What Is SIBO, and Why Is It So Confusing?

Many people struggle with bloating, gas, heartburn, constipation, or diarrhea, and get confused by conflicting information online about good gut health.

They often start their journey with an IBS diagnosis, which really means serious conditions have been ruled out, without explaining what is actually happening. 

Research is increasingly pointing to SIBO, or Small Intestinal Bacterial Overgrowth, as the real issue for a large share of IBS patients, with estimates ranging from 45% to 80%. 

SIBO happens when bacteria that belong in the colon start over growing in the small intestine, fermenting food and creating gas.

This creates a range of symptoms: Burping, chronic bloating that worsens through the day (some describe it as feeling six months pregnant), abdominal cramping, and changes in bowel habits, from constipation to urgency and diarrhea. Beyond digestion, people can experience low energy, brain fog, skin issues like acne or eczema, and joint or muscle pain.

Alexa Ress, a holistic nutrition and functional medicine certified health coach who specializes in SIBO, IBS, and gut health, explains that there are actually three types of bacterial overgrowth, based on which gas is produced:

1. hydrogen-dominant SIBO
2. methane (now called Intestinal Methanogen Overgrowth, or IMO)
3. hydrogen sulfide (Intestinal Sulfide Overproduction). 

Hydrogen tends to bring diarrhea and bloating; methane is linked to constipation, nausea, and sometimes weight gain; hydrogen sulfide often brings more pain, including bladder or joint pain. Many people have a combination of SIBO types.

SIBO: Testing and Treatment

Breath testing is the most common way to identify SIBO. It’s non-invasive: You drink a sugar solution and breathe into a tube every 20 minutes for 2 hours so overgrowth can be measured and gas identified. Hydrogen and methane are the most widely tested gases; in the US, the Trio-Smart test can also measure hydrogen sulfide. 

Testing matters because treatment differs by gas type. Rifaximin, the antibiotic GI doctors most commonly prescribe, works well for hydrogen but not methane, which needs an additional antibiotic or different herbal antimicrobials.

Unfortunately, recurrence is common. Nearly 45% of people relapse within nine months of one round of rifaximin, and close to half relapse within a year. That’s why treating the underlying cause, not just killing the microbes, matters so much.

Why Bacterial Overgrowth Happens

SIBO isn’t an infection; it happens when the body’s natural defenses weaken. Those defenses include stomach acid, pancreatic enzymes, bile, an intact ileocecal valve, and a healthy gut microbiome and nervous system. 

Chronic stress plays a real role here, because when your body is in survival mode, digestion shuts down. Many people are also disconnected from their bodies, unable to recognize hunger cues or eat mindfully.

Alexa teaches clients how to eat again: Putting phones away, slowing down, noticing color and taste, and even taking a few deep breaths before a meal to activate the vagus nerve and prepare digestion. This helps the body release the stomach acid, enzymes, and bile needed to break food down, rather than leaving undigested food to feed microbes.

Diet: Finding the Middle Ground

Interestingly, by the time clients reach Alexa, they’re usually underfed rather than overfed, having restricted their diets out of fear and discomfort. While fermented foods and fiber are often recommended for gut health, they can backfire for someone with active SIBO. 

Alexa rarely uses a strict SIBO diet anymore; instead, she removes the biggest offenders and works to expand a very limited diet slowly, sometimes one bite at a time, helping clients rebuild trust with food rather than staying stuck in restriction. 

Healing isn’t about permanent limitation, it’s about returning to a full, nutrient-rich diet, and avoiding the perfectionism and all-or-nothing thinking that can add more stress to an already stressed system.

Supporting Gut Motility

The migrating motor complex (MMC) is the gut’s housekeeping wave that clears leftover food and bacteria between meals, but it only activates during fasting periods, roughly 90-120 minutes after eating. 

Spacing meals three to five hours apart supports this process, along with mindful eating, good sleep and wake cycles, and prokinetic supplements when needed.

Biofilm disruptors are also useful, especially for people who’ve relapsed, since bacteria can shield themselves in protective communities that antimicrobials struggle to penetrate. Options range from gentle ones like NAC to more targeted natural formulas.

Natural vs. Conventional Antimicrobials

Both approaches have a place. Herbal antimicrobials like berberine, oregano oil, neem, and thyme oil can be as effective as antibiotics in some studies, though natural doesn’t mean automatically safe, berberine, for instance, can interact with medications. 

Foundational work always comes first: Nutrition, meal rhythm, motility, and inflammation, especially for sensitive individuals, before adding antimicrobials that can trigger die-off symptoms.

Constipation, Structural Support, and the Bigger Picture

For constipation, Alexa focuses on daily, complete bowel movements using magnesium, kiwi fruit, coconut water, vitamin C, and partially hydrolyzed guar gum, always starting low and slow. Structural issues, such as those following endometriosis or abdominal surgery, may benefit from visceral manipulation therapy.

The ripple effects of healing the gut are enormous: better skin, energy, mood, concentration, and even improvements in vaginal and bladder health, since these systems are deeply interconnected. As I often say, this is the paradox of the gut: the more severe your symptoms, the slower and gentler your approach needs to be. Small, steady changes outperform aggressive ones every time.

If you want to learn more about Alexa you can find her on Instagram @seekingguthealth and Facebook @Seeking Gut Health. Alexa also offers a free Ultimate SIBO Guide and a SIBO Free Life Method Program, along with one-on-one, personalized consultations through her website, SeekingGutHealth.com. 

A Note from Dr. Doni

I, too, help a lot of people in my practice with SIBO and gut health, and I completely agree with Alexa about how important it is to address the gut microbiome in order to restore healthy immune system function. Conditions such as allergies, autoimmunity, as well as infections, like HPV, all improve as the gut heals.

Optimizing your health is absolutely possible. There are more and more ways to support healing that don’t require expensive treatments or complicated protocols. For this, it is important to address the underlying causes of health issues by working with a practitioner who can help you look deeper to uncover the root causes of your health issue, and help you to prioritize what to address first, so that you are finally able to break the pattern. 

And that’s exactly what I do in my one-on-one practice, and online programs, including my Leaky Gut Program, where I teach you how to heal your digestion in a safe and effective way. You can read about it and join in here.

In my book Master Your Stress Reset Your Health, I explain how stress, trauma, toxins, and a lack of recovery, can keep us stuck in “stress mode” and lead to various health issues, including leaky gut, food sensitivities, bacterial overgrowth, autoimmunity, and susceptibility to infections. I also teach you how my individualized approach to recovery makes all the difference.

Start by taking my Stress Type® Quiz to understand how stress is impacting you today, and then follow my Stress Recovery Protocol and C.A.R.E. Method to support your body and nervous system to heal using diet changes, and natural approaches including time in nature. 

TAKE THE FREE STRESS QUIZ TO FIND OUT YOUR STRESS TYPE:

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If you’re dealing with HPV and want to prevent cervical cancer, I welcome you to join me over on Instagram @drdoniwilson and on my website at clearhpvnow.com. You can download my free HPV Recovery Guide and watch videos of women who’ve implemented my HPV Protocol and found freedom from high-risk HPV. I want for you to feel hope that you can heal too.

If you’d like to get a better sense of my approach, I welcome you to join my next free How to Get Rid of HPV online workshop where I help you to create a plan to get HPV out of your life for good. From there, you might choose to join the Heal HPV Kickstart Program, for the initial steps of my protocol, including diet changes and supplements, over the next 30 days.

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Or you can begin with the comprehensive Say Goodbye to HPV Program, which includes everything you need to implement my full protocol and to address all eight susceptibilities to HPV, including helping you to resolve underlying emotional stress and trauma. 

If you have any questions, please don’t hesitate to reach out to my office. My team and I would be happy to connect with you and help you. Click here to set up a call with my team.

Thank you, everyone, for listening in to How Humans Heal and learning all about how Alexa is helping people heal from SIBO and IBS through personalized, root-cause-focused plans. If you haven’t already subscribed, I welcome you to subscribe so you don’t miss the next episode. 

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Disclaimer: This specific article and all other Content, Products, and Services of this Website are NOT intended as, and must not be understood or construed as, medical care or advice, naturopathic medical care or advice, the practice of medicine, or the practice of counseling care, nor can it be understood or construed as providing any form of medical diagnosis, treatment,  natural HPV cure, or prevention of any disease.