I’ve searched the posts and have found a few from several years ago about similar news I just received. I’m wondering about current experiences, including more about biologics. 

Im a 20 year j poucher after a UC diagnosis. Since 2013 I’ve been treated with antibiotics 2-3 times for pouchitis after suffering with it unknowingly for likely over a decade. Thought I was doing pretty darn great. I’ve never had symptoms as bad as it became by 2013. My GI is not a fan of regular antibiotics saying it ultimately decreases in efficacy. 

Well now my endoscopy results last year and this year show more inflammation and she suspects indeterminant colitis or crohns. A small bowel series and blood work are next.

ultimately, though, it seems she has me headed for biologics after more testing and consulting me about which course of treatment to choose. 

Yes, I’m devasted. After nearly 30 years of disease, misdiagnoses and complications, I was always grateful it wasn’t crohns. Now I’m hearing the stories about possible misdiagnosis again, maybe I didn’t need a j pouch but they know more now than 20 years ago, maybe it didn’t present as crohns until now, maybe they won’t be able to know for sure even with testing what it is. 

I’m left with questions like did this trigger because of massive stress the last few years? What am I in for now that I know this could be progressive? Why have I only been given antibiotics a few times in 4 years unlike other people when I felt so much better afterwards? (Doc said antibiotics can make crohns symptoms feel better but it’s not pouchitis that I have).

And last, she says if I don’t go with the biologics to hopefully heal and keep the pouch healthy, I’m likely to ultimately lose the pouch. So.....I’m starting to read about these biologics and I’m not thrilled about side effects and injections after being med free for decades.

One thing I was grateful for after antibiotics was that I was able to exercise for the first time in my life and drop excess weight and felt great for the first time in my life. Now I’m reading about massive and rapid weight gain with biologics and that people can’t seem to prevent it with diet and exercise. This greatly adds to my upset as being overweight was not only not fun, but physically uncomfortable in many of the usual ways. I really don’t want to go down that path again of meds that help one thing but have major downsides  

Has anyone had experience with battling sudden  and significant weight gain on biologics? Is one biologic any worse than another in this regard? Googling seems to indicate they all cause weight gain, particularly for middle aged women. 

Original Post

Hi, BlueFlame! Like you I have an uncertain diagnosis, though it's been uncertain for longer. I can't change your doctor's mind, but long-term antibiotics work great for many of us. I was on Cipro alone from 2009-2014, and have added Flagyl since then. I would have preferred rotating among several antibiotics, but I couldn't find others that worked for me. I've had no particular side effects. The Cipro did indeed lose efficacy, but adding Flagyl took care of that. Some do get side effects, of course, but I've been very well served by long-term antibiotics. Heck, I just today finished up a week of scuba diving in the Caribbean!

Other folks here have gotten great results from biologics, and the bad side effects really are quite rare. Don't fret, just find something that makes your life work.

Good luck!

Thank you for that, Scott. Yes, really no changing her mind. She keeps throwing out pouch failure looking long term if I decline biologics. 

One thing I know is a no carb, no sugar diet helps me greatly. I haven’t followed it in a long time though and my symptoms seem to follow when I fall off the wagon.

Doc isn’t going to like it, but I think I may need to explore alternative diet more before going down the medication rabbit hole. I’m not good about saying no to doctors but I’m not so sure about this. Clearly the docs aren’t either. 

Rotating antibiotics is a valid and preferred way to manage pouchitis ("inflammation of the pouch") prior to going to biologics. (Like 1 antibiotic for 2 weeks, then another for 2 weeks, then switch back, etc.). If your further testing doesn't show inflammation elsewhere in the bowel, then it sounds like it is indeed "pouchitis" although there are likely different "causes" of pouchitis-it could be inflammation of the pouch somehow triggered by an overgrowth of bacteria (which antibiotics seem to help, as might a major diet change, like low FODMAP) or it could be "crohns of the pouch or crowns-like" or some might refer to it as IBD of the pouch-I have heard that after a couple decades of a pouch, that histologicslly (on a microscope slide) that the tissue of our pouch, technically small bowel, actually begins to look much more like the architecture of a large bowel on the slide.  To be honest, a good work up should be done to rule out other involvement, but if inflammation is al in the pouch, what they call it isn't as important as how they treat it.

when rotating antibiotics wasn't cutting it for my chronic pouchitis, my Dr recommended immuran plus a biological. I was not keen to try a biologic just yet, since I have never tried immuran back in my UC days. Doc gave it a low chance of working, but agreed to let me add immuran to my rotating antibiotics. It took 3 months to build up in my system and has been working great for 2.5 years. I tried to go off the antibiotics, but symptoms crept back, so for me, the combo of rotating antibiotics plus immuran works well-regardless what the exact "cause" of the inflammation was. Plus, I love that I still have the biologics in my back pocket if/when my current regimen stops working.

This article is pre-biologic options, but clearly rotating anitiniotics is a valid treatment, as are other immunosuppressant options. Shouldn't have to go straight to biologics if you don't want to. https://www.researchgate.net/p...28ace5c7ee000000.pdf





Thank you, Jja. I’m told some granulation showed above the pouch last year. She now sees more inflammation and ulcers in and above the pouch. She says it’s not fecal backwash. Perhaps the addition of some granulation and now ulcers that’s suggestive of crohns is why she’s saying it’s not pouchitis. She told me antibiotics might make me feel better but won’t heal the ulcers. 

Last year she sent me for a small Bowel series and no additional ulceration was found higher up. She’s sending me for the same this year and says she suspects there would be more than what she can view with the endoscopy. Last year I turned my diet around for a few weeks before the small bowel series and the test came back clean. I have a few weeks before the small bowel series again, so I’ll work on my diet again. 

The doctor says at this point nothing I do or don’t do will matter. I know that’s not correct. What I don’t know is if I can heal the ulcers without medications. It seems I also need to look at some new diet things first that have been suggested to me. I’m not ruling out biologics but I’m hesitant knowing the doctor so quickly dismissed diet factors. 

Blueflame, if the diet helps, but you only follow it when a test is coming up, then it's doing more harm than good, by masking your usual state. It's reasonable to try if it's a diet you'll be able to follow.

Yes, agreed Scott. I’ve been thinking on that. At the same time, if being consistently responsible in what I eat brings things in line, I owe it to myself to make that effort before resorting to meds that create other problems. I remain open to all treatments. Just feel like this has been a flying leap to biologics. 

My one caution is that it's easy to fall into the trap of assuming that the risks from medication are worse than the risks from untreated (or inadequately treated) disease. As a general rule, the opposite is true. Good luck!

The prior posts by JJA and Scott are right on. I have been rotating antibiotics to treat pouch inflammation since 1995. As long as you rotate there is no decrease in efficacy. While I have kept the pouch inflammation in check, I developed inflammation above the J Pouch in 2007. I changed my diet to include less carbs and sugars in 2012 after a scope showed very bad inflammation and my subsequent scopes were better. In 2015 I began taking Remicade, which has cut my antibiotic dosages in half. The Remicade has essentially eliminated the pouch inflammation but the inflammation above the pouch has proved more resistant to treatment. It is believed that this inflammation may be due in part to fecal stasis above the pouch because my J Pouch inlet was narrowed due to scarring and inflammation. 

Regarding side effects on biologics, I have had none. No weight gain. Nothing. I have been on Remicade for 2 years. I still take antibiotics but in significantly lower dosages. I maintain a modified Paleo diet. Limiting carb and sugar intake is a huge key, in my opinion, and based on my experience which is now 25 years treating a J Pouch for various issues.

Last edited by CTBarrister

Thank you CTBarrister. Agreed on carbs and sugar. I’ve found the same, as have others. Finally an article from Mayo acknowledged it. My experience is doctors do not acknowledge this and, at best, say everyone finds what works best. 

I’m starting to look at organic, too, as there’s much info on that and some fellow IBDers have found benefit. 

Do you have/have you had ulcers and granulation? This is the new thing my endoscopy shows, not just inflammation. And the doctor insists inflammation above my pouch isn’t fecal backwash. 

To answer you yes and yes to ulcers and granulation. All biopsies negative. My doctor said the fecal backwash/fecal stasis from the narrowed J pouch inlet created small intestine bacterial overgrowth. This was back in 2012 and I counteracted it by reducing carbs and sugars. My diet prior to 2013 was horrendous. I am a foodie and 2010-2012 one of my clients roped me into a dinner club that went to very high end restaurants in New York and Connecticut and I got carried away with it and paid the price. I did improve the situation with changing my diet but the inflammation just above the Pouch is what has been most resistant including to Remicade. I suspect if the J Pouch inlet was widened and there was a sphincter preventing backwash stool it wouldn't be an issue, but there is no backwash valve like there is with the colon. 

I have now lived with all of this for a long time (25 years) and hopefully will keep it in check for another 25.

Regarding organic- I do eat some organic foods. Most important is avoiding anything processed. I try to eat mostly whole foods. I have a yogurt for breakfast and salad for lunch every day. My diet is fairly healthy with occasional cheating but I adhere to it for the most part.

Last edited by CTBarrister

Thanks, again, CTBarrister.

Biopsies were negative for what? My biopsies were negative for abnormal cells/cancer. She’s telling me we’re next doing a blood test for Crohns and the small bowel series to look for more ulceration. She seems certain it’s Crohns or indeterminate colitis. 

My biopsies were negative for the same, just have inflammation. I am suspected to have Crohn's but all diagnostic testing was inconclusive and frankly it's a complete waste of your time because whether it's Crohn's, pouchitis or "new IBD variant", it's going to have to be treated and all treatments for these disorders on people like us are exactly the same. Your Doc's diagnosis is probably correct but it doesn't matter because it's likely not going to change anything as far as treatment. My doctors stopped wasting time with diagnostic testing for the same reasons a long time ago.

I had the Prometheus blood test. Total waste of time. It was read by two pathologists - at Mount Sinai and one on the west coast - as inconclusive. Even if it was conclusive it wouldn't matter. So it's a waste of your time IMHO.

Last edited by CTBarrister

I understand what your saying but I’ve lived with the belief I’ve been disease free 27 years with the colitis diagnosis and j pouch surgery. I was always grateful it wasn’t Crohns. 

I also have struggled with medicine side effects a lot. There are some big ones with biologics so I don’t understand why she’s jumping to that first. On the weight gain, middle aged women are most prone, while men are least prone. 

Biologics work well for many people and docs want to find ways to alleviate suffering. I don't see a reason why you couldn't try immunosuppressants and/or antibiotics and/or budesonide (which are all (maybe not antibiotics) treatments for various IBD conditions as a first go (the risk being it maybtake several months to see if they are working and you run the risk of inflammation/ulcers/granulation getting worse, and when things get worse it can be harder to get back under control) before biologics. It's your body, so you should have the final word. I would straight up ask the doc why she is not considering non-biologic options if that is something you would like to try. They are not usually the only option or even necessarily the first go to for treating Crohns or UC either. Treating/not treating and all the treatment options have there own set of risks/potential side effects.

you need a doc you feel is listening to, can answer your questions about treatment Rex's, and that you feel you can trust. It is definitely your perigotove to ask "Why doesn't it make sense to try X?" "Or why don't you recommend trying Y first" - she may have reasons that make sense, given your unique situation, but you need to feel comfortable with the reasons/rationale.

My doctors also pushed biologics first for the same reasons, and because they believed them to be safe. I was put on Entocort before biologics but that was at my request. I can understand your concerns. You don't know about side effects until you try them. Nothing ventured nothing gained, or lost. Ultimately they may be your best option, but I agree with JJA that you might want to try Entocort/Budesonide first.

Last edited by CTBarrister

Thanks again. Yes, I didn’t even know questions to ask about treatment as I’m researching after meeting with her. She’s good but abrupt and not open to suggestion. I’m to have a follow up consult with her PA team to discuss treatment, followed by a treatment plan appointment a week later with her. I’ll be asking about all options now that I know more. 

Blue Flame,

Just remember it's your body and you get to decide the course of treatment.  I would suggest that you be forward with your doctor and tell her what you want to do, after you come to a decision.  Like you, I was very resistant to the idea of biologics when they were first presented to me by my doctors.  I eventually decided it would be wise for me to pursue it., but did not do so until years after they were first urged upon me.  You may not have reached that point yet.  I eventually reached the point where I felt that we needed to try something else.  Good luck with it.

JJA, thank you, too, for your very thoughtful reply. Somehow I missed the last one. So very helpful. I’ll be rereading all this as things proceed. I hope you are well.

I can say I completely changed my diet 5 days ago and added some new recommended things for healing this. My symptoms have backed way off. I can even lie on my stomach, which is something that normally sends me straight to the bathroom. I know the doctor may resist my wanting to take this one step at a time, but when she tells me diet and probiotics won’t help while I know otherwise, I’m a bit resistant to aggressive meds right out of the gate.  

OP, I was one of those who was misdiagnosed as well and came here to express my outrage (was told I had UC but now they say Crohns). Some posters, like Scott F,  said essentially, "aren't you glad your surgeon didn't mess up the J-Pouch procedure because that would have been mal-practice." So apparently, misdiagnosis is totally in bounds. Apparently, Scott is a doctor and he seems way too sympathetic to other doctors.

To me, it would be no different than performing a double-mastectomy on someone who didn't have breast cancer but rather a harmless lump and then saying "yeah but hey, look what a great job I did with your surgery, you're not dead or anything."   

Fact is, my surgeon gets paid for cutting. If he had told me I had Crohns and not UC he would have never seen me again and he wouldn't have received the S-ton of money he got from my insurance company.

I’ve been traveling and just got home, so just now I’m finding time to check in.

Blueflame, I have been on one biologic or another for over a decade. It was for enteropathic arthritis and I did not develop chronic pouchitis until a couple of years ago. I did wind up taking antibiotics chronically, but my GI did not like the long term issues with them. Ultimately, he encouraged me to start Remicade with oral Imuran. That was about a year and a half ago. I was able to completely stop the antibiotics and my pouchitis symptoms compketely resolved. But, I did gain weight on the Remicade, over 30 pounds since starting it. So, I am not happy about that. I had gained back some weight I lost from a program while on other biologics (Humira, Simponi, Cimzia), but not as much or as rapidly as the Remicade. Maybe it boosted my appetite, but it definitely is something I need to address.

Rustyskyline- I think to compare having a colectomy and j-pouch procedure for presumed UC that later manifests as Crohn’s to performing a double mastectomy when no cancer existed is a false comparison. You are entitled to believe what you want, but that does not make it a realistic approach.

First, IBD is very difficult to diagnose accurately, even today, let alone 20 years ago.

Second, IBD can change over time so that the real underlying disease becomes apparent as the disease progresses. Unless all the clues are present, you cannot be sure. While there are some features that can confirm Crohn’s, you can never fully rule it out.

Third, a colectomy is absolutely appropriate for severe colitis even with a Crohn’s diagnosis (it is just the j-pouch that would be in question, and even that is not an absolute). So, if your colon was trashed, it needed to come out regardless of the diagnosis. The difference would be whether you wound up with an ostomy or not. So to presume that you would avoid surgery all together if you had Crohn’s is not correct. Patients with Crohn’s actually have more surgery over time, due to strictures and fistulas.

So, while I can understand disappointment and anger with a changed diagnosis, outrage seems out of place. Doctors do the best they can with the tools and knowledge base available at the time. Crystal balls are not in their medical bags. They are humans like the rest of us.


Jan, thank you for your reply. I truly appreciate everyone’s input. This board is the only one I’ve found that provides this level of information and support. 

Rustyskyline, I hear your frustration. It can be a bumpy road. I hope you find good health. 


You're right, it's not a fair comparison. The colon is involved in so many bodily functions and it is virtually impossible to not experience a significant loss in quality of life post colectomy; the these changes will last the rest of one's life. Versus mammary glands which have esthetic value only and whose function can be easily reproduced artificially. So, no comparison. 

Update: Waiting on small bowel series results. Changed my diet and feel amazing. 

Just discovered something. I didn’t realize a sleep aid I was taking for a long time was an NSAID! Now I’m wondering if the ulceration is due to that. I’ve left my doctor a message as all along I’ve been saying/thinking I wasn’t taking an NSAID. 


The message from the doctor is this NSAID wouldn’t affect ulcers or IBD. The sleep aid was diphenhydramine. At one point as a gel cap with that being the medicine exclusively, and then as an ingredient in Tylenol PM. 

I’ve read the drug is an NSAID, but when it’s Tylenol PM it’s not an NSAID.  Doesn’t make sense to me. 

 I’m frankly frustrated now and less confident about what I might have going on. I don’t yet have answers as to why she is proposing straight skip to biologics. 

If anyone has thoughts I’d really appreciate it. I have left a message for with the doctor about my concerns. 

Diphenhydramine is an antihistamine (Benadryl). It works well as a sleep aid because of the drowsiness it causes as a side effect. It's not an NSAID and unfortunately can't explain the ulceration. Bummer.

You're describing your doctor's advice as "skipping" to biologics. This suggests that there's something you believe you should try first, for whatever reasons. Do you know what that is, or are you mostly just hoping something exists? Since you're not really on board with the doctor's diagnosis, it will be hard to come to an agreement about treatment.  If you don't want to be treated for Crohn's, but your doctor is convinced of the diagnosis (it sounds like testing is still going on?), then you might even have to switch doctors.

Less drastically, you could ask the doctor what treatment alternatives exist, since you are worried about biologics. You could ask how certain the Crohn's diagnosis is, and ask about trying to treat the next-most-likely alternative. You could consider trying a biologic for a few months to see if it makes you feel better and whether it causes the side effects you're particularly concerned about. You can always stop it if it's not working, or causing side effects you don't want to put up with.

I've live with the  possibility of a Crohn's diagnosis for nearly 40 years. At times I was in denial, and at times I went along with my doctor's advice. My J-pouch was, in part, treatment for the next-most-likely alternative to Crohn's. At the time I hoped the pouch would last a few years. I got lucky, and either 1) I don't have Crohn's, or 2) my Crohn's is going easy on me.

Whatever you do next, try to pay attention to how it's really going, and be open to a change (even an unwelcome one) if it turns out to be necessary. Untreated Crohn's is sometimes much worse than weight gain. The folks here with fistulas and such can attest to that.

Thank you, that’s helpful Scott. 

The doctor called back and was clear I’ll lose the pouch if I do nothing. I’m to meet with her IBD team to discuss treatment options. She is saying biologics are recommended in a case like mine because they are most effective, and because I have many years of life expectancy (requiring pouch care). 

She wasn’t saying no to other treatments and asked that I meet with the team about treatment options. 

It is tough to accept after believing I had UC. And if a med has side effects, I typically get them in spades. I don’t like feeling like crap with side effects. It’s not just about weight gain. It’s also the risks with biologics. And with other treatments headaches, nausea and dizziness are typical side effects; I’m prone to those things. I was miserable for years with med side effects so I’m not excited about that possibility either. I know it’s the lesser of possible problems, but I just want to feel well. 

To be continued, I suppose. 

Last edited by BlueFlame

Hang in there Blueflame. I was a mess when I was told that I had Crohns instead of UC too. That opens up a whole realm of possible fiascos. I also had my pouch for over 20 years before the change in my diagnosis which one doctor informed me is quite common with people who really have Crohns. Biologics are scary but Remicade was a life saver for me. Do your research and make a choice that you can live with. I had no weight gain on the Remicade; the worst thing I experienced initially was really bad nasal congestion for the first month or two. I am so happy for the good years that I had with my J pouch...it let me get through all my younger years without an ileostomy. Even after all the bad stuff that has happened, I wouldn't have changed my decision to go for the J pouch. My colon was a mess when they took it out and all these drugs weren't available in 1999 when I made the decision to go J pouch. Hopefully time will be your friend and allow you to accept this change in diagnosis. I was also on Cimzia and Humira with no weight gain but neither of those worked for me personally. Good luck with what you decide and know that you are not alone with this changed diagnosis thing. Plus, they sometimes do J pouches in Crohns patients depending on how their disease presents itself. So even if your initial diagnosis was Crohns, you may have ended up with a J pouch anyway. 

Thank you very much, LORI726. 

I guess I’ve been walking around in ignorant bliss. Mild symptoms of bloating and occasional mild incontinence or urgency that I’ve always easily fixed with diet, Imodium and Gas X. No pain or bleeding. 

I’m certainly not looking for trouble, but I guess what I’ve considered my “normal” are symptoms of not feeling/being well. 

Yes, my colon was wrecked. I feel nothing like what I had then, but I guess the colon didn’t deteriorate overnight either. 


As I mentioned previously what the actual diagnosis is is kind of irrelevant. It's chronic inflammation and regardless of what it's called it has to be treated. More variants of IBD exist than they know but they all have to be treated and the treatments are the same.  I went from a UC to a tentative Crohn's diagnosis 15 years after getting a J Pouch which has never been confirmed despite multiple diagnostic tests that were a waste of time and money. The treatments for bowl inflammation of the pouch and ileum are all the same. So as Scott already said you have to explore what other treatment options exist and if the answer is none, your choices will be to use biologics or lose the pouch. I have taken Remicade for 2 years and it works very well on J Pouch inflammation but not as well on inflammation above the Pouch. That's been my experience anyway. Entyvio and other biologics exist as well, and can be supplemented with rotating antibiotics as in my case. 

Last edited by CTBarrister

Since being on this sight, I have found it most bothersome to read that diagnosis doesn’t matter. I agree when it comes to biologic treatment, Colitis and Crohns can have very similar, if not the same  biologic treatment. But there are differences in  treatment of small bowel and large bowel.  My diagnosis has never been IBS  or indeterminate IBS, it has always been UC. I certainly had symptoms of Crohns, but my UC treatment remained the same.  And I did have the Prometheus test and it wasn’t a BS test, quite important . It provided substantiation I had UC. Additionally, it supported continuing treatment options - creating a Kpouch, which is not advised for a Crohns diagnosis. My entire medical treatment has been based on my UC diagnosis.  We are all entitled to our opinions and beliefs, and may have the best doctors treating us telling us many differing opinions.  But I believe  with all my doctors and treatment my diagnosis IS important. Symptoms fluctuate, treatment fluctuates, but original diagnosis has never fluctuated for me. It comes across very callous that one should not put any weight into their diagnosis let alone minimizing when one opts for a test that could corroborate diagnosis. Nothing is typically concrete in our world of GI disorders, but I believe the original determination matters. 

I think you are confusing diagnosis in people who still have their colons and diagnosis in people who have had their colons removed which is most of the people on this board. This board is the J pouch group and those who have J Pouches do not have colons, thus UC isn't a applicable diagnosis for those with chronic inflammation of a J Pouch. In this latter group, diagnosis as between Pouchitis and Crohn's doesn't matter and is only the source of money being spent unnecessarily and I have had two J Pouch specialists admit this to me.

If it is important my doctors sure don't think so because they gave up trying to figure it out a long time ago. Two J Pouch specialists, at Yale and at Mount Sinai, have specifically told me my diagnosis will not alter the way they treat me because chronic inflammation in the ileum is treated with the same progression of drugs- antibiotics, topical enemas, biologics, etc. Remicade is the preferred first choice biological drug for inflammation of the J Pouch. 

If you still have your colon the above analysis doesn't apply and that may be where you are becoming confused. Once your colon is gone UC is not a diagnosis, chronic inflammation is pouchitis or Crohn's and the treatments are the same for both.

The Prometheus test is not taken seriously or as conclusive by most diagnostic experts I have spoken to and I was specifically told it is not even the golf or silver medal diagnostic test- capsule endoscopy is gold and MRI Endoscopy is silver. 

I had a UC diagnosis for 20 years, had surgery on the basis of that diagnosis and then after 22 years of J Pouch inflammation my diagnosis is Crohn's - operatively, not conclusively. However there was no evidence whatsoever of Crohn's for my first 35 years having IBD. It developed after I had the surgery and has done so with others. All diagnostic testing pre surgery was UC and all diagnostic testing since surgery has been inconclusive.

If you think diagnosis matters for a person who has chronic inflammation of a J Pouch, please explain why and how diagnosis would impact on their treatment? My own doctors and specialists have not been able to answer this, so if you can I would like to hear the explanation of how diagnosis matters to those in the same situation as me, which is more than a few people on this board.

Last edited by CTBarrister

There are some decisions that would be influenced by the presence (or absence) of a Crohn's diagnosis. For example, the set of surgical options considered appropriate could be quite different. Additionally, if puzzling symptoms are present the set of possible causes is different for those with Crohn's vs. a UC diagnosis. Nevertheless, the basic medications and choices among them are indeed the same for both diseases, as CT says. And sometimes, as in my case, the true underlying diagnosis remains a bit mysterious.

Still waiting for small bowel series results and treatment plan. In the meantime, I’m wondering why my doctor said no to antibiotics last year when she saw inflammation and some ulceration that may indicate Crohns. At the time she didn’t prescribe anything, said it’s not pouchitis, antibiotic use would be ineffective if used routinely and come back in a year for another endoscopy. 

If antibiotics are cycled as part of Crohns treatment and clearly I had something going on last year, why no treatment? I had symptoms, whether pouchitis or Crohns. 

BlueFlame, antibiotics aren't really used to treat Crohn's disease per se. They are used to treat pouchitis, from several different causes. Granulation and ulceration above the pouch isn't pouchitis. So your doctor is suggesting things that tend to work best for what you seem to have.

Trying antibiotics would likely do no direct harm, and it's possible that you'd feel better. There is some risk that they would delay the treatment more likely to preserve your pouch, so there is that consideration.


What is/was sometimes diagnosed as Crohn's in the ileum above the J Pouch is now considered a result of SIBO.  SIBO was not even being discussed until around 10 years ago, and it is most definitely treated with antibiotics.  The problem I have above the pouch, which is the same problem many J Pouchers have, is backwash stool going back into the ileum due to the J Pouch inlet not having a backsplash valve, as the colon does to prevent such backsplash.  My SIBO is compounded by the fact that in addition to the backwash, I have a very small J Pouch inlet which was narrowed due to surgical scarring and swelling from inflammation.  This causes fecal stasis, and SIBO, according to my docs. At my worst in 2012 I was getting a sensation of blockages all the time. I took Entocort and a high dosage of antibiotics at that time, and changed my diet, with very good results.

You are correct that traditional Crohn's Disease is not treated with antibiotics first.  But, in patients who have a J Pouch and a pattern of inflammation above the pouch, an experienced specialist will want to look at the possibility of SIBO depending on the pattern of inflammation.

I have granulation and ulcers in the area just north of J Pouch inlet, same as BlueFlame.  They were NEVER there before 2007.  My specialist who scoped me 1992-2007 always took pics above the pouch in the neoterminal ileum. The symptoms in this area developed many years after surgery.  The explanation for them is what I have stated above.  This was also born out on MRI Enterography and CT Enterography exams which showed the bowel walls thickened as well in these areas.  These are diagnostic tests that are far more reliable than Prometheus for this type of situation.  In my case, I have a tentative, unconfirmed diagnosis of Crohn's Disease.  It is treated the same as pouchitis in my case.  And for many others who have carried both diagnoses.

Whether you call it Crohn's or something else, the methods of treating it are likely the same in the same order.  It's important to consider that it's a new disease afflicting your new biology, meaning my UC diagnosis was not wrong.  I always felt that I was cured of UC after surgery. I never felt the same way after surgery as I did before when suffering with the UC.  I have been managing a different bowel disorder.

Last edited by CTBarrister

My doctor says it’s not backwash, that this isn’t possible. Then she added reference to seeing cobblestoning and ulceration in the pouch this year. Last year it was above the pouch with pouch inflammation. 


How is that she thinks backwash is not possible? Did your J Pouch come with a backwash valve? Or does she think that it's not what is causing the ulcerated areas inside the pouch?  Which would make sense because backwash only creates problems above the pouch.

Also, how far above the J Pouch inlet are/was the ulcerated and granulated areas?

Last edited by CTBarrister


I’m not clear why she says SIBO isn’t possible and she did not say I have a valve. I need to understand that better when I see her.  The affected area was right above the pouch last year and this year. Inside the pouch is new this year and she says she’s certain the small bowel series will show more inflammation further up. 

What you are describing is indicative of inflammation from backwash stool.  If they find no inflammation further up, just right above the J Pouch inlet, there is pretty much no other explanation for it.

What you have described sounds exactly like what I have, with one difference: the inflammation inside the J Pouch has disappeared since I started taking Remicade.

Are you the only J Pouch patient of your doctor?  

Last edited by CTBarrister

CT, no she’s quite experienced from what I can tell. She’s exceptionally resolute in her diagnoses and communications which is a bit of a challenge.

It sounds like the treatment she’s suggesting is the same as you are taking. She’s very brief so I don’t yet know if she would intend to include antibiotics with the biologic. I just know she’s saying this needs more than just antibiotics. 

I’m to meet with her IBD team next week to discuss options. I’ve gone from not wanting meds because this just can’t be, to being willing to start with the Imuran route. I’d like to see how that and diet goes before biologics. 

Imuran is a very different drug and my body rejected it almost immediately.  It made my liver chemistries go haywire.  I was tried on it back in the 1990s.

BlueFlame, good luck in the meeting with your IBD team next week and hope that you are equally resolute in asking questions and advocating a course of treatment for yourself.  Hopefully this discussion armed you with some questions to ask.

I am doing great with Imuran, including liver functions, and I even have fatty liver disease. Actually, I was on a variety of biologics for my arthritis until pouchitis became chronic. My GI suggested the combo of Imuran and Remicade as the one with the most data for pouchitis treatment. Of note, Imuran used with Remicade is a lower dose than when used alone. It helps prevent antibody formation against the Remicade.


The status is clear as mud. Small bowel series results are now in and say chronic pouchitis. Does not say crohns, which is the new concern. I’ve left a message asking the doctor to clarify as her notes say to follow up as planned for IBD treatment. It’s not clear if Crohns is ruled out or not. 

Received a reply. Crohns isn’t evident in bowel, but is in pouch. They’ll explain more when I go in Monday. That’s a big difference from chronic pouchitis in her first message. Really frustrated. 

Well, you can either make yourself crazy trying prove or disprove a diagnosis and never get a clear answer, or you can accept chronic pouchitis as a diagnosis and just take it from there. Go with what works. Treatment is essentially the same based on signs and symptoms, regardless.

I know it does not seem very scientific, but sometimes there simply is no clear cut answer. Remember, you cannot completely rule out Crohn’s, as diagnostic certainties are often not present, at least not with today’s diagnostics. This is where the skill and knowledge base of your doctor comes into play. There is such a thing as Crohn's of the pouch, without other involvement.

Personally, I’d be pleased that my disease is confined to this small area (for now). Perhaps with effective treatment, it can stay that way.


Last edited by Jan Dollar

Jan, are you saying chronic pouchitis may also be treated with biologics? I understand what you’re saying, but wouldn’t it make sense to take this in steps? I have had no treatment in years. Not even antibiotics. Why not start there, then go to imuran, then biologics if needed?

I’m not looking to take risks or be in denial. But I feel well, especially after getting back on my diet. Why not start with antibiotics, recheck and see how things are looking?

I agree in the take one step at a time approach. However, you need to be aggressive in treating chronic inflammation, and not dawdle if you are stagnating or regressing with any one treatment.  If the antibiotics are not achieving success (and the proof will come in your scopes), you should go to the next step sooner rather than later.

I also agree with Jan on not getting caught up in diagnostic slowdowns.  The diagnosis, as between pouchitis and Crohn's, does not matter for reasons that have already been stated.  It's chronic inflammation, whatever you have is whatever you have, and it needs to be treated regardless of what it is called.

Blueflame, as I already mentioned, Remicade is a treatment for chronic pouchitis whether it's diagnosed as Chrohn's or not.  It is a proven treatment of pouch inflammation.  It eviscerated my pouch inflammation but not my neoterminal ileum inflammation. You gotta forget the words "pouchitis" and "Chrohn's" and instead use the words "chronic inflammation."  What you call it beyond that simply does not matter.

Last edited by CTBarrister

I also do not understand when you say Crohn's in the pouch is a "big difference" from chronic pouchitis.  It isn't.  Both are treated the same.  Both are species of chronic inflammation and cannot be allowed to go untreated.  If you think chronic pouchitis left untreated cannot lead to something bad happening, you would be badly mistaken.  The Cleveland Clinic study on rectal cuff cancer patients showed that many had severe pouchitis, some cases of which had not been properly treated.

I agree, it makes sense to opt for antibiotic treatment as a first option. But, if you are not symptomatic while having chronic inflammation, it is a little more tricky. Also, if your doctor is quite convinced this is more likely to be Crohn’s of the pouch, and not the ordinary run-of-the-mill pouchitis, a more aggressive approach may be considered. Hopefully, when you are at your next appointment, you will get the full details about your doctor’s plans. Make sure to ask all the questions you asked us. Protocols are changing all the time.

And yes, I am on biologics for chronic pouchitis. But, I did try antibiotics first. I became antibiotic dependant and was rotating three different antibiotics. Bottom line, my GI felt that the long term risks of chronic antibiotic use were worse than the risks of biologics. Plus, understand, I had already been on biologics for years for enteropathic arthritis. The main change was to Remicade and adding Imuran.


My doc explained and I am of the belief that there are different "causes" of "pouchitis" or inflammation of the pouch, and there are no easy diagnostic test to determine what the "cause" is. This is why docs will often cycle through the treatments in the pouchitis article I posted earlier in this thread first (and then biologics, which came along after the article was written), to see if you can get a good response. If chronic rotating antibiotics stop symptoms and clear up inflammation on scope, great-and probably not "IBD of the pouch or Crohns of the pouch" If it takes immuran and/or biologics to successfully treat, it is probably some ityoe of IBD-related root cause. 

I was adamant when I started hearing "it may be crohns" because I was mainly worried that it might mean I was now susaceptibke to disease throughout my digestive system, and in 30 years there had never been signs of that. Any inflamation i have now is restricted to the pouch.i like to think of it as "IBD of the pouch". If someone asks, I say I have an inflammatory bowel disease. I don't say UC, and I don't say Crohns, and frankly, if you don't have a pouch "pouchitis" just prompts more questions. But ultimately what I call it doesn't matter because I have found a treatment that works (immuran plus rotating antibiotics) and if/when that stops working, I will start on one of the biologics. 

If it is not clear cut crohns diagnosis, I see no reason why you couldn't start with rotating antibiotic treatment (maybe with budesonide-a designer, non-systemic steroid to jump start healing of inflammation), then if it doesn't work try something else or or if you start to feel uncomfortable with long term antibiotics and more comfortable with another treatment, go that route. BIOLOGICS as a first line treatment is not an unreasonable choice if it is what YOU want, but if you'd rather wait on that treatment and try other things first, there is no reason not to.

Thank you everyone, as always. 

Met with the IBD team today and definitely taking steps back to sort this out more. More tests, etc. 

One interesting thing is the doctor has been telling me there’s more inflammation this year compared to last. Today the IBD tesm told me less was seen this year and the inflammation leading into the pouch last year was not present this year. 

Last edited by BlueFlame

Update and wondering thoughts before my next appointment:

Blood work shows folate and B12 in low normal range. CRP elevated. Prometheus result: pattern not consistent with IBD. Small bowel series indicates chronic pouchitis, less inflammation than last year and no inflammation just above the pouch this year (had some last year). Endoscopy showed a crohns like cobblestone patch with ulcer. Biopsy showed no granuloma or abnormal cells.

Original diagnosis of UC 32 years ago. J pouch for 27 years. Treated a few times for pouchitis. 

With this possible crohns scare two months ago, I went hard core on bowel rest, followed by all organic and Whole Foods, alternative supplements, lots of water, no caffeine/alcohol/sugar/carbs and switched to some alternative foods to get rid of possible triggers. I’ve just added in B12 and folate by supplement and veggies; I had completely excluded this from my diet so I’m not inclined to think it’s an absorption issue.

 I feel so much better physically. The symptoms I could “feel” before dietary changes felt like pouchitis. I don’t feel symptoms now. The fatigue is lifting and I think will continue to improve when I get back to exercise and the B12 and folate build up. 

Sooooo, I’m wondering thoughts before this appointment as I think about questions to ask. 

My thought is to continue my current course and ask to repeat tests in 6 months or so. 

I’m also aware of the issues with the promethius test and find the results curious.....though I’m grateful for the overall picture. 

My Prometheus test produced the exact same result. My GI didn’t believe it and told me he didn’t think the test was reliable at all. What would be more reliable is an MRI Enterography. As I mentioned my diagnosis is likely Crohn’s notwithstanding the above. But the correct diagnosis is actually irrelevant because it all boils down to whether you have a condition that needs to be treated. If so then the only important question is your response to the treatment.

Last edited by CTBarrister

I am with CT on this. You have plenty of info to point toward chronic pouchitis. The chronic inflammation likely led to the deficiencies. Prometheus results are a red herring and essentially meaningless. Diet may well keep you on track, but don’t rule out treatment in the future, or beat yourself up if diet does not work long term.

My B12 was also low and I responded very well to supllements. I only take it twice a week now and my numbers are quite high. My folate was always within range, though. My B1 and Vitamin D were also low. I always have eaten wide variety of foods.


Jan Dollar posted:

I am doing great with Imuran, including liver functions, and I even have fatty liver disease. Actually, I was on a variety of biologics for my arthritis until pouchitis became chronic. My GI suggested the combo of Imuran and Remicade as the one with the most data for pouchitis treatment. Of note, Imuran used with Remicade is a lower dose than when used alone. It helps prevent antibody formation against the Remicade.


Hi Jan, I have been on Remicade with Imuran for 14 months and my Gİ says it's time to stop Imuran now. Just as you, I started Imuran along with Remicade to prevent antibody formation. My Imuran dose is 2 x 2 a day (50 mg each). I am a bit concerned about going off of Imuran because I have been doing great lately. Humira never worked for me. And  I don't want my Remicade treatment fail.

I suggested tapering off Imuran gradually but my GI thinks otherwise. He wants to end the treatment all at once at the end of this month and go on with Remicade only.

BTW, my blood work has always been good throughout the treatment, no side effects from Imuran or Remicade. And I also have hepatomegalia and fatty liver ( grade I-II).

I wonder why he is so determined to end the Imuran treatment, and why not to stop it gradually. any ideas? Thanks.



Thank you CT and Jan. I like the idea of an MR Enterography. Wonder why it’s not been considered, but I’ll surely ask. 

CT, you mentioned you eat yogurt. What type? Do you take VSL and how much?

I’ve switched to all goats milk for dairy, and goats milk kefir. VSL made me miserable and I felt I was wasting money between that and the lack of definitive guidance on how much to take. I now understand it takes time to adjust to the probiotic and went thru that misery with another brand I’m happy with. But the scope will be more telling so I’m not ruling out VSL.

I felt like VSL III was a waste of money as well.  I was tried on it a few times, cold turkey off antibiotics, and it was a dramatic fail.

I eat all kinds of yogurts, but I like the Yoplait lowfat probiotics yogurts, Noosa, and Chobani.  I eat a yogurt for breakfast and another one as an afternoon snack but with the snack yogurts I stick to 100 calorie or less with low sugar and fat.

As far as the MRI Enterography, it's much better for diagnostic purposes than the Prometheus test because it also isolates the location of the inflammation especially up the pipeline so to speak. It's an almost 3 hour test and I posted  a thread about mine here:


I posted that thread over 5 years ago and I am glad I did because I don't remember the details so well and that thread served as a journal of my experiences with the MRE.  Right when that test was done I was at my worst point in the 25 years of managing the pouch issues and things have been much better since then with vastly improved diet and Remicade starting in 2015.

Last edited by CTBarrister

CT, thanks for the MRE thread. Very informative. I suppose if there’s no apparent thickening, it could also indicate lack of disease progression at this time. Such a crap shoot.....pun intended. 

Linguist, it appears that the jury is still out regarding whether combination therapy with a biologic and immunosuppressant should continue long term. There is a concern regarding lymphoma with long term therapy with azathiopurine. But, the key is if you are in full remission before considering stopping one or another treatment. The immunosuppressant makes it possible to sustain lower doses of Remicade over time, by suppressing anti-Remicade antibodies.

I was able to find this article. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5479343/

Your azathioprine dose is higher than mine. I only take 50mg daily, and have since the beginning of my treatment. Perhaps because I am also on treatment for my arthritis in addition to IBD, there has been no discussion of stopping any treatment. It has been 18 months for my combination therapy.



Two months into this journey and they don’t know what to make of my mixed results. Really annoyed at the communication confusion. Now I’m told the cobblestoning appeared in the small bowel series last year, but not this year. If all the flip flops are straight, this year it’s inflammation and ulcer in pouch only. But, once again I see the doctor in two weeks. 

For now it’ll be treated as chronic pouchitis, but also scheduling an MR Enterography.

And at two months of testing I’m just now being prescribed antibiotics. All I know for now is Cipro and flagyl, likely at least a month. I’ve never taken them more than two weeks, and never together. Really hoping I’m not knocked on my butt with nausea. Last time I told the doctor I had this symptom she said that doesn’t happen. I’ve since learned otherwise. Next time I mentioned it to another doc in the practice and he said he could prescribe something if I had nausea, but I didn’t need it. 

The care plan is coming along but really annoyed about communication, having a doctor who multiple times is making me feel things are in my head, disregards things I say and treatment possibilities. Just been down that road a few too many times in 3 decades and not tolerant of that crap. 

Grateful, but tired and annoyed.

Blueflame, I hope the Cipro and Flagyl do the trick for you. I looked up Cipro and Flagyl, and nausea is prominently listed as a possible adverse reaction for both. It’s not in your head. Perhaps taking them with a meal (non-dairy) might help.

Yes, thanks Scott. Even the Rx literature says the same. Such a basic thing.

Doctors don’t like the internet for educating ourselves and this doctor said talk to the experts in her office rather than what I read on the internet .....as though I wasn’t going to talk to them. It’s about advocating for ourselves and I’m frankly annoyed today that much hasn’t changed in decades.

I was told they haven’t seen Promethius results that indicate pattern inconsistent with IBD when there’s a clear history. Then there’s the lab that didn’t even run the test until I called directly myself and learned they had a system glitch.

Finally, I was initially told yesterday by the PA that an MR Enterography was not warranted since the small bowel series was clear. Today I get a call that the doctor wants it done. I’m quite certain it never would’ve come up had I not learned about the test on this board.

Heck, I had multiple doctors send me away with no answers for 13 years until I discovered the word pouvhitis on this board.

This seems basic stuff that specialists should be on top of without the patient internet education they are quick to shut down. 


Well they didn’t see my Prometheus test which said pattern inconsistent with IBD despite that I have had IBD for 45 years documented on scopes. Like I said it’s a nonsense test and inconclusive. My GI has two pathologists on west and east coast, both of very high expert pedigree, look at the results and they couldn’t draw any conclusions.

The MRE isn’t necessarily going to give you closure on a diagnosis and as I mentioned I don’t think “proper” or correct diagnosis is or should be driving your treatment. The MRE will provide information on the location and extent of the inflammation upstream. These tests should be viewed as guides for treatment and markers for your response to treatment. Any Doctor who wants to see a Prometheus result before determining a course of treatment for his or her patient is not someone I would be a patient of for very long.

I have taken antibiotics for 22 years continuously and always take with food and was never nauseated by any.

Regardless of everything else I think you should go to a different GI specialist going forward. Find someone experienced with treating Pouch inflammation and related issues.

Good luck. If you improve with antibiotics you can stay on them but will need to rotate as previously discussed.

Last edited by CTBarrister

The story continues, as these things go. I continue to feel better. MRE on Monday. 

Just a tidbit to share that I received from Prometheus:

The sensitivity of our IBD panel is 72% which is posted at the bottom of the report. This indicates that we are unable to detect IBD in ~28% of IBD positive patients. The UC marker ANCA antibody is produced in the large bowel, so with resection, this reduces our ability to detect IBD / UC.

The positive outcome of a negative IBD result, is that the initial diagnosis is more likely.

Last edited by BlueFlame

The Prometheus results should be ignored, totally. IMHO this test is just a money grab by pathologists much like propofol was a few years back by anesthesiologists. Then when everyone started doing it became a craze until patients objected because it is 15 times the cost of conscious sedation which they do not tell you upfront when giving you a choice. As far as Prometheus they give something to the Docs like kickbacks for pushing these tests even though responsible and ethical doctors know they don’t really mean anything. Someone is making money it but it’s not you!

I had an intelligent and honest debate with my GI about the merits of using propofol to sedate scope patients. In the end  he gave in to me because logic compelled him to do so. They mainly do it for reasons of making money for anesthesiologists and moving patients in and out of recovery rooms as quickly possible. Not because it’s actually better. MONEY GRAB for the specialist and the facility as they can scope more people and make more money. All of us should be calling a spade a spade. They will NEVER put propofol in my body.

BF, hit the ignore button on Prometheus results and move on to the MRE which will actually provide some reasonably conclusive scientific evidence. Good luck and review my thread on same. It’s not a horrible test, just long.

Last edited by CTBarrister

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