What to Expect: Week 1 of Herbal Antibiotics

So you took your breath test, you’re finally diagnosed with SIBO (either hydrogen dominant, methane dominant, or both), you’ve chosen a SIBO diet that works for you, and now you’re ready to begin treatment.

I am convinced that a couple of rounds of antibiotics in HS from all of my acute bronchitis infections is part of what got me in this mess in the first place, so you can bet I was not about to pop some Rifaximin for 2 weeks.


(note: If you’ve chosen to go the pharmaceutical route, that’s totally cool. I just had prior digestive issues like GERD, gastritis, esophagitis, and possible leaky gut. I didn’t want to do further damage. This was the right choice for me. Make the right choice for you :))

Anywho… for whatever reason you have chosen the natural route.


(Convinced this is how all of my friends see me.)

If you’re at all like me, you were probably excited to kick this SIBO thing in the butt, but nervous because you’ve probably heard about this thing called the Herxheimer Reaction, aka the overgrowth/bad bacteria inside of you is literally dying off and out of your body (i.e. “die off”) and you in turn feel like your time has come and you are soon going to meet the good Lord Himself.

Most common illnesses and medications have symptoms and side effects we all know about. Amoxicillin can give you really bad stomach pain. Zofran can give you headaches. Pepto Bismol tablets can give you a black tongue (which is a whole other story for another day). But SIBO is so NEW and there’s still much research to be done, so there wasn’t much I could find on what to expect from taking herbal antibiotics.

So… I created this handy dandy guide to record my own experience as well as to hopefully mentally prepare someone for things they might expect when taking herbal antibiotics. I’m writing this first week on day 10, but I’m on a 28 day course so I’ll split them into separate posts.

My Herbal Antibiotic Protocol

Allicillin – 1 pill with breakfast, lunch, + dinner
Berberine – 1 pill with breakfast, lunch, + dinner
Oil of Oregano – 2x a day (was less strict on taking this)
Interfase Plus – 1 pill between meals (2x a day)
MotilPro – 1 pill between meals (2x a day)
Betaine HCL – 2 with each meal
Digestive Enzymes – 2 with each meal
Probiotic – 1 scoop upon waking


A lot of pills, isn’t it?

The important thing to note here is that every person is different. I’ve talked to some people who thought Berberine was a God-send and for others it made them violently ill. My experience will likely be different from yours, but hopefully this will at least give you an idea of what to expect if you’re on similar herbals.

In addition, some advice – this is an overwhelming number of pills/supplements. I was already taking the enzymes/probiotic. Then, I started with the HCL and to see how I did with it. For most, that won’t give you any sort of bad side effects unless you’ve got other stuff going on. With those as a part of my regular routine, it wasn’t too difficult to add the herbals to my routine. I also used a pill organizer so it was waaaaay easier to remember everything.

Processed with VSCO with c1 preset

With that said, let’s carry on.


Day 1: Just got back from traveling yesterday and I am pretty beat. Feeling dehydrated. Drinking lots of water today and started the day with some celery juice (come on HCL production). Did oregano and berberine for breakfast. Biofilm at 10:30. Throat feels a little inflammed and I’m pretty bloated/constipated. Taking all these pills feels like a second meal. I’m not even hungry at all. Also, feel kind of sweaty/gross and like I smell bad. Ugh. Am I hotter than usual?! The brain fog is real.

Day 2: Woke up nice and early (around 5:30am). Went to bed with chills last night and feel hot and achey this morning. Holy moly my bowel movements are rancid. I guess this really means bacteria is dying?

Oh boy. We have cramping people. We have cramping. We have period. For real!? The pain. Oh my goodness, the pain. Can I take tylenol? Feel like I’m going to die taking this many pills. Do you poop more on your period? No complaints there. Lots of complaints in the pain department. I fell asleep because the pain was so bad. Caved and popped some tylenol. Skipped my lunchtime herbals because I can’t handle the SIBO die off and period. Still hot and sweaty. I smell like a fart. I’m bloated and emotional. Can’t stop crying. My head hurts and my body aches. How can you feel constipated when you’ve gone to the bathroom?! This was a bad time for lady time to appear.

Day 3: Woke up feeling like my tummy was in a little boxing match yesterday and is now soaking in an ice bath. Wore my retainer because I noticed I’ve been grinding my teeth (which is giving me headaches upon waking). Headache did get worse throughout the day, though. Still feeling hot and sweaty. Took a nap today. My body hurts and it’s so hard to get out of bed. The FATIGUE is the devil. Still bloated and not hungry whatsoever. Making myself eat and take pills. I’ve never felt so exhausted. Tried an epsom salt bath. Gave me a headache and felt dehydrated afterwards. Feeling super depressed and like a huge burden to everyone. Is it too late to do elemental? I don’t want to do this anymore.

Day 4: Finally slept well and woke up without a headache (thank you lavender essential oil + my diffuser). Finally feeling a little bit calmer today. Less depression/anxiety. Don’t really have a mood. I just kind of feel like I’m existing, you know? Making no negative or positive contributions to society. Feel like I can still smell the antimicrobials through my pores. Sam (my boyfriend) says he doesn’t smell me, but I don’t know if I believe him. Maybe I’m going crazy. C turned to D today. That’s new. Still not all there mentally, but brain fog has lifted a bit to where I can focus better at work today. The belching and bloating is rough today. Skipped dinner pills. It’s just so difficult to take the full dosage. Tummy was throbbing.

Day 5: Woke up super early. I drove 8 hours home to be with family for the rest of treatment. Anxious to be on the road. Feeling pretty constipated today. Had some abdominal pain (not a common symptom for me) and diarrhea after lunch. Pain. Bloating. It feels like someone set fire to my stomach. Tummy feels like a block and it’s pulsating. Like a heartbeat. Skipped lunch and dinner pills. Didn’t handle anything well the rest of the night. Didn’t eat much.

Day 6: Woke up nice and early again. My throat hurts. Celery juice and some breakfast helped. Still feeling pretty fatigued and bloated today. Sticking to the allicin and berberine today. My throat burns and tummy feels like it has spasms. Fatigue hit pretty bad and some stomach pains before lunch… which turned into painful d. THE PAIN. WHY THE TUMMY PAIN. I don’t want to eat anymore, yucka yuck.

Day 7: Woke up feeling a little more rested today. Tummy is gurgly and I’m low energy. Haven’t gone to the bathroom today. Feeling constipated and bloated after lunch. WHY DOES EVERYTHING TASTE LIKE GARLIC. It’s foul.


I’m scared to eat and my throat is still bothering me. Still have some tummy pain here and there. Very irritable. Keep fighting with/ignoring everyone who is trying to help. What if I never get better? What if I’m like this forever? What if nothing works for me? I don’t want to get married feeling like this. I don’t want to lose my job. I feel like I’m kidding myself by being hopeful. I am getting worse and worse.

*insert crippling depression here*

Took an epsom salt bath. Feel worse and nauseous.


So I know that’s a weird/depressing place to leave off… but I promise it gets better. There is more to come next week!

Week 1 Conclusion

Beginning herbal antibiotics was extremely difficult for me. I expected some side effects, but I didn’t know it’d be anything like this. The start of my period made things 257x worse, but I think one of the big things I wasn’t expecting was the mental side effects.

Because the overgrowth eats up all the nutrients that are in your body (a fun SIBO symptom is malabsorption), you’re not getting the nutrients you need to be a mentally sane person (even if you’re eating a perfect diet). It makes sense that you’d feel anxious/depressed/brain fog. I wish I would have known that going into it so I would’ve felt less crazy going through it. It escalated for me being on herbals. So know you’re not crazy, even taking supplements won’t do much until you rid yourself of the SIBO.

MY BIGGEST ADVICE: I went head-on and took the full dose my naturopath recommended I take. We didn’t come up with a plan for me to introduce the antimicrobials. So I did a reset day 8 (didn’t take anything) and began reintroducing week 2 and did MUCH better with that. That way it may not be SO intense and you have some time to get used to it.

Overall, it isn’t a pleasant experience, but PRESS ON. You’re getting rid of these nasty little buggers and getting to a point where you can hopefully rid yourself of SIBO and begin healing your gut again. I almost gave up on day 8, but was encouraged and I’ll share more with you why in next week’s post 😉

I hope this guide is helpful and encouraging. Starting your SIBO treatment can be nerve-wracking and often difficult, but feeling a little crappy means (most times) that it is WORKING and you are getting rid of that nasty bacteria! If you have any questions/comments, please send them my way. Remember, this is just my experience. Yours could be completely different. I’d love to hear what it was like for you/what you learned through your herbal antibiotic process. Stay tuned for next week’s diary. It gets better, I promise!

4 thoughts on “What to Expect: Week 1 of Herbal Antibiotics

  1. My first round extremely similar to yours. This was a year and a half ago and im now back on them. Side effects not as bad this time around but definately still struggling. I have been treating this and underlying issues this whole time. It seems i may have similar things to you so am keen to see how you go with your protocols. Thankyou for sharing your stories.


    • Chloe,
      So happy to hear your second experience isn’t as rough as your first!

      I’m hoping that will be my case as well. I’m having some anxiety about doing a second round, but I know with some of the groundwork I’ve laid and the new ones I’ll be taking are more catered to my specific bacteria–so I don’t think it’ll be as bad either.

      Thank you for sharing that! That’s encouraging!


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