3 times a day. Be aware that glutamine capsules are not potent enough to give you the benefits you need, and the powder is the recommended formulation. In my current flare and C. diff infection, the glutamine is not a magic fix, but it does play a role in speeding up the healing of my intestinal lining. If you are interested in learning more about leaky gut, the gut microbiome, and autoimmunity, I would highly recommend listening to some of Alessio Fasano’s talks on YouTube such as this one. Note: his focus is more on the role of gluten in leaky gut and autoimmune disease, but he also elaborates on many other interesting concepts.
Manuka honey: I had never heard of manuka honey until a friend told me about it while I was in the hospital. Manuka honey is a special type of honey from New Zealand which contains a high level of an antibacterial compound called methylglyoxal (MG). Although MG is found in small quantities in other honeys, it is found in high concentration in the nectar of manuka flowers, which is where manuka honey comes from. There is a grading system for manuka honey (UMF grading system) that ensures the purity and quality the honey so that you know you are getting the MG concentration stated on the bottle. What really got me interested in manuka honey is this scientific article which demonstrated that manuka honey is bactericidal against C. diff, meaning it can effective kill C. diff just like an antibiotic would (some antibiotics are only bacteriostatic, meaning it just prevents new bacteria from forming, but bactericidal means it can actually kill established bacteria). I personally love the taste of honey, so I happily eat a few spoonfuls a day! In addition to treating C. diff, manuka honey has been proven to improve antioxidant status and reduce inflammation in rats with both IBS and ulcerative colitis. The only downside to manuka honey is that it is very expensive and goes for about $40 for a 9 ounce bottle. However, when you compare that to 70+ days in a hospital and $100,000 in medical bills, it really doesn’t seem that bad. I alternate between two different brands of manuka honey: Comvita UMF 15+ and Steen’s UMF 15. I chose Comvita because it was the same brand used in the study mentioned above. I also like Steen’s because their product keep the entire honey comb which leaves behind the nutritious “bee bread” and pollen.
Absorb Plus: When I was unable to eat solid foods in the hospital, I was restricted to TPN (getting “food” through an IV) and an enteral diet (liquid shakes consisting of pre-digested protein, carbohydrates, etc.). The idea of an enteral diet is to give your bowels a rest to allow them to heal. The enteral shakes provided by the hospital were disgusting and loaded with sugar, artificial sugars, and emulsifiers like carageenan, all of which can aggravate ulcerative colitis. As an alternative to this, I purchased my own enteral shakes. One option is Kate Farms Peptide 1.5 shakes which taste like a vanilla shake, but for me the taste of it got real old real quick. I recently switched to Compleat which tastes much better and is covered by insurance! I also like a product called Absorb Plus. This “shake” comes in a powder form that you mix up yourself in a Blender Bottle, and it was created by Jini Patel Thompson, author of the awesome book, Listen to Your Gut (for anyone who has ulcerative colitis or Crohn’s Disease, I highly recommend reading this book). Jini Patel Thompson has Crohn’s Disease and has done decades of research on inflammatory bowel disease, and her product is specifically designed for people with inflammatory bowel disease. The Absorb Plus shakes come in many delicious flavors as well (my favorite is Chocolate Royale), and they are tasty enough that I do not need to force them down to get them in. Even now that I can eat solid foods again, I still consume at least one Absorb Plus shake a day since it provides me with essential proteins, nutrients, and amino acids (including glutamine, which no other enteral shakes contain) that help with my severe malnutrition and weight loss.
Probiotics: Probiotics are a tough product to recommend because there is so much we don’t know about them. By getting a fecal transplant, I was doing the ultimate probiotic supplementation by inoculating my gut with thousands of different microbes, many of which can’t be cultured in a lab. Most probiotic supplements on the market will generally give you no more than ten strains of “good” bacteria, and it is all a guess as to which bacteria are the most beneficial for your body. Because of these unknowns, I decided to choose my probiotic based on a manufacturer I trust. I use the Natren Healthy Start System which is a combination of three different powdered probiotics: Lactobacillus acidophilus DDS-1, Bifidobacterium bifidum Malyoth, and Lactobacillus bulgaricus LB-51. Natren has been doing clinical trial research for 30 years and maintains strict guidelines for the potency of their products. They keep all three bacterial strains separated in their own bottles to prevent them from competing with one another, but you can mix them together when you are ready to use them. I add my probiotics to my Absorb Plus shake. The powder is good because it is readily absorbed by the body, even if you are having a lot of diarrhea. Note: these must be refrigerated.
Protein powder: When I am healthy, I do not use protein powder since I get all the protein I need in my diet. However, I was extremely malnourished in the hospital and needed every bit of help I could get. At my lowest, I weighed 86 pounds which put me at a BMI of 15.2 (anything less than 18.5 is underweight). In addition to the TPN and Absorb Plus shakes, I used Amazing Grass Amazing Protein Digest to get an extra boost of protein. I mixed it in my unsweetened coconut milk yogurt which actually gave it a nice vanilla flavor. This protein powder is plant based, sweetened with Stevia, contains prebiotics (food for probiotics), and also contains the probiotic Bacillus subtilus.
A note on disinfecting:
C. diff is a spore-forming bacteria, meaning it is very difficult to kill. Because it can survive for months (even years) on non-living surfaces, you need to disinfect your bathroom and house so you don’t re-infect yourself or others. The only way to do this is with bleach. Alcohol wipes are not effective! Mix 1 part bleach to 10 parts water and focus on cleaning surfaces that are touched by hands like doorknobs, refrigerator handles, shared cups, toilet flushers, and toilet seats. I personally found it easier to use bleach wipes. Be aware that the Clorox and Lysol disinfecting wipes you get at the store do NOT contain bleach. The only bleach wipes I could find were Clorox Healthcare Bleach Germicidal Wipes. You can get them on Amazon here.