The Mysteries and Underdiagnosis of SIBO

In 2017, shortly after she turned 32, Phoebe Lapine had just spent the past three years doing a health check to make up for her ailing thyroid, the result of Hashimoto’s uncontrolled thyroiditis. She followed a gluten-free diet, drank kombucha and took prebiotics, and finally felt her best when she noticed strange intestinal symptoms: belching during meals, stomach upset and a bloated stomach that just wouldn’t empty. She turned to a functional doctor who quickly gave her a diagnosis: small intestinal bacterial overgrowth (SIBO), an intestinal condition not uncommon for hypothyroid patients.

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Lapine, who lives in New York, had never heard of it, nor had her endocrinologist warned about the possibility of developing it. The diagnosis was a relief: “It’s not just between my ears; the bloating just sticks to my body like an inner tube,” Lapine, now 36, recalls thinking. But the treatment turned out to be an odyssey in itself. It would take six weeks on antimicrobial drugs and another six months on a restricted diet before her digestion returned to normal and the bloating finally disappeared.Lapine, a nutrition and health writer and chef, wrote her SIBO journey in early 2018, sharing SIBO-appropriate recipes on her blog and podcast. how lucky she was.

“I’ve been getting a lot of messages and emails from really sick, desperate people. They reach from all over the world and say, ‘Nobody here where I live knows what this is,’ says Lapine. She answered the first few notes, but when the avalanche didn’t stop, she set up an automatic reply with links to online resources.

SIBO is a notoriously underdiagnosed condition, despite research suggesting it may be a leading cause of irritable bowel syndrome (IBS). About 11% of people worldwide suffer from IBS, a ‘trash can diagnosis’ that many patients with a variety of digestive problems receive when doctors can’t pinpoint a more precise cause. Their symptoms can be managed through diet and a handful of supplements and medications, but a cure was long thought to be out of the question. “People were demoted to ‘learn to live with it’. When SIBO came along, it really offered some treatments and solutions,” said Dr. Nirala Jacobi, a naturopathic physician whose online platform “The SIBO Doctor” offers courses on the condition for both practitioners and patients. But while 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 still goes unrecognized,” Jacobi says.

SIBO is the abnormal and prolific growth of bacteria or archaea – a single-celled organism that is older than bacteria – in the small intestine. The bacteria or archaea disrupt normal digestion by competing with patients for food. Instead of letting the small intestine digest food and release nutrients into the bloodstream, the bacteria or archaea get there first and ferment the food. During the fermentation process, the bacteria release hydrogen and the archaea release methane, causing bloating. While SIBO has served as the umbrella term for both types of overgrowth, experts now prefer to differentiate between them and refer to archaeal 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 cause a range of IBS problems: most commonly diarrhea from the production of hydrogen and hydrogen sulfide and constipation from methane, although there can be both or neither. Over time, in addition to intestinal discomfort, gas production leads to poor absorption of fat, carbohydrates and proteins by damaging the intestinal wall, creating what is known as a ‘leaky gut’. This also causes vitamin deficiencies, the most acute being B12 deficiencies, leading to weakness and fatigue (and in advanced cases, mental confusion).

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

Go to the cause

By the time patients reach Dr. Calling David Borenstein at Manhattan Integrative Medicine, they’ve consulted an average of three GIs for him, with no 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 treat it are gastroenterologists,” says Borenstein, an integrative and functional physician. “They’ll give you an antibiotic. It often helps, but the SIBO comes right back because they don’t address the cause of the problem.”

Diagnosing SIBO and IMO is easy. A breath test is a non-invasive procedure that measures hydrogen and methane gas levels (including hydrogen sulfide, depending on the type of test) by having patients blow into plastic tubes or bags every 30 minutes for three hours after taking a lactulose substrate. A few more tests may be needed to narrow down the underlying conditions of SIBO and IMO, but a patient history is the best place to start.

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

Proton pump inhibitors — a common reflux drug that reduces the amount of acid the stomach produces — may have compromised the stomach’s ability to kill bacteria. In that case, the stomach acid level should be checked. An underperforming thyroid may have slowed a patient’s MMC, so a full thyroid panel should be done. Abdominal surgery — a hysterectomy, a laparoscopy to investigate possible endometriosis, a hernia — may have caused scar tissue on the small bowel wall that squeezes the bowel and restricts its flow, like a kink in a garden hose. Imaging and further exploration can detect that.

Then a solution can be tailored to the patient. Much of that involves prescribing a prokinetic, a drug that improves motility.

In the meantime, the excess bacteria and archaea can be eliminated in three ways. The first option many doctors opt for is a two-week course 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 neomycin or metronidazole for IMO , as archaea are resistant only to rifaximin. 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 particularly unruly cases, some resort to the elemental diet, a liquid formula of pre-digested nutrients that gives the digestive tract a break, starving the bacteria or archaea in the process. The basic diet is the nuclear option as it is the most challenging for patients as they cannot eat solid food or drink anything but water for two to three weeks.

A medical and holistic alliance

The origins of SIBO research can be traced back to our improved understanding of the microbiome and, in particular, the 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 mental 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 been characterizing key bacteria in the small intestine for the past two decades. Last year, they published a paper showing the sequences of the microbiome in the duodenum, jejunum, ileum and colon for the first time. And they addressed SIBO as a major contributing factor to IBS.

Pimentel’s research caught the attention of Allison Siebecker, a naturopath who had conducted her own SIBO research and led awareness campaigns in the holistic community. In 2010, she became one of the first SIBO experts to create an online resource,, of information about the condition for both physicians and patients. She invited Pimentel to speak at the 2015 SIBO Symposium, an annual conference she had begun hosting a year earlier, where the leading US SIBO researchers presented their findings on the condition and treatments. Pimentel and Siebecker have continued to work together ever since.

“What’s interesting in the naturopathic community is that they tend to see patients that a lot of western doctors can’t resolve, and I think that was the case for IBS and SIBO in the beginning,” Pimentel says. “The naturopathic community saw many of these patients and also recognized the treatments earlier than Western medicine.”

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

More awareness

Medical schools are beginning to include more material about the microbiome and dysbiosis, but practicing physicians may not have received that training.

“I trained as a doctor 20 years ago and SIBO was not known then,” explains Dr Ana Esteban, an intensive care physician who now specializes in SIBO. “Nobody talked about the microbiome. So my generation is educating the next generation of doctors. Professionals like me inform ourselves, but we just have to specialize, pay for courses out of pocket, find the time and resources, because we want to. There is no institutional aid.”

As more online resources like those of Siebecker and Jacobi pop up, patients are increasingly rejecting diagnoses of the trash and seeking doctors who really want to investigate their digestive issues.

“A lot of people are still being told to eat fiber and learn to live with their IBS,” Jacobi says. “Due to the internet and social media, people just don’t accept that anymore and they are looking for answers.”

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