Do probiotics make SIBO worse or help you heal?
- thegutremedy
- Jul 30
- 8 min read
Updated: Aug 16
What is SIBO?
For years, we’ve been told that Small Intestinal Bacterial Overgrowth (SIBO) is exactly what the name says - too many bacteria in the small intestine. Doctors and functional medicine practitioners have been treating it like that for decades, throwing antibiotics and harsh antimicrobials at it to ‘kill off’ the bacteria.
Here’s the thing though, we now know that’s not really what’s going on. The small intestine isn’t supposed to be sterile, instead it has its own microbiome that’s different from the large intestine. Research now shows that SIBO is less about ‘too many’ bacteria and more about the wrong balance of bacteria [1]. This is called dysbiosis.
That’s a game-changer because if you believe SIBO is just overgrowth, all you’ll ever do is try to kill bacteria. And trust me, I’ve done round after round of antimicrobials… it didn’t get me anywhere. But when you see it as dysbiosis, it makes sense to focus on rebuilding a healthy microbiome, not just nuking it and hoping for the best (I talk more about that here).
My experience - Using probiotics when antimicrobials failed
Like most people who get a SIBO diagnosis, my first instinct was to wipe it out and kill all the bacteria! I did what every practitioner and Reddit post told me to do, round after round of antibiotics, herbal antimicrobials, and never-ending strict diets (including about 4 months eating chicken, rice and carrots - all low FODMAP, low histamine, low oxalate and low salicylate!)
And guess what? Nothing got better.
My symptoms got worse. The pain, the burning, the lack of appetite, the feeling of constantly being full, the food intolerances, the brain fog…it all stayed, but now my gut was even more sensitive than before.
At that point, probiotics were the last thing on my mind. Everything I’d read told me to not take probiotics with SIBO, as they just feeding the overgrowth! The thought of adding more bacteria felt like pouring petrol on a fire, but I had hit rock bottom. Out of sheer desperation, I decided to carefully try probiotics, one strain at a time, starting very low.
Slowly, the bloating and pain eased slightly. My gut felt calmer. I could finally eat more than those three ‘safe’ foods without spiralling into agony.
That’s when it clicked for me: SIBO isn’t a simple overgrowth problem. It’s a microbiome imbalance. And you can’t fix an imbalance by just wiping everything out - you need to rebuild. Probiotics weren’t the enemy.
This personal journey completely changed my view: for many with SIBO, probiotics aren’t the enemy - they’re a huge part of the solution. I would argue that it is almost impossible to permanently cure SIBO without the use of probiotics (be that in supplements or food form).
Why probiotics are controversial for SIBO
If you’ve spent even five minutes in a SIBO Facebook group or Reddit thread, you’ve probably seen this advice:
‘Don’t take probiotics - they’ll just make your SIBO worse.’
I believed this too. It made perfect sense when I thought SIBO was just ‘too many bacteria’. Why would you add more bacteria to an overgrowth?
This fear is baked into a lot of old SIBO protocols. The focus has always been on eradication - kill off bacteria with antibiotics or antimicrobials, starve them with low-carb or low-FODMAP diets, and hope your gut magically resets itself.
But here’s what I’ve learned the hard way: you can’t starve or nuke your way out of dysbiosis.
The idea that probiotics ‘make SIBO worse’ simply isn’t backed by research. In fact, clinical studies are starting to show the opposite - probiotics can reduce symptoms, improve gut motility, and help prevent relapse [5].
So yes, probiotics are controversial, but that’s because the conversation is still stuck on an outdated understanding of SIBO.
How probiotics actually help SIBO
Once I realised SIBO wasn’t just about too many bacteria, probiotics started making sense. They’re not there to pile more bugs into your gut, they’re there to fix the imbalance.
I like to think of it like this: imagine your gut lining has a certain number of parking spaces. Bacteria need to park in those spaces to live and thrive. When all the spaces are full, no new bacteria can move in.
In SIBO, many of those spaces are taken up by problem bacteria - the ones causing bloating, pain, and inflammation. When you introduce the right probiotics, they drive in and take over some of those spots, pushing the troublemakers out. It’s not about adding more cars to the lot; it’s about changing who gets the parking spaces.
Additionally, some probiotics naturally produce antimicrobial compounds. For example, Lactobacillus reuteri can create reuterin [6], a substance that directly inhibits harmful bacteria in the gut. This means probiotics can actually help kill the bad guys instead of feeding them.
On top of that:
They calm inflammation - Probiotics help repair the gut wall, which is often damaged in SIBO [7].
They help with motility - Certain strains improve how well food and bacteria move through the gut, stopping things from getting stagnant [8].
They rebalance your microbiome - After antimicrobials or restrictive diets, your gut needs rebuilding. Probiotics bring in the good guys to restore order [5].
When you see SIBO as dysbiosis, probiotics stop looking like a threat and start looking like the very thing that can rebalance your gut and help you finally heal.
Best probiotics for SIBO (what actually worked for me)
When I first started trying probiotics for SIBO, I had no idea which ones would help and which might make me feel worse. After a lot of trial and error, these were the ones that truly made a difference for me:
Probiotics I personally used
Dose: Started at 0.2 scoops and worked up slowly
Why it’s helpful: Many people with SIBO struggle to tolerate probiotics that produce D-lactate, a byproduct of fermentation that can cause symptoms like brain fog, fatigue, and bloating. This blend is specifically formulated with low-histamine, non-D-lactate-producing strains, making it much easier to tolerate for sensitive guts. It helps rebalance gut flora without triggering those common reactions.
My experience: This was my first step into probiotics. Because it’s low-histamine and D-lactate free, my gut handled it well. It calmed inflammation and felt like a safe starting point when everything else flared me.
Dose: Began with ¼ capsule for a few days, slowly increased to 2 capsules daily
Why it’s helpful: Spore-based probiotics like this one are tough survivors that can push out harmful bacteria by competing for resources. Some Bacillus species also produce natural antimicrobial compounds that directly inhibit gut pathogens.
My experience: This was a game-changer. It didn’t cause bloating or discomfort, and over time I noticed better digestion and fewer flare-ups.
Dose: 1 capsule, 1–2 times daily with meals
Why it’s helpful: This beneficial yeast doesn’t colonize your gut but helps kick out harmful bacteria and yeasts. It’s particularly helpful for managing diarrhea and calming inflammation.
My experience: One of my earliest wins, this helped balance my gut flora and helped some food intolerances.
Dose: 1 tablespoon daily (but start much lower - just a drop or two)
Why it’s helpful: This food-based probiotic has an extremely high CFU count, meaning it’s packed with beneficial bacteria that can outcompete harmful strains. Because it’s food-based, many people (myself included) find it gentler than high-dose supplements.
My experience: Once I eased into it, it became a simple and effective way to feed my gut the good guys every day.
Other options worth considering
I didn’t personally use these, but they’re highly regarded for SIBO and have helped many people:
Gastrus – BioGaia (L. Reuteri DSM 17938) → Produces reuterin, a natural antimicrobial that inhibits pathogenic bacteria; especially useful for methane-dominant SIBO.
Ideal Bowel Support – Jarrow Formulas (L. Plantarum 299v) → Helps reduce gut inflammation and may block harmful bacteria from sticking to the intestinal wall.
NB: None of these probiotics are sponsored or affiliate links - they’re all genuine recommendations based on my own experience and what I’ve seen help others I’ve worked with.
A quick word on individual responses
Probiotics are highly individual. What works brilliantly for one person might do nothing (or even cause a temporary flare) for another. That doesn’t mean probiotics are bad for SIBO, it just means your microbiome is unique.
Sometimes probiotics can make symptoms feel worse before they get better. In that case, it’s often worth reducing the dose and sticking with it a little longer to see if your gut settles, before trying a different probiotic.
I now have a list of over 40 different probiotics that I’ve seen help people I’ve worked with. But there’s no way to predict exactly which ones you’ll respond to without some gentle trial and error. Go slow, listen to your body, and introduce one probiotic at a time.
When and how to start probiotics for SIBO
Starting probiotics when you’ve got SIBO can feel terrifying - I was absolutely convinced they’d make me worse. Dosage is everything, and getting that right can mean the difference between relief and a flare.
When to start
Alongside antimicrobials: Some people introduce probiotics during a course of antibiotics or herbal antimicrobials to help protect and rebuild the microbiome as they go.
After antimicrobials: Others wait until they’ve finished treatment and then start probiotics to repair the gut and keep symptoms from returning.
On their own: Like me, you might find that antimicrobials don’t work for you at all. Probiotics can instead be used as a standalone approach to rebalance your microbiome.
How to introduce them
Start ridiculously low: I’m talking about a sprinkle of a capsule or a drop of cultured coconut. Jumping straight into full doses is a recipe for flares.
One at a time: Only add one probiotic at a time. This is the only way to know which strain is helping and which isn’t.
Go slow: Stick with a low dose for several days or even a week before considering an increase. Your gut needs time to adjust.
Watch symptoms carefully: Some temporary bloating or discomfort can actually be a good sign as it often means the probiotics are doing their job. If it’s too much, just lower the dose rather than stopping completely.
How long to take them
Gut healing is not an overnight job. I used probiotics for months, slowly increasing and layering different strains. Many people continue using probiotics long-term to maintain a balanced gut and prevent relapse.
Not every probiotic will work for every person, but I genuinely believe that pretty much everyone can eventually find at least one probiotic they tolerate and benefit from. The tricky part is that there’s no way to know which one it’ll be for you without some careful trial and error.
This is why it’s so important to start low and add just one probiotic at a time. Sometimes probiotics can make symptoms feel worse before they get better, which is why reducing the dose and giving it a little more time can help.
But equally, if it feels like probiotics are really not working for you, even at a tiny dose, it’s okay to stop and try something else. SIBO recovery is deeply individual, and pushing through with something that’s clearly not helping won’t speed up healing.
To sum up:
For years, I was told probiotics would only make my SIBO worse. I avoided them, stuck to antimicrobials, and lived on restrictive diets…and I got absolutely nowhere.
It wasn’t until I started experimenting with probiotics, VERY slowly, one strain at a time, that things began to shift. My gut calmed, I could eat more foods, and I finally felt like I was moving toward real healing.
Probiotics aren’t a magic bullet, and they won’t work the same way for everyone. But in my experience - and from working with many others with SIBO - there’s almost always at least one probiotic that your gut will tolerate and benefit from. Finding it just takes patience, trial and error, and a willingness to listen to your body (and not just panic if the first one you try seems to cause a flare up!).
If you’ve been stuck in the endless cycle of killing protocols and restrictive diets, maybe it’s time to try a different approach. The right probiotic could be the missing piece in your SIBO puzzle.
References:
Comments