You feel bloated after almost every meal. Someone online says “SIBO.” Now you are wondering whether bad bacteria have taken over your gut.
Here is the twist. In SIBO, the bacteria are usually not bad at all. They are ordinary gut residents that ended up in the wrong neighborhood, in the wrong numbers.
Short answer
SIBO, small intestinal bacterial overgrowth, means too many bacteria in the small intestine, causing gut symptoms. The bacteria are typically colon residents in the wrong place.
Your stomach acid, gut movement and the valve between your small and large intestine normally keep the small intestine lightly populated. When those defenses slip, colon-type bacteria can build up. Diagnosis belongs with a clinician, and the common breath tests have real limits.
This is general wellness information, not medical advice. It does not diagnose anything. If your gut symptoms worry you, talk with a qualified healthcare provider.
Flore data
What we see in our own microbiome reports
Our data can’t show SIBO. Stool reports read the colon, not the small intestine. They can show the methane side of the story. Methanobrevibacter smithii appears to be the key microbe behind breath methane, and it is an archaeon, not a bacterium (ACG, 2020). Among 7,299 people with de-identified reports and symptom records, it was flagged above our reference range for:
- 16.3% of people who reported bloating (510 of 3,128)
- 17.6% of people who reported gassiness (415 of 2,356)
- 15.2% of people who reported constipation (426 of 2,801)
- 10.7% of people with no digestive complaints (115 of 1,070)
That lines up with the ACG guideline, which notes that constipation is associated with higher breath methane and stool M. smithii. It is still an association. Most people with these symptoms did not have the flag. A stool flag does not diagnose SIBO or methane overgrowth. That takes a clinician and the tests below.
How we ran these numbers: Flore has analyzed 23,000+ microbiome reports. This section uses the 7,299 people whose de-identified records include both report flags and the symptoms they told us about. A “flag” means a microbe was above our reference range in that person’s stool report. It is not a diagnosis. Symptoms are self-reported. “No digestive complaints” means people who reported other concerns (such as mood, skin or energy) but none of our digestive tags. These are people who came to Flore, not a random sample of the public. Groups under 20 people are never reported. Every figure is an association, not proof of cause.
What SIBO is
The American College of Gastroenterology defines SIBO as “the presence of excessive numbers of bacteria in the small bowel, causing gastrointestinal symptoms” (ACG, 2020). The concept started with people who had clear risk factors that let the small bowel be colonized by colonic microbes (Bushyhead and Quigley, 2022).
So SIBO is a where and how many problem. Most of your gut bacteria are supposed to live in the colon, which holds the large majority of the roughly 38 trillion bacteria in an adult body (Sender, Fuchs and Milo, 2016). Healthy people have fewer than 1,000 colony-forming units per milliliter in the small bowel (ACG, 2020).
That is the same idea we cover in how to know when a gut bacterium is bad: location can matter as much as identity. And it is a clean example of why “bad” bacteria can be good somewhere else.
How your body keeps the small intestine quiet
- Stomach acid. Gastric acid acts as “a gatekeeper preventing the overgrowth of bacteria in the upper GI tract,” and most bacteria in food can’t survive it (ACG, 2020).
- Movement. Waves of muscle activity sweep food, secretions and bacteria toward the colon (ACG, 2020).
- A one-way valve. The ileocecal valve between the small and large intestine limits backflow of colon contents (ACG, 2020).
What raises the risk
The ACG guideline lists conditions that weaken those defenses (ACG, 2020):
- Low stomach acid, including after stomach surgery or with autoimmune gastritis. See low stomach acid (hypochlorhydria).
- Slowed gut movement, for example with diabetes or scleroderma, or with medicines such as opioids, antidiarrheals and anticholinergics.
- Surgery that leaves a blind loop, or removal of the ileocecal valve.
- Advanced age and female sex are also associated with SIBO.
The guideline also reviews acid-reducing medicines (proton pump inhibitors) as a possible factor. Don’t stop a prescribed medicine on your own. Talk to your clinician.
What SIBO can feel like
Typical symptoms are abdominal pain, bloating and diarrhea, and, more rarely, trouble absorbing nutrients (StatPearls). Those symptoms overlap with many other gut conditions, which is why SIBO is hard to call from symptoms alone. See IBS vs. SIBO for how the two get confused. Fungal overgrowth can look similar too: SIFO.
How SIBO is tested
Small-bowel aspirate. During an endoscopy, a clinician draws fluid from the small intestine and sends it for culture. A count of 1,000 or more colony-forming units per milliliter is “generally considered diagnostic” (ACG, 2020). It is invasive, needs sedation and is expensive, and it is not an established gold standard because it can’t reach the whole small bowel (ACG, 2020).
Breath tests. You drink glucose or lactulose, then breathe into tubes over a couple of hours. Bacteria ferment the sugar into hydrogen and methane, which show up in your breath. Under the North American Consensus, a hydrogen rise of 20 ppm or more within 90 minutes is positive for SIBO, and methane of 10 ppm or more is methane-positive (Rezaie et al., 2017). The ACG calls high methane intestinal methanogen overgrowth (IMO), because methane comes from methanogens, which are archaea, not bacteria (ACG, 2020).
The limits of breath testing
Breath tests are cheap, simple and safe. They are also imperfect, and gastroenterologists say so:
- The ACG guideline states that current breath tests “have low sensitivity and specificity.” Across studies, lactulose tests caught between 31% and 68% of cases confirmed by culture (ACG, 2020).
- Lactulose can give false positives when it reaches the colon quickly and colon bacteria ferment it. Glucose is absorbed early, so it can miss overgrowth farther down (ACG, 2020).
- In one study, breath tests and small-bowel aspirates agreed only about 65% of the time (ACG, 2020).
- Reviews argue that heavy reliance on breath tests, lactulose especially, has led to overdiagnosis of SIBO (Quigley, 2025; Kholwadwala and Quigley, 2025).
The takeaway: a breath test result is one input. A clinician puts it together with your symptoms, history and risk factors.
Can a stool test show SIBO?
No. Stool mostly reflects the colon, where most gut bacteria live. SIBO is about the small intestine. A stool-based microbiome test, including the one Flore uses, is not a SIBO test. Here is how an at-home microbiome test works and what it is built to show.
Where Flore fits
If you think you have SIBO, start with your clinician. Diagnosis and management are theirs, and they should hear about any supplement you plan to take, probiotics included.
Flore works on the bigger picture: the colon community that holds most of your gut bacteria. An at-home gut microbiome test shows who lives there and in what proportion. Flore builds a personalized probiotic-and-prebiotic formula from that data, and you retest so the next formula reflects what changed. It is wellness support, not a SIBO test, a diagnosis or a treatment.
Flore (formerly Sun Genomics) builds personalized probiotics from your own gut microbiome. Your sample is read by a CLIA-certified partner lab. Flore builds and makes your formula from the results. That work spans 10 years, 18,700+ people served, 23,000+ microbiome reports analyzed and 40,000+ personalized formulations.
Educational, structure/function information. Not medical advice, and not intended to diagnose, treat, cure or prevent any disease.
Frequently asked questions
What is SIBO?
Small intestinal bacterial overgrowth (SIBO) is the presence of excessive numbers of bacteria in the small bowel, causing gastrointestinal symptoms (ACG Clinical Guideline, 2020). The bacteria involved are usually types that normally live in the colon. It is a problem of location and amount.
How is SIBO tested?
Two ways. A clinician can take a fluid sample from the small intestine during an endoscopy and culture it; a count of 1,000 or more colony-forming units per milliliter is considered diagnostic (ACG, 2020). More often, a glucose or lactulose breath test is used. A hydrogen rise of 20 ppm or more within 90 minutes is considered positive, and methane of 10 ppm or more is considered methane-positive (North American Consensus, 2017).
How accurate are SIBO breath tests?
Less accurate than most people assume. The ACG guideline notes that current breath tests have low sensitivity and specificity. Lactulose tests can give false positives when the sugar reaches the colon quickly, and glucose tests can miss overgrowth farther down the small intestine. Gastroenterology reviews warn that reliance on breath tests, especially lactulose, has led to overdiagnosis (Quigley, 2025; Kholwadwala and Quigley, 2025).
Can a stool test diagnose SIBO?
No. Stool mainly reflects the colon, where most gut bacteria live (Sender, Fuchs and Milo, 2016). SIBO is about the small intestine, which is assessed with breath testing or a small-bowel sample. A Flore microbiome test is not a SIBO test.
What causes SIBO?
Anything that weakens the small intestine’s normal defenses. The ACG guideline lists reduced stomach acid, slowed gut motility (for example with diabetes, scleroderma or medicines such as opioids), surgery that leaves a blind loop, and loss of the ileocecal valve between the small and large intestine. Advanced age and female sex are also associated with SIBO.
Are methane-making microbes more common in people with bloating or constipation?
In Flore’s de-identified data on 7,299 people, Methanobrevibacter smithii was flagged above reference for 16.3% of people reporting bloating (510 of 3,128) and 15.2% reporting constipation (426 of 2,801), versus 10.7% of people with no digestive complaints (115 of 1,070). That is an association in stool reports. It does not diagnose SIBO or methane overgrowth.
Should I take a probiotic if I think I have SIBO?
Talk to your clinician first. SIBO is diagnosed and managed by a healthcare provider, and they should know about any supplement you plan to start, probiotics included.
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Sources
- Flore internal analysis of de-identified, aggregated report flags and self-reported symptoms, 7,299 people, November 2026. Groups under 20 not reported. Associations only.
- Pimentel M, Saad RJ, Long MD, Rao SSC. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Am J Gastroenterol. 2020;115(2):165-178. PMID 32023228
- Rezaie A, et al. Hydrogen and methane-based breath testing in gastrointestinal disorders: the North American Consensus. Am J Gastroenterol. 2017;112(5):775-784. PMID 28323273
- Bushyhead D, Quigley EMM. Small intestinal bacterial overgrowth: pathophysiology and its implications for definition and management. Gastroenterology. 2022;163(3):593-607. PMID 35398346
- Quigley EM. Small intestinal bacterial overgrowth: from malabsorption to misinterpretation. Minerva Gastroenterol. 2025;71(1):65-73. PMID 39804239
- Kholwadwala AS, Quigley EMM. Small intestinal bacterial overgrowth and intestinal methanogen overgrowth: are they overdiagnosed? Acta Gastroenterol Latinoam. 2025;55(4):276-291. PMID 41821875
- Sorathia SJ, Chippa V, Rivas JM. Small Intestinal Bacterial Overgrowth. StatPearls (NCBI Bookshelf). PMID 31536241
- Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533. PMID 27541692
Flore was formerly Sun Genomics. This article is general wellness information and is not medical advice, diagnosis or treatment. Statements have not been evaluated by the FDA. Talk to a qualified healthcare provider about your health.