Small Intestinal Bacterial Overgrowth, or SIBO, is a common problem that millions of people are walking with every day, treated with medications without getting to the underlying cause. SIBO raises its ugly head when bacteria normally found in the large intestine grow out of control in the small intestine.
This disrupts digestion and nutrient absorption, leading to symptoms like gas, bloating, abdominal pain, constipation, or diarrhea. Many people are turning to probiotics and fermented foods for gut health support, but when it comes to SIBO, the mixed messages people get are confusing.
Let me break down the science behind probiotics, fermented foods, and how the correct dietary approach can improve your gut health, without making the problem worse.
Probiotics, Prebiotics, and Postbiotics: What Actually Are They?
Probiotics are beneficial bacteria that contribute to a healthy gut environment. They support digestion, boost the immune function, and help maintain the right balance between good and bad bacteria.
Research shows a healthy gut should have about 80% good microorganisms and only about 20% bad microorganisms. While many people think of probiotics as capsules or powders, the best source of probiotics is fermented foods like sauerkraut, kimchi, miso, and kefir.
These natural, food-based sources of the friendly microbes have sustained health in the gut for tens of thousands of years.
Prebiotics, on the other hand, are the fibers and plant compounds that nourish the beneficial bacteria. Humans can’t digest prebiotics, but the bacteria in your gut can. Feeding beneficial microbes with high-fiber, plant-based foods helps them survive and thrive.
Postbiotics are compounds made by beneficial bacteria from fiber. These compounds are short-chain fatty acids (like butyrate), enzymes, and other compounds that have direct anti-inflammatory, immune-boosting, and healing effects in the gut and beyond. While the term “postbiotic” may be unfamiliar to you, its health benefits have been well recognized for decades.
The Link Between SIBO and an Imbalance of Gut Bacteria
SIBO, known as dysbiosis, is important to our conversation. In the case of SIBO, the problem begins when bacteria normally confined to the colon migrate into the small intestine. This causes fermentation of carbohydrates in the small intestine, leading to excess gas, cramping, and inflammation.
Because probiotics are bacteria, the common belief is that taking them should help reduce or eliminate the symptoms of SIBO. However, it’s not always the case.
In fact, taking the wrong strains of probiotics, especially those that contain lactobacillus or bifidobacteria in capsule form, may worsen symptoms in some people with SIBO. That’s why it’s important to get a personalized approach.
Two Important Ways Fermented Foods Differ from Probiotic Supplements
First, they provide a greater diversity of microbial strains. Unlike probiotic supplements that often contain only one or two strains, fermented foods contain dozens of naturally occurring strains of microbes. These microorganisms have lived inside humans forever and know how to survive and function more effectively in the digestive tract.
Fermented foods contain fewer live organisms than high-dose probiotic supplements. While that might sound like a disadvantage, it’s actually beneficial for people suffering from SIBO.
Fermented foods offer a gentle introduction of microbes without flooding the digestive tract with microorganisms. For people with an overgrowth of microorganisms in the small intestine, small doses are often better tolerated.
The Role of Plant-Based Fiber in Feeding the Right Bacteria
The beneficial bacteria that contribute to long-term gut health need the right environment and food sources to grow and populate inside the large intestine. That’s where fiber comes in.
Diets rich in fiber from whole plant foods—like vegetables, legumes, nuts, seeds, and fruits—help feed beneficial bacteria in the colon. These bacteria then produce postbiotics like butyrate, acetate, and propionate. These naturally occurring compounds strengthen the gut lining, reduce inflammation, and regulate immune function.
Research has shown that a high-fiber diet increases the abundance of beneficial bacteria and increases bacterial diversity. A more diverse microbiome is associated with better health outcomes, such as better digestion and elimination, mood regulation, and a stronger immune system.
To recover from SIBO, it is important to slowly reintroduce fiber through cooked vegetables, soaked legumes, and fermented foods to help restore a balance in gut bacteria without causing a flare-up.
Postbiotics: The Unsung Heroes of Gut Health
While probiotics get most of the attention, it’s actually the postbiotics—the compounds produced when bacteria digest fiber—that do much of the heavy lifting in your gut.
One of the most important is butyrate, a short-chain fatty acid produced when bacteria ferment plant-based fibers. Butyrate helps repair the lining of the small and large intestine, the colon, reduces inflammation, boosts the immune system, and much more.
Other postbiotics include antimicrobial peptides, vitamins (like vitamin K and B12), and enzymes that aid digestion. These byproducts also help maintain a low pH in the gut, making it harder for harmful microbes to thrive.
In short, while probiotics help seed the gut, and fiber helps feed the microbes, it’s the postbiotics that deliver many of the health benefits.
Practical Steps for Using Fermented Foods in SIBO Recovery
If you’ve been diagnosed with SIBO, here’s a practical roadmap for using fermented foods and plant fiber to support your recovery:
Start Low and Go Slow
Introduce fermented foods like sauerkraut juice, kombucha, fermented beets or carrots, or small amounts of kimchi in tiny servings—1 teaspoon at a time. As long as you don’t produce excess gas or bloating, continue to increase the dosage slowly.
Choose the Right Fermented foods
Choose raw, unpasteurized versions of fermented foods from the refrigerated section. Pasteurization found in unrefrigerated foods like saurkrout or pickles kills the beneficial microbes, forgoing the probiotic effect.
Reintroduce Fiber Gradually
Begin with well-cooked, easy-to-digest vegetables like zucchini, carrots, and spinach. Soaking legumes before cooking makes them easier to digest.
A Lot of People Avoid FODMAP Foods unnecessarily
Many People go on a very restrictive FODMAP diet. FODMAPs are considered highly fermentable carbs that are rapidly fermented in the small intestine. However, after treating thousands of people with digestive problems, including SIBO, I have found that personalizing the diet is in the patient’s best interest to eliminate the symptoms of SIBO.
I order a blood test for patients with SIBO and all digestive disorders. This test screens for delayed food allergies. This type of allergic reaction produces symptoms anywhere from three hours up to three days after ingesting the offending foods. Sometimes the reactions can occur up to five days after ingesting the offending foods.
Work with a Functional Medicine Practitioner
My advice is to work with a functional medicine physician who has years of experience in treating patients with SIBO.
SIBO often requires more than just dietary changes. Herbal antibiotics, digestive enzymes, and specific foods are needed to fully eradicate the overgrowth before rebuilding the microbiome.
Final Thoughts
SIBO is a complex condition that doesn’t have a one-size-fits-all solution. While certain probiotics can be part of the recovery process, food-based sources—particularly fermented vegetables and cultured foods—offer a more balanced, sustainable approach for most people. When combined with a diet rich in plant-based fiber, these foods help support a healthier, more diverse microbiome.
In the end, it’s not just about adding probiotics. It’s about creating the right environment so beneficial microbes can thrive, die, and leave behind postbiotic compounds to help keep your gut in balance.