I’m ready to share my 28-day Rifaximin and Neomycin SIBO journal.

As soon as I mentioned I’d be starting Rifaximin + Neomycin again, everyone started asking me to share what the days were like on it; side effects, ups, downs, etc.

So I chose to document the 28 days, and now that they are over (ended on June 28, 2018), I wanted this to be as helpful and useful as possible for anyone who might come across this blog post without me needing to give every single last detail about each of the 28 days. 

So with that….

My 28-Day Rifaximin and Neomycin SIBO Journal

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My 28-Day Rifaximin and Neomycin SIBO Journal agutsygirl.com

I used a small notebook, in fact, it’s just my journal and I used the last 28 pages of it for this little experiment.

At the top of each day I wrote (example): Day 1: Rifaximin + Neomycin Friday, June 1, 2018.

Updated in 2024 to add: If I had to do my entire journey over, I would have used the Ahara Dinacharya journal. This 28-day journal was created from a decade of experience, and would have made these 28 days FAR easier to record, manage, and evaluate. 

Beneath each day, I had 6 sections. They included (in order):

  1. Food: where I recorded the things I ate (not quantities, just types)
  2. Medicine: where I recorded any and all medicine taken
  3. Supplements: where I recorded any and all supplements taken
  4. Mood: how I was feeling
  5. Workout: what I did for a workout
  6. Notes: all miscellaneous notes

My 28-Day Rifaximin and Neomycin SIBO Journal agutsygirl.com #sibo #fodmap #guthealth

Here we are the key (consistent) things from the 28 days:

  1. My food didn’t change a ton. I toggled between no, low, and high-FODMAP, depending on the day, how I was feeling, and what I was comfortable with.
  2. Every single day from Day 1 – Day 14, my medicines consisted of Rifaximin x 3 per day, Neomycin x 2 per day, LDN (low dose naltrexone) at night before bed, WP Thyroid on an empty stomach immediately upon waking up each day. 
  3. Once Day 15 hit, all medicine was the same except no more Neomycin.
  4. Almost every single day, my supplements stayed consistent with just digestive enzymes, HCL, and Adrenal Glandular. There was a period of time when I took Atrantil (2-3 times per day x’s 2 pills per time) as well.
  5. I was working out almost every single day, and barely ever was it “light and easy.”

Interesting/telling things from the 28 days on Rifaximin and Neomycin

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SIBO healing My 28-Day Rifaximin and Neomycin SIBO Journal agutsygirl.com

Days 1 – 14 (Rifaximin + Neomycin)

Day 1

I felt great until 4pm when I started feeling semi-nauseous.

Just prior to starting, though, I had been low-FODMAP so I wasn’t expecting to feel anything less than great.

I also forgot to eat FODMAPs on day 1, so there was that.

Day 2

I still didn’t have any bloat, but the nausea started hitting me.

I got some ginger mints and that worked wonders.

It was a Saturday so I had a long, 8-mile run that day which I noted left me completely wiped out and fatigued. 

Day 4 (a major high)

I made note that night: “No bloat. No gas. 2 great BM’s. Almost no nausea. Very tired around 3pm, but I also only got 6 hours of sleep last night. Still no back acne returned.”

But then Day 5 Hit (and BAM!)

Most of the rest of the 28 days would be misery.

That day I did a hard 20-minute workout, and I made note: “Sometime after workout = bloat, bad at night with huge bloat.”

I also then commented, “Correlation between the hard workouts, my lower back, and bloat?”

The SUPER BLOAT Continues

And on day 8 my notes said:

Super bloat all day. Sitting in lower stomach. Lower back made it worse after early morning workout. So bloated I could barely breathe. Left-side pain-like gas and nausea.

I start getting super paranoid

Paranoid that nothing is going to work this time, and I dig deep back into all the research.

On day 10 I noted: “Methanogens are tough characters (Dr. Pimental). I was so tired in the morning, felt super blah, dozed off about an hour, bloated and sitting in my lower gut.”

By This Point

I’m eating all the FODMAPs because I continue telling myself to, “just trust the process.”

But it feels like hell, and on day 12 I note:

Feeling so uncomfortable in my clothes – nothing fits, left-side pain all day. My mouth is highly irritated.

At the beginning of that week

Days 10-13, I was in New York for work. When I get home and settled on day 14, I noted:

Horrible fatigue today. A lot of nausea. Coffee aversions. Overall down day.

This is not a day I can forget because I got out of bed that morning thinking (remembering) how it was around day 13/14 of the previous SIBO antibiotic cycles when seemingly overnight I felt 100% again.

I had so much hope, but not even an hour after waking up, I was back in bed, thinking maybe I had the flu. I felt miserable.

And when I did spring back to life, I began having the coffee aversions, which lasted for most of the rest of the 28 days. Who was I anyways?! But that was day 14, which meant the final day of Neomycin.

Days 15-28 (Rifaximin only)


On day 15, all nausea went away.

Don’t you dare think this is made up, either.

It’s a very common side effect of Neomycin.

The nausea is the worst.

I did a hard 20-minute workout that day, and at night I felt so fatigued, drained, and my throat even hurt some.

By the way, at this point in the game, my weight was still creeping up some.

The next day

On day 16, I felt achy and sick again. I was so achy that I even had to take some Advil to get through the day (which I never, ever have to do unless my female monthly friend is visiting).

Because I was getting so afraid, I figured I might as well start Atrantil to see if that would help.

I was insane (yes, looking back, just pure insanity) and ran an “easy” 7 miles that day. 

And looking back

It’s no surprise, then, that on day 17 I was still so achy and had to take Advil yet again.

I also developed a stye in my eye. But at least I completely took the day off from working out that day.

I should mention

Even though I was on the struggle bus this entire time, I was going to the bathroom every single day like a normal person with BM’s that were just fine. T

hat was my sign for hope that repair could happen. 

On Day 19

I didn’t eat much, but here’s what I did eat: coffee, coconut milk, monk fruit, chicken, honey mustard, Chipotle Rice Bowl with that huge heaping of guacamole, booch, peanut butter, espresso coconut chips. And overall I just felt off and blah.

I noted,

I’m bloated, lower stomach sloshing, frustrated – mad – sad, I think it’s just time to follow the tried-tested-true diet for me.

So on Day 20

I stopped eating the FODMAPs and grains, dairy, and anything else that’s “technically” encouraged during the antibiotic protocol.

And I also started fasting again, and fasted for 14 hours that night/morning.

I stayed the course

But on day 22 felt the super bloat again, noting: “All this bloat — when I started Atrantil again?” But I stayed with the Atrantil through day day 24.

On day 25

I cut the Atrantil cold turkey.

Day 25 was miserable (I also ran 6 miles that day), but I decided to finish my last few days with some FODMAPs and grains and carbs sprinkled in here and there, but no Atrantil. 

Day 26

My food list looked like this:

  • coffee with coconut milk and monk fruit
  • smoothie (Elmhurst Milked Unsweetened Hazelnut, kale, spinach, Swiss chard, banana, blueberries, hempseeds)
  • Banana
  • Paleo Bar
  • pork rinds
  • collard greens with homemade dressing (olive oil, cinnamon, apple cider vinegar)
  • chicken
  • turkey
  • flaxseed + pumpkin seeds
  • 100% chocolate
  • walnuts
  • almond butter

Medicine: Rifaximin x 3, WP Thyroid, LDN

Supplements: HCL, enzymes, L-Glutamine, collagen, adrenal glandular

Mood: great

Workout: Nia’s workout (which is straight lifting) + a 1-mile walk

Notes: BEST day yet! ZERO bloat. 

I finished day 27-28 the exact same. No bloat; perfection

Rifaximin Side Effects

This is a question I get all the time, 

I heard the side effects from Rifaximin are really bad. Did you experience any Rifaximin side effects?

The answer is, “No.” And I think I took it a total of 4 times throughout my journey.

I did, however, have awful nausea from the Neomycin each time I took that.

Just because I did not have Rifaximin side effects doesn’t mean there aren’t any. 

Wrap Up from My Rifaximin and Neomycin Experience

And there you have it….my 28-day Rifaximin and Neomycin SIBO journal.

What’s the point of keeping a meticulous journal so we can see progression (or regression for that matter) like my 28-day Rifaximin and Neomycin SIBO journal if we’re not going to act upon the findings? 

While I did want to keep track of all this so I could share the experience and journey with those who have SIBO and/or are thinking about doing the antibiotics, I also wanted to do it for myself – to understand exactly what to do next and why. 

Because listen, my testing results for anything underlying are still inconclusive. Numbers are off, but specific tests are still negative (i.e. I don’t have Lyme disease).

I will never stop seeking the real answers (i.e. mold test, the Colonoscopy and Endoscopy, etc.) as to why I would relapse 4 times now when my lifestyle would (otherwise) indicate a relapse should never occur.

However, upon studying my 28-day Rifaximin and Neomycin SIBO journal, there are things I know for sure. I can draw many conclusions, and I can take the very worst days and see possible connections for why they were the very worst days.

Questions? Ask in the comments below or EMAIL ME.

Updated in 2024 to add: I am healed. I have had no relapse since this time period.

Gut Healing: ELEVATED

If it has, and if you want to dig in deeper, I’m inviting you to join Gut Healing: ELEVATED.

This is a 30-day PROCESS. It’s the FRAMEWORK and a detailed outline for what to do, day-by-day for 30 days to learn everything you can not only about the gut, but about how you will apply it for YOU and your own journey.

It’s my decade+ – long journey wrapped in one package with everything I learned, how I healed, and the SYSTEM that got me from there to here.

Gut Healing for Beginners ELEVATED with guthealingforbeginners.com

If you liked this post, you might also enjoy:

  1. Best Supplements for SIBO {based off experience + research}
  2. What Caused Your SIBO
  3. How I Healed SIBO Long Term


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  1. What are your conclusions about your experience with Antrantil? You r journal seems to conclude it made you worse.

    1. Hi – Yes, THIS time it DID make me worse. That hasn’t always been the case, though, which is why I don’t want to say too much negative about it. I have a planned post for Atrantil coming as well.

  2. Hello, I’ve just been diagnosed with SIBO and I have to start having Rixaximin and do this for 10 days. My question is, do you think that I should eat a low FODMAPs diet at a time, or when I finish the treatment? Thank you so much. I love all the content you provide since it helps others in the same situation as you. XX Irene

    1. Hi Irene – That’s all in my e-book, but I always ate FODMAPs during treatment (and most definitely for 10 days). You don’t have to eat a ton, but it’s generally accepted that you should be eating some so the antibiotic can do its job and fight off the bacteria.

    1. Hi Deena –

      No, I get my Rifaximin from a pharmacy in Australia. I wrote about it via a post called, “Waiting on Rifaximin.” And no, I haven’t lost ALL of it yet, but it hasn’t even been a week since I ended it. That said, ALL bloat weight is gone and the scale continues to go down without making any changes (except the changes to chill the #$%^ out). I know you wondered about my Ginger mints, too. They are these – affil link – https://amzn.to/2lTlQGY + I also use Ginger Chews frequently – https://amzn.to/2NkTeTo Hope that all helps!

  3. Going to be honest, your diet during most of this protocol sounds like the exact opposite of what it should be for someone with SIBO. If you’ve got SIBO, the microbiota in your small intestine is very out of balance, and your good probiotic bacteria populations are too weak. FODMAP’s, dairy, grains are going to make the situation worse, not better (independent of whether or not you’re taking antibiotics). You need to stop the disaccharide sugars, grains and starches for a while 100%. There should be no bloating.

    If you’re bloated it means bacteria and/or yeasts are present (at the wrong places in your gut) that are metabolizing what you’re eating and producing gases. That’s not good and the exact opposite of what you want. You’re taking large amounts of antibiotics to reduce or kill off the population of these things, but at the same time you’re eating FODMAP’s and feeding the buggers. It’s not going to work nearly as effectively.

    I know there’s a theory being tossed around that you should feed the bacteria while taking antibiotics, but I’ve seen zero evidence of this. You don’t feed a pathogen while you’re trying to kill it.

    You want to do the opposite: Starve the bad bacteria out. Attack them with antibiotics and biofilm busters. Don’t feed them. If it was me (as I’ve done this already), I would be eating a very basic zero FODMAP diet during the antibiotics. After the antibiotics, I would be eating *very* strong probiotic yogurt, and over time trying to *slowly* introduce prebiotics such as Inulin and arabinogalactan.

    It may take several waves of antibiotics followed by very strong probiotics to shift the microbiota in your small intestine back into balance. If you can’t tolerate Inulin it means your gut is still too out of balance and you need to work on it more. Prebiotics like Inulin feed the parts of your microbiota that need to be strong in order to recover from SIBO. Unfortunately, some types of bad bacteria can also metabolize Inulin, and if your overgrowth is still present it won’t work.

  4. What dosage of the Rifaximin and Neomycin did you take each dose (1200mg and 1000mg or smaller)? How many times a day?

    I want to tell my doctor how to write the protocol.

    Thank you

  5. Can one be bloated and have no pain or gas? I look 3-4 months pregnant, and I’m a MAN, and have been either constipated or loose, but don’t have any pain.

  6. Hi Sarah,

    Thanks for providing your experience with us. So what would be your conclusion after this rifaximin + neomycin treatment? Was it better or worse when you stopped eating fodmaps? Did you take probiotics while you were on those antibiotics?

  7. I was confused because I thought rifaximin and neomycin would make you loose weight because I thought it targeted archaea in the gut like methanogens and lactic associated archaea. Does it only target bacteria and not archaea or like only gram positive or gram negative? I took a medication that disturbed the balance of my gut flora and so I have an imbalance of methanogens (archaea) when I need more good bacteria instead of archaea. I thought after this class that the H gas produced by the bacteria is partly consumed by the methanogens and other archaea, but if you have too many methanogens and it consumes all of the gas you absorb more calories than average and have methane gas so I was trying to kill off the methanogen population or get a sort of antibiotic that targets archaea in order to keep more bacteria and lose weight and maintain as I did before. Do you know what domain of microbes those medications target? I don’t quite have the same problems, but I know archaea in the small intestines is harder to get rid of

  8. hello … I would like to know what doctor you were dealing with here in mexico I do not find anyone who treated me I did not even want to do the sibo test I found a laboratory but I think they only do it in hydrogen and do not know how to give doses I do not know what to do I have histaminosis

  9. My son started to have many belching distension reflux gases and he had an endoscopy tests and he got bacteria in the biopsy and he was given rifaximin but he continues with some burps he no longer eats gluten and they are treated by non-erosive reflux but I think the problem is the sibo but they do not listen to me or know how to treat it

  10. Hi Sara,
    I am about to start a new job around the same time as starting the antibiotics. I’m trying to stay optimistic and hoping I will get through this with minimal side effects at work. Any suggestions on what to have on hand besides ginger mints and Atrantil?

    1. My apologies Sarah. I didn’t catch that I left off the “h” off in your name.

  11. Hi, what exactly does the Atrantil do? I have some on hand and about to start a Xifaxan/Neomycin course. (got the xifaxan, waiting on the neomycin). Also, was the weight you gained just water weight? It’s been a nightmare trying to keep my weight down let alone lose. Did your weight come off after?

  12. Hello what kind of digestive enzymes did you buy ? And which kind of HCL ? And in what dosage for each ? Thanks

  13. Oh gosh, I’m so glad I found this post! I started a 14 day cycle of Rifaximin 7 days ago and feel way worse than I felt before. I was starting to think something is wrong. My stomach pain and bloating went from a 3 to a 7/8 since starting it. I almost wanted to throw in the towel today, but I’m going to stick it out. Thanks for the detailed journal of your experience!

  14. Hi Sarah,
    Have you ever gotten any answers as to what that fluid build up in the lower abdomen is? Whenever I have a bad recurrence of SIBO it seems like my lower abdomen fills with some sort of heavy fluid. The doctors keep saying that it is fat, but fat doesn’t appear one day and disappear the next. Sometimes the fluid is more bothersome to me than the bloating and gas pains and I would love to understand what it is that’s going on. I am on week four right now of a terrible SIBO outbreak after being good for a year and I am still waiting on my insurance company to approve my prescription. Each day my pain and symptoms are getting worse. It is so unacceptable for them to drag it out for this long.

  15. I am currently going through the same antibiotic treatment but for 10 days plus the Atrantil.

    I get severe itching because my SIBO dr believes I have leaky gut. Now that all my bacteria is dying and going into my blood stream the itch is unbelievable and worse than before. After reading your story and seeing how you got worse before you got better helps me think I’m not going through all this for no reason.

    Did you ever experience any itching?

  16. when you say specific tests were negative, does that mean your breath test was negative?
    p.s, thank you thank you thank you…. just thank you for this

  17. Hi, Sarah,
    I’m curious as to how you are now? are you cured? Can you eat freely, unrestricted?
    Im on my second round of Xifaxan and terrified that I won’t turn around. Before taking any Xifaxan, I could maintain a flat tummy by eating lowfodmap, but having started Xifaxan, I have been bloated 24/7. I’m scared.

  18. Hi Sarah,

    I re-read your posts constantly to help me know that there is an end in sight. My doctor and I have treated all my underlying issues (for 8 months) and have finally gotten to SIBO. I have SIBO-C and one round of Rifaximin didn’t work. 2 months later and a flight to the USA for neomycin, and I’m now on day 7 of the combo. 🤞🏽 How long after completing the antibiotics did you start to see (1) debloating, and (2) weight loss?

    Thanks for being such an inspiration and support to us lost souls!

  19. Sarah, I am being prescribed a protocol with both these plus a redo of the herbal protocol along with short chain fatty acid I am deficient in and some other things. YOu were just put on the medicine, is that right?

  20. Hi Sarah! Thank you so much for sharing your story. I have been dealing with SIBO for 9 years, three antibiotic treatments and I’m on my 4th relapse. This gives me hope! I’ve just been prescribed this antibiotic combo but am so nervous about the “hearing loss” side effect of neomycin. Did you have an side effects like that or were nervous about it at all? I’m hydrogen dominant with elevated methane (but only just a bit). Thinking about taking the Rifaxamin with Atrantil instead. Would love your thoughts!

    1. I hear the hearing loss concern all the time, but I’ve never known of anyone to actually have hearing loss due to it. I’ve taken neomycin like 3 times; my hearing is just fine. Hope you’re getting close to your forever healing!

  21. Yo. I am fascinated that you mentioned left side pain in one of your days here because that’s been a persistent thing for me as well and I also have hydrogen dominant (confirmed) and hydrogen sulfide (presumed) issues. Also noticed your best day was when you had L-Glutamine (tho it was also your last day of this protocol so it could also be the accumulation of things) but it’s interesting to me because when I started taking things with that and adding amino acids in my life I finally started feeling less dead! I think the sulfur piece has what’s been keeping me ill after yearsss of, like you, doing all the right things/food/lifestyle/meds wise! The discovery of hydrogen sulfide sibo is so exciting but I wish there was more established research. I introduced my doc who is experienced with sibo to its existence…..anyways thanks for what you do!!

  22. Wow! Those were some heavy workouts! Isn’t one supposed to just do light workouts… yoga or something like that, while we’re healing?
    And you were able to have coffee too? I have IBS-c with sibo and leaky gut…I cannot touch coffee… it’s something I miss every single day!

  23. Hi there. I am curious why, and how, your doctor put you on a 28 day supply of Rifaximin. Is that a double dose? My doctor has never prescribed more than a 14 day protocol. Did the back to back really help and did she/he prescribe it all at once? Thanks!

  24. Hi Sarah,

    I’ve been following you for some time and am so appreciative for all you share with us to provide us glimmers of hope on our sibo journeys. I’m about to start my third round of antibiotics, and am wondering if you did anything special to prep prior to starting on day 1? My current doctor has me on biofilm disrupters (it’s been nearly 2 months now) thinking that this is the piece missing from previous protocols lack of success. Did you ever incorporate biofilm disrupters or anything else in advance of starting the antibiotics that you think contributed to your successful final treatment?
    Thanks again 🙏❤️

  25. I realize that this post was originally from 2020, but I see you updated it as of 2024 that you haven’t had any relapses. Were there any die-off symptoms during this 28-day protocol? I had been taking herbal medications that caused a lot of stomach cramping/discomfort seemingly in my small intestine, so I went to Xifaxan. I felt better on Xifaxan and had no side effects, but still having constipation. I then moved to Xifaxan + Neomycin. I have been having very smelly flatulence and loose, but not diarrheal stools in the am (so it reversed the constipation). I would say that there is less bloat, too. However, as of Day 5, I have only had 1 normal BM, and there is the smell issue :-/. I am thinking that this might be die-off? Did you have any die-off symptoms?

  26. Thanks for your reply! I have moved past that stage to one marked mainly by extreme fatigue, poor sleep, and seemingly an even more bloated belly…:-(( Still trying to get out and exercise, though. Three follow-up questions: 1) I see that you did a 28-day cycle of Rifaximin + Neomycin for first 14 days. Often, it seems that most (but not all) doctors recommend 14-days both only, including Pimentel. Did you move to a 28-day cycle because you had had relapses before with only 14 days, or did you go directly to the 28-day cycle? 2) Did you have any relapses after your initial post where you had to repeat the 28-day cycle. I know that you said recently that you have had any recent relapses; 3) I saw you did Atranil. Have you ever tried Iberogast? I have IMO, which I had back in 2018 and had pretty well resolved with Xifaxan + Neomycin, but a brush with COVID in September really messed up my gut, so it came back in full force.

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