The Mysteries and Underdiagnosis of SIBO

10 minute read

In 2017, shortly after she turned 32, Phoebe Lapine had just spent the previous three years overhauling her health to make up for her ailing thyroid, the result of unchecked Hashimoto’s thyroiditis. She was following a gluten-free diet, drinking kombucha and taking prebiotics, and finally feeling her best when she noticed peculiar gut symptoms starting to rear their head: burping during meals, stomach discomfort, and a bloated belly that simply would not deflate. She turned to a functional doctor who quickly gave her a diagnosis: small intestinal bacterial overgrowth (SIBO), a gut condition not uncommon for hypothyroid patients.

Lapine, who lives in New York, had never heard of it, nor had her endocrinologist warned of the possibility of developing it. The diagnosis was a relief: “It’s not all in my head; the bloating is just sticking to my body like an inner tube,” Lapine, now 36, remembers thinking. But treatment proved to be an odyssey in and of itself. It would take six weeks of antimicrobial medicines and another six months of a restricted diet for her digestion to feel normal again, and for the bloat to finally go away. Lapine, a food and health writer and chef, chronicled her SIBO journey and shared SIBO-appropriate recipes on her blog and podcast in early 2018. That’s when she learned how lucky she’d been.

“I’ve gotten many, many messages and emails from really sick, desperate people. They reach out from all over the world and are like, ‘No one here where I live knows what this is,’” Lapine says. She answered the first few notes, but when the avalanche didn’t let up, she set up an automatic response with links to online resources.

SIBO is a notoriously underdiagnosed condition, despite research suggesting it may be a chief cause of irritable bowel syndrome (IBS). Approximately 11% of people worldwide suffer from IBS, a “wastebasket diagnosis” many patients with an array of digestive issues are given when doctors can’t pinpoint a more precise cause. Their symptoms can be managed through diet and a handful of supplements and medications, but for a long time, a cure was considered to be out of the question. “People were relegated to ‘learn to live with it.’ When SIBO came along, it really offered some cures and solutions,” says Dr. Nirala Jacobi, a naturopathic doctor whose online platform “The SIBO Doctor” offers courses on the disorder for both practitioners and patients. But although Jacobi and others have led an awareness crusade, many practices fall short when it comes to SIBO diagnosis and treatment. “I still hear from patients every day that they go to the gastroenterologist and it’s still not being recognized,” says Jacobi.

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SIBO is the abnormal and prolific growth of either bacteria or archaea—a single-celled organism older than bacteria—in the small intestine. The bacteria or archaea interfere with normal digestion by competing with patients for food. Instead of allowing the small intestine to digest food and release nutrients into the bloodstream, the bacteria or archaea get there first and ferment the food. In the fermentation process, the bacteria release hydrogen, and the archaea release methane, creating the appearance of bloating. Although SIBO has served as the umbrella term for both kinds of overgrowth, experts now prefer to differentiate between them and refer to archaea excess as intestinal methanogen overgrowth, or IMO. Certain bacteria can also produce another gas, hydrogen sulfide, but this type of SIBO does not have its own name. In addition to bloating, fermentation can create a range of IBS issues: usually diarrhea from hydrogen and hydrogen sulfide production, and constipation from methane, although there can be both or neither. Over time, in addition to bowel discomfort, gas production leads to poor fat, carbohydrate, and protein absorption by damaging the intestinal wall lining, creating what’s called “leaky gut.” This also causes vitamin deficiencies, the most acute of which are B-12 deficiencies, leading to weakness and fatigue (and in advanced cases, mental confusion).

Read More: What We Know About Leaky Gut Syndrome

Understanding how and why bacteria or archaea start to overgrow in the small intestine is crucial to treating SIBO and IMO. Although they are digestive disorders, they’re almost always a symptom of another underlying issue: motility dysfunction, or the slow transit of food through the small intestine.

Getting to the root cause

By the time patients call up Dr. David Borenstein’s clinic at Manhattan Integrative Medicine, they’ve consulted three GIs before him, on average, without success. Either treatments were ineffective, or after a temporary reprieve, the SIBO or IMO relapsed. According to some studies, relapse rates are as high as 45%.

“Most of the people who do treat it are gastroenterologists,” says Borenstein, an integrative and functional doctor. “They’ll give you an antibiotic. A lot of the time, it helps, but the SIBO will come right back because they’re not treating the root cause of the problem.”

Diagnosing SIBO and IMO is simple. A breath test is a noninvasive procedure that measures hydrogen and methane gas levels (hydrogen sulfide too, depending on the kind of test) by having patients blow into plastic tubes or bags every 30 minutes for three hours after ingesting a lactulose substrate. Narrowing down the conditions underlying SIBO and IMO may require a few more tests, but a patient history is the best place to start.

A bad episode of food poisoning—or several—can have damaged the patient’s migrating motor complex (MMC), a system that sweeps the small intestine clean like a dishwasher every 90 minutes and which, if impaired, may leave food debris and bacteria behind, allowing them to multiply. The IBS Smart test looks in the blood for anti-CdtB and anti-vinculin, antibodies produced to fight food poisoning. Their presence can indicate post-infectious IBS and suggest that the MMC has been weakened.

Proton pump inhibitors—a common reflux medication that decreases the amount of acid the stomach produces—can have compromised the stomach’s capacity to kill bacteria. In that case, stomach acid levels should be checked. An underperforming thyroid can have slowed a patient’s MMC, so a full thyroid panel ought to be done. Abdominal surgery—a hysterectomy, a laparoscopy to explore possible endometriosis, a hernia—can have produced scar tissue on the small intestine wall that pinches the intestine and obstructs flow, like a kink in a garden hose. Imaging and further exploration can detect that.

Then a solution can be tailored to the patient. Many involve prescribing a prokinetic agent, a medication that enhances motility.

In the meantime, the excess bacteria and archaea can be eliminated one of three ways. The first option many doctors opt for is a two-week regimen of antibiotics—specifically rifaximin, the first and only U.S. Food and Drug Administration–approved IBS drug, for SIBO, or a combination of rifaximin with either neomycin or metronidazole for IMO, since archaea resist rifaximin alone. For a gentler approach, some practitioners prefer to prescribe herbal antimicrobials such as allicin, oregano, berberine, neem, and cinnamon for four to six weeks. For especially recalcitrant cases, some resort to the elemental diet, a liquid formula of predigested nutrients that gives the digestive tract a break, starving the bacteria or archaea in the process. The elemental diet is the nuclear option, as it’s the most challenging one for patients, considering they can’t eat solid food or drink anything besides water for two to three weeks.

A medical and holistic alliance

The origins of SIBO research trace back to our improved understanding of the microbiome and, specifically, to advances presented by Dr. Mark Pimentel, a gastroenterologist and executive director of the Medically Associated Science and Technology (MAST) Program at Cedars-Sinai Medical Center. In 1999—before the term microbiome had even gone mainstream—Pimentel published a paper showing that IBS was not a psychological disorder, as was commonly believed at the time; rather, it was the result of bacterial dysbiosis, or an imbalance of the gut’s microbial community.

Pimentel and his team at Cedars-Sinai have spent the past two decades characterizing the major bacteria in the small intestine. Last year, they published a paper that showed the sequences of the microbiome in the duodenum, the jejunum, the ileum and the colon for the first time. And they homed in on SIBO as an important contributing factor to IBS.

Pimentel’s research caught the attention of Allison Siebecker, a naturopathic physician who had been conducting her own SIBO research and leading awareness campaigns in the holistic community. In 2010, she became one of the first SIBO experts to create an online resource,, with information about the disorder for both physicians and patients. She invited Pimentel to speak at the 2015 SIBO Symposium, an annual conference she’d started organizing a year prior, where the leading U.S. SIBO researchers presented their findings on the disorder and treatments. Pimentel and Siebecker have continued to collaborate since then.

“What’s interesting in the naturopathic community is that they tend to see patients that a lot of Western physicians aren’t able to sort out, and I think that was the case for IBS and SIBO in the beginning,” Pimentel says. “The naturopathic community was seeing a lot of these patients and then also recognizing the treatments sooner than Western medicine.”

While Pimentel pioneered the use of rifaximin as both an IBS and a SIBO treatment, naturopaths like Siebecker had already been touting herbal antimicrobials as an equally effective treatment method.

More awareness

Medical schools are beginning to include more material on the microbiome and dysbiosis, but practicing doctors may not have received that education.

“I trained to be a doctor 20 years ago, and at the time, SIBO was not known,” explains Dr. Ana Esteban, an intensive-care doctor who now specializes in SIBO. “No one talked about the microbiome. So my generation is training the next generation of doctors. Professionals like me are informing ourselves, but we have to specialize on our own, paying for courses out of pocket, finding the time and resources, because we want to. There’s no institutional help.”

As more online resources like Siebecker’s and Jacobi’s crop up, patients are increasingly turning down wastebasket diagnoses and seeking out doctors who will truly probe their digestive issues.

“A lot of people are still told to eat fiber and learn to live with their IBS,” says Jacobi. “Now because of the Internet and social media, people are just not willing to put up with that anymore and are looking for answers.”

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