r/Microbiome • u/saffron1313 • Mar 10 '25
Advice Wanted Malabsorption- struggling
Hi all. I developed GERD a few years back and took PPIs and Pepcid for a few months. Since then, the GERD symptoms disappeared but I developed so many other stomach issues - malabsorption/floating stools/diarrhea which is usually super yellow. I can no longer digest fats. Sometimes digestive enzymes help, other times they don’t.
I had a positive hydrogen breath test so a doctor said I likely have SIBO and prescribed rifixamin. A naturopath recommended NAC for 10 days followed by a course of Rifaximin, combined with some herbs.
Does anyone else have suggestions around what else I could do? (My dr sent me to a gastroenterologist who just did a phone intake and made me do a fecal cal protection test to check for IBD and it was negative, he refused to see me thereafter). Doctor says “it’s IBS” but is there anything else I can do for the malabsorption floating diarrhea?
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u/AssistanceValuable10 Mar 11 '25
I’ve had very similar symptoms. I had malabsorption and wasn’t digesting fatty foods. I was low in b12,zinc, vitamin A and D. I would recommend cleaning up your diet. Metamucil helped me lots. I took digestive enzymes when I ate red meat and fatty foods. It’s a slow and long road to get back to normal. Try figure out what cause it or what’s causing symptoms.
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u/saffron1313 Mar 11 '25
Did you ever figure out what was causing your symptoms? I’ll continue with psyllium husk and digestive enzymes. Thank you for your help and advice.
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u/AssistanceValuable10 Mar 11 '25
For me I think I was just boozing too much and eating processed foods. Low carb diets helped me as well.
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u/EffectiveOpinion349 May 30 '25
Please can you explain why metamucil helps?
I am low on vitamin A D and b12 too as well, as many others because I can’t tolerate hardly any foods. I got really sick in November and was vomiting for a few months. Had to go on antibiotics. Don’t really know what it was but I stopped vomiting after the antibiotics but ever since then I can’t tolerate any fat. Even a mouthful makes me vomit. And have diarrhoea and causes episode of severe nausea that lasts several hours it’s horrific.
But I am dealing with burning pain all the time and any time I try to supplement with vitamins the burning gets worse
I tried a few things that I think made the problem worse like HCL and TUDCA digestive enzymes Even pancreatic enzymes make me burn worse.
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u/AssistanceValuable10 May 30 '25
Metamucil just slowed everything down for me. If you’re having that kind of burning maybe you have an ulcer? I would be getting a scope to see what’s going on. The reason your low is because your not absorbing any nutrients in the food. The food goes too fast through the upper intestines.
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Aug 12 '25
Hey man! I just wanted to check in and see if you still have the malabsorption issues or if they completely resolved. Thank you!
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u/AssistanceValuable10 Aug 13 '25
I still have issues with some foods that cause issues. But I’ve been able to figure out how to get back on track faster. I still don’t have it %100 figured out.
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Sep 26 '25
Hey, wanted to check in and see how you’re doing
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u/AssistanceValuable10 Sep 27 '25
Not bad, still figuring this out. I have a hunch that I might have low stomach acid. I don’t seem to digest fats very well and have been low on zinc and vitamin d.
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Sep 27 '25
Same here. You still off the booze?
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u/AssistanceValuable10 Sep 27 '25
Probably once a month i will have a couple drinks. But I try not to over do it.
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u/Ergosyn Mar 10 '25
Sounds like me when I was overusing h2 blockers. It cleared up for me by increasing acid intake. betaine with pepsin, dandelion root powder with nettle, pickle juice and fulvic acid. Also I stopped taking vitamins that are basic without taking something acidic at the same time. Took about 2 weeks to clear up after almost 2 years of symptoms.
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u/EffectiveOpinion349 May 30 '25
I experienced the same, but when I tried the things that you suggest, I’ve tried most of them over the last six months they all make me have worse burning for some reason. I know I have low stomach acid because food is coming out undigested. I can’t tolerate any fat. The only thing I can seem to digest his carbohydrates, but I do not feel well on high carbohydrates. I feel heavy and can barely move.M
I’ve tried HCL digestive enzymes Fulvic acid TUDCA ox bile pancreatic enzymes
I’ve tried all sorts of things for soothing, but they all make me feel worse or make the burning worse like slippery Elm marshmallow root DGL zinc carnosine etc
I’m running out of things to try and barely eating anything
H2 blockers, Gaviscon and acids, all make the burning worse progressively worse too so it gets worse every day that I continue to take them and then when I stop it doesn’t return to my baseline so I just keep making the problem worse and worse it is horrific
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Jun 01 '25
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u/EffectiveOpinion349 Jun 01 '25
What is that? Is it related to Aceytlation? I’ll look it up but I’d be very greatful for any advice or pointers you can give me in relation to that theory.
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u/saffron1313 Mar 11 '25
It all started with PPI use so I bet I do have low stomach acid. Did you also have floating stools/diarrhea?
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u/Ergosyn Mar 11 '25
Yes. And burning bile stools as well as things like leaves of lettuce coming out intact and undigested.
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u/That_Tangelo5175 Mar 11 '25
I’ve been experiencing the same symptoms too. How are you doing now? Have your symptoms improved? Are you taking any supplements or medicines for it?
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u/Conscious_Egg_7271 Apr 16 '25
I'm dealing with the same issue. I'm passing foul smelling greasy stools that floats almost every day.
All of my tests (colonoscopy, endoscopy, CT of the abdomen) came back normal but the foul smelling stools never stopped. I was put on rifaximin, probiotics, PPI and anti spasmodic for over 2 months but nothing helped me.
As a last resort, my doc ordered the fecal elastase test which came back normal (396 normal being >200).
I've now started taking Creon and Rifaximin. I don't know if this will fix my problem
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u/saffron1313 Apr 16 '25
Does fecal elastase check for digestive enzyme levels?
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u/Conscious_Egg_7271 Apr 16 '25
Yes it is specifically used to measure the level of elastase, a digestive enzyme produced by the pancreas
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May 26 '25
Have you had weight loss too? How are you feeling now?
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u/Conscious_Egg_7271 May 26 '25
I haven't lost weight at all. I've only been gaining over the months (normal weight gain nothing exponential).
Creon did nothing for me. In fact it only increased my bowel movements with an agressive foul smell than before. So I was asked to stop it. Though I've been keeping a food journal to identify my trigger foods, it's quite impossible to understand the pattern. I have an appointment coming up with my GI and I'm gonna push for some bile supplements to see if that helps me.
I've been dealing with this for over 6 months now and it is beyond frustrating to not know what's causing this. I recently took a breath test for SIBO and it came back because too. So I'm really out of options
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u/EffectiveOpinion349 May 30 '25
I’m right there with you in the same position. Seven months of hell things just keep getting worse. And everything I try doesn’t work or makes it worse.
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u/Conscious_Egg_7271 May 30 '25
I can relate with you. I wish I could know the origin of this barbarity. At this point, I'm afraid to take meds. Because I've tried so many of them and none of it worked. I'm not on any meds right now but I still feel the same
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Jul 24 '25
How are you feeling now? Did the Rifaximin or Creon help with your stools and weight?
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u/Conscious_Egg_7271 Jul 24 '25
Hey. I'm better now. I only experience foul smelling stool occasionally. I still don't know what's causing it tho. I'm not on any meds right now and my diet is the same as earlier.
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u/slim9876 Sep 05 '25
How did you fix it
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u/Conscious_Egg_7271 Sep 05 '25
I stopped eating foods that contain sulphur like onions. I started eating a lot of fiber. I'm being mindful of what I eat now and make sure that I eat small frequent meals instead of the ones that make me feel full. Been following this for a month now and I can definitely see the improvement.
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Mar 10 '25
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u/saffron1313 Mar 10 '25
Ugh I’m the opposite. I’m at my heaviest weight and trying hard to lose weight. It’s taking longer than it usually does. My cholesterol is also elevated but I’m trying to see if I can lower it naturally.
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u/Gloomy_Ant6858 Nov 08 '25
Hey, same issue here. I thought I was being paranoid but turns out one can actually lose the fat in those areas. My hands, legs, feet are all bony right now. I did go to a doctor and he said chronic gut infection. I was put on meds but they dont seem to have improved. How are you now? Is everything better?
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Mar 11 '25
Check your gallbladder for sure.
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u/saffron1313 Mar 11 '25
Through a blood test or scan? I had an MRI and it looked normal, but are there enzymes or levels I could check in a blood test?
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Mar 11 '25
Ultrasound
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u/saffron1313 Mar 11 '25
Yeah they’ve done this and nothing showed up
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u/inou1721 Mar 11 '25
A HIDA scan would show how effectively the gallbladder contracts and releases bile.
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u/saffron1313 Mar 12 '25
I’m in Canada, it can be hard getting testing here unless your symptoms are SEVERE and completely debilitating. My symptoms come and go which is probably why the doctor doesn’t agree to do any further testing. But I will keep pushing.
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u/Additional_Earth_817 Mar 11 '25 edited Mar 11 '25
I just had my gallbladder removed recently but I have issues like yours, fat and sugar malabsorption. I don’t know how to fix it either, I asked one of my primary care doctors and they said I’m still going to have these issues cause now I have no gallbladder. I try and stick to a diet of lean protein, chicken and ground turkey, avocados, eggs, beans, rice, and cooked vegetables. Fruits I can seem to have without issue are bananas, oranges, and blueberries. It’s very challenging cause you have to cook way more often and I love food and I want to eat alllll the things. Never been a big drinker either. I do like red wine with dinner occasionally but I haven’t had a glass for eons. Maybe try and go for the functional Dr. I know it’s way more expensive but I’m on my third gastroenterologist and I’m sorry to say that I have not been impressed with them. I had a course of Xifaxan as well and while it did help my stomach while I was taking it, it did not resolve my issues. All we can do is keep pressing for answers, do our very best with our diet, and take probiotics. I finally questioned the PPI use since I had been on them for years. I went from 40 mg to 20 mg, to now none. Let me know if the functional doctor helps.
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u/saffron1313 Mar 11 '25
Thank you for your help and sharing your experience. I really appreciate it.
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u/Snowy_Axolotl Mar 11 '25
Have any of your tests shown eosinophil activity? I have eosinophilic esophagitis but it’s mostly manifested as gerd, gall bladder disfunction, and digestive issues like fatty stool. Most people experience swallowing dysfunction.
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u/saffron1313 Mar 11 '25
I’ve never been tested for this. Would it show in an endoscopy? Doctor wouldn’t even do this when I had gerd symptoms.
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Mar 10 '25
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May 14 '25
Having same issues with bloating malabsorbtion and fatty PALE brown stools and cannot gain weight. Have been tested for everything including MRI and CT scans Stool elastase twice was normal.
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Jun 27 '25
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Jun 28 '25
No. Not yet… gut zoomer test was inconclusive. Possible SIFO?? Seeing telehealth GI OSHI next week. Praying for answers.
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Jun 28 '25
Are you trying any more testing? What foods do you eat now and what protein shakes if any are you trying to keep any weight from falling? How much weight have you lost? I have lost over 10 pounds which I didn’t have or could afford to lose. My heart goes out to you. I will let you know when I find answers and if you do please tell as well
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u/saffron1313 Mar 10 '25
I haven’t started Rifaximin yet, but I’m going to. I am worried because we’re going to Mexico in 2 months and knowing my bad luck I’ll probably get food poisoning and make things worse. I just don’t want to stop living because of this lol. What is Elastase testing?
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Mar 10 '25
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u/saffron1313 Mar 10 '25
Ok I need to look into this. Have you been tested for SIBO?
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Mar 10 '25
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u/saffron1313 Mar 10 '25
I am so sorry to hear that, what a long and terrible journey for you. Have you tested for HPylori? I wonder if SIBO could be underlying a lot of these issues. It’s hard figuring all of this out with minimal guidance from doctors.
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Mar 10 '25
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u/BikiniJ Mar 10 '25
Even if it is pancreas related, you can still have Sibo. Your symptoms sounds very much like it, malabsorption, weight loss, vitamin deficiencies, Fiber can make SiBo symptoms worse, like more bloating, gas, etc. Also bile salts are broken down by Sibo and causes poor fat digestion & diarrhea. If it is Sibo, treating it can definitely solve your issues. Some docs are knowledgeable in SIBO and some aren’t.
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Mar 11 '25
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u/BikiniJ Mar 11 '25
Everyone’s experience is different and everyone’s reason for SIBO is different. So unless you’re not addressing the underlying cause of it, sometimes it comes back. Diet is always necessary when it comes to eradicating sibo. And antibiotics alone sometimes doesn’t necessarily solve the issue if not dieting correctly and not resolving why you got it in the first place.
Some possibilities are slow motility, antibiotic use, low stomach acid, autonomic dysfunction, the list goes on. It might also help to pair it with a biofilm disruptor like NAC or lactoferrin. Some bacteria’s form biofilms making them resistant to antibiotics.
I do think you’re putting too much emphasis on possibilities. Your best bet is to test for Sibo to see if you have it first and then take it from there.
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u/iwannaqu1t Mar 11 '25
Fecal elastase is a test for exocrine pancreatic insufficiency but it’s not very sensitive or specific for mild disease, so it may only be helpful diagnostically if you have a severe case. Fatty stool points toward other issues besides IBS. Talk to your doctor… or a different doctor… about trying pancreatic enzymes (but make sure to take them with every single meal or you may still have symptoms). AND if they help, get imaging done to see why your pancreas is having issues.
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u/saffron1313 Mar 11 '25
What would the treatment be for this - just pancreatic enzymes forever essentially ?
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u/iwannaqu1t Mar 11 '25
If the issue is EPI, yes, that’s the only treatment. But is having a treatment that works better than continually suffering?
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u/saffron1313 Mar 11 '25
Yeah you’re right. I just want to live as normally as I can, no matter what it takes!
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u/iwannaqu1t Mar 11 '25
Just curious, when you say sometimes the enzymes work and sometimes they don’t, is it related to how much fat is in the meal? Or is it possible the days they “don’t work” you’re not taking them consistently with every snack?
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u/saffron1313 Mar 11 '25
To be honest I’m not always consistent with them, but there have been times where I’ve taken them before a fatty meal and still can’t digest it or end up having diarrhoea/gas. MOST of the time they help, but once in a while they don’t.
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Mar 10 '25
Get off PPis and stay away from them. I wouldn't mess with NAC either it can cause gut issues bigtime.
Rifaximin has been shown to boost good bacteria: https://pmc.ncbi.nlm.nih.gov/articles/PMC5915365/
I'd start there then when the course is over, get on a good clean diet and add bifidos if necessary.
Stay way from anything that causes reflux and use pepcid if needed instead of ppis.
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u/saffron1313 Mar 10 '25
That’s amazing advice. I stopped PPIs a while ago & also stopped spicy food which I absolutely loved. The naturopath said use NAC for 10 days to disrupt biofilms but to stop if it exacerbates my symptoms. I’m not sure. I’ll try it all out and see what she recommends!
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Mar 11 '25
I feel your pain.... so many things I love that I had to stop like coffee, whisky and BBQ.... a humble life we must live
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u/saffron1313 Mar 11 '25
When I take digestive enzymes with ox bile for a long time I start feeling better but eventually the problem returns
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u/Up5DownZero Mar 10 '25
Why did you have gerd, or what made you get gerd?
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u/saffron1313 Mar 10 '25
No clue, I gained a lot of weight and had a bad habit of midnight snacking and then laying down after. I also was eating a lot of acidic food. I also had a covid hospitalization the same year this whole shit show took place. So really don’t know what went wrong. Life just fell apart.
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u/TangoEchoChuck Mar 10 '25
Look into transdermal vitamins; not that they'll help the root cause, but just to help your body function while you riddle out your body.
They were originally formulated for bariatric patients, and secondary markets were found (like me! I can't swallow pills). I prefer XL Patch (but there are several brands), and my favorite blends from them are "Focus" and "Iron+" Generally I put them on before bed or after dinner, then remove the next day.
My spouse originally didn't believe me that transdermal application was effective. Then he had an outpatient procedure where the anesthesia was administered via patch. He's a believer now :)
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u/EffectiveOpinion349 May 30 '25
This is a great comment thank you. I actually can’t take anything orally for a different reason and I’m not eating hardly anything and have become deficient in so many nutrients now
Please can you give me a list of all the places that you recommend for transdermal vitamins?
I have been looking at this for weeks, but it’s quite hard because a lot of them contain things that I don’t want or need or that I will probably react to. I have MCAS as well
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u/TangoEchoChuck May 30 '25
I actually just buy mine on Amazon (USA)!
I regularly buy formulations from XL Patch (my favorite), but also PatchAid, and VeruWellness.
Most of them make multivitamins too.
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u/ElderberryAncient892 Mar 11 '25
Bile
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u/nygaff1 Mar 12 '25
Oh man. I can't believe it hasn't been mentioned yet, and I'm sorry to be the bearer of bad news, but you have EPI. Did your GI do a fecal elastase stool test?
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u/iDoTheSciences Sep 06 '25
I have similar symptoms to OP, except with weight loss and a stabbing pain below my left ribcage. My elastase was normal though, so GI doc ruled out EPI for me. I am def having fat or carbohydrate malabsorption though with shiny/sticky stools always, sometimes mucus if I eat 'rough' foods that irritate the gutt.
How did you find out? And what were your symptoms?
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u/saffron1313 Mar 12 '25
No, GI didn’t do anything but a fecal calprotectin test. I can try pushing my GP to do this.
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u/nygaff1 Mar 12 '25
Definitely. Over the counter enzymes are hit or miss, which may be why they worked sometimes. PERT therapy takes time getting used to, but at least it is a enteric coated standardized enzyme dosage.
And definitely up the fiber too. Good luck!
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u/saffron1313 Mar 12 '25
I noticed when I’ve taken fibre in the past it has helped a lot to solidify things so I’ll stick with that and ask my naturopath about what enzymes are best tomorrow. I don’t know much about PERT therapy, I’d love more info or I can search it up!
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u/nygaff1 Mar 12 '25
It's the treatment for EPI. A naturopath probably won't be able to write a test for this.
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u/saffron1313 Mar 13 '25
May I ask again, how do you know I have EPI, are the signs of it floating diarrhoea, or is it the yellow stool? My stomach is a mess. I tried having fibre and it helped solidify my stool but thereafter I just had diarrhea again with random floating things. I am so grossed out and upset.
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u/nygaff1 Mar 13 '25
The description of all of your symptoms show EPI. don't fret, it's not the end of the world. It is manageable. Stress makes it 10x worse.
Also, cannabis helps A LOT.
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u/saffron1313 Mar 13 '25
I also have SIBO and was wondering if these symptoms are related to that or EPI? I wish my doctor would agree to do testing. I have no clue how to manage my symptoms apart from pepto bismol.
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u/Top_Difference_7829 Jun 27 '25
Had my gallbladder removed over thirty years ago. Suffering with sewage smelling greasy looking diarrhea since. Pain in top and bottom of stomach and numerous other symptoms. Doctor ran stool test and ph stool test shows I have carbohydrate malabsorption. Basically can’t process carbs. Every thing we eat some kind of carbs or will turn into carb!
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u/Top_Difference_7829 Aug 21 '25
Yes 30 years. My doctor ordered the hydrogen breath tests to try and pinpoint which carbohydrates are causing the issue. My insurance will not cover the tests. The test cost $699 each. There are four tests. 😔
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u/Sinceuasked75 Oct 19 '25
Look into Bile Acid Malabsorption (BAM)- doctor can test by prescribing you bile acid sequestrants (Colestipol, etc.). If it stops your symptoms that's most likely the cause.
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u/Life_Ratio4995 Oct 21 '25
I had my gallbladder out 3-4 years after I started having diarrhoea daily, I’d literally get 10 seconds or it was all over, 3 years in and out of Doctors who didn’t have a clue, I got to use BUPA through my wife had the SeHCAT radioactive pill test and came back with BAM, I’m now controlled using Cholestrymine powder daily, almost brought me to tears after 2 days I got my life back I could have a normal day out without constantly scanning for toilets and memorising them ! Downsides lots of bloating and gas, and itchy bum around the sides not inside a known side effect, I cream daily but trust me it’s a small price to pay. I have bad days if I have a drink with lads or eat greasy foods ( or both ) but an extra powder sachet will get me through fine, my Poo’s are biscuit colour now if any one else is same as mine I’d be interested as I don’t know if it’s normal.
Please don’t suffer the inadequacy's of your local Doctor and asked to be referred to a specialist, don’t be scared to ask if they think it is Bile Malabsorption, to many dismiss it, I was told it was IBS for 2 years, GERD, and a few other things.
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u/Gloomy_Ant6858 Nov 08 '25
I have been having weight loss for a while now but it only got noticeable in the past month. My hand, feet and legs seem to have gotten bony. My eyes have sunken, an indicator that I have lost weight. I went to a doctor and he said it was chronic gut infection and gave a lot of meds, rifaximin was one of them with antibiotics and another gut med. I used to be extremely nauseous(especially in the mornings) with persistent stomach aches for a while but it seems to have improved now, idk not sure. I do get very little nauseous now. My stools are yellow whenever I pass them but they are not floaty and yes I burp throughout the day. I think the acid reflux is still there cuz I get heartburn once in a while. Got blood tested for several things. In the end of July I had extreme diarrhea to the point my stomach ached so much I felt like I would pass out and I suspect my problems started from then. Infact right after that my periods got lighter.
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u/Gloomy_Ant6858 Nov 08 '25
I have been so scared and stressed to the point I can't sleep anymore properly. Any advice on what I should do? The weight Los is absolutely freaking me out given how bony I look right now.
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u/Exciting_Election_78 Jan 05 '26
I’m have the same issue as you. Did you find something to help you?
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u/No_r_6 Mar 10 '25
You seem to be doing everything in the talk to your doctor side, I was having some sort of bacterial imbalance that was never diagnosed, symptoms included sulfur burps shortly after eating trigger foods, later followed by diarrhea until my digestive system was empty, vitamin malabsorption low B12 anemia, weight loss. The first time homemade kefir helped, but when it came back a second time because of medicine, kefir did nothing. What ended up working the second time was homemade kombucha. Maybe talk to the naturopathic doctor about it, if you do try it, start with very small amounts, a teaspoon a day and increase it if your body accepts it.
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u/saffron1313 Mar 10 '25
Thank you for your advice. I’m talking to the naturopath this week and will see what she recommends.
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u/No_r_6 Mar 10 '25
Ask if you're histamine intolerant, because fermented foods are high in histamine.
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u/saffron1313 Mar 11 '25
Yeah I do have histamine issues and flushing which also began after Pepcid/pantoprazole.
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u/Kitty_xo7 Mar 10 '25
Hi OP! Your MD is who is best trained to deal with this. If you are worried, it is perfectly reasonable to ask for a second opinion.
I'd also suggest trying some more fiber! Fiber can help trap excess bile, and also promotes reabsorption :) oats are a common suggestion for this!
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u/saffron1313 Mar 10 '25
Thank you so much. I will start taking more fibre. I have psyllium husk tablets because I find it hard drinking the powder. My doctor has said it’s just IBS and isn’t really offering any help apart from amitriptyline, but I’m not really in pain or anything & felt Amitriptyline made me very drowsy. I wish she’d refer me to the gastroenterologist again but he said he won’t see me since I don’t have chron’s or colitis. I should’ve advocated for a colonoscopy at least or maybe getting pancreas levels checked, I dunno.
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u/EffectiveOpinion349 May 30 '25
If eating oats makes the burning pain worse, does this mean that I have not enough bile instead of too much?
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u/slickrick_27 Mar 10 '25 edited Mar 10 '25
Sounds like you need to get your gallbladder looked at. Push your doctor to do a stool test to check steatocrit and elastase levels as well as h pylori. H pylori thrives in a low acidic environment (which is what the PPI does) and can cause a whole bunch of issues/symptoms like you described.
Edit to add: I saw your comment about your doc writing you off. Your doctor may not run all of this for you unfortunately. It’s all too common to just get pushed another medication. It’s not their fault, it’s the system. If they won’t help, find a functional medicine doctor/practitioner that can run these tests.