SIBO

Too much bacteria, in the wrong place

SIBO, small intestinal bacterial overgrowth, happens when bacteria that normally live further down the gut grow in the small intestine instead, where there should be relatively few. It's diagnosed with a breath test that measures gases, hydrogen and methane, produced when these bacteria ferment sugar. In a study of 443 patients tested for symptoms like bloating, 53 had a positive result.

Source: PubMed, Preferential usage of rifaximin for the treatment of hydrogen-positive small intestinal bacterial overgrowth

A targeted antibiotic clears it, most of the time

The main treatment is rifaximin, an antibiotic that stays mostly in the gut rather than being absorbed into the bloodstream. In that same study, response rates varied by gas type: 47.4% of patients with hydrogen-positive SIBO responded to treatment, compared with 80% of those positive for both hydrogen and methane. A separate study of 19 patients found rifaximin normalised breath test results in the majority of cases within two weeks of finishing treatment.

Source: Rifaximin for small intestinal bacterial overgrowth in patients without irritable bowel syndrome

SIBO changes body chemistry beyond digestion

Researchers studying SIBO patients found that those with diarrhoea-type SIBO had higher blood levels of serotonin and higher levels of its breakdown product in urine, both linked to how much hydrogen the breath test detected. This shows SIBO doesn't just cause digestive symptoms, it measurably shifts body chemistry connected to gut-brain signalling too. The type of gas matters too. A different organism, Methanobrevibacter smithii, is responsible for a positive methane breath test rather than hydrogen, and its overgrowth has been specifically linked to the constipation-predominant form of IBS, a distinct pattern from the diarrhoea-type SIBO described above.

Source: Serotonin Pathway of Tryptophan Metabolism in Small Intestinal Bacterial Overgrowth

It usually comes down to two specific bacteria

For a long time, doctors assumed SIBO happened because bacteria from the colon simply moved backward into the small intestine. Newer sequencing studies have found something more specific. In a study using detailed gene sequencing on 38 people, just two types of bacteria, Escherichia coli and Klebsiella, made up 40.24% of all the bacteria found in the overgrown small intestine. These aren't colon bacteria that wandered up. They are specific species that multiply in place.

A separate study of 224 patients measured inflammation directly in fluid taken from the small intestine. People with SIBO were more than twice as likely to have raised levels of an inflammatory marker called IL-1β. Klebsiella specifically was linked to two other inflammatory markers, IL-6 and TNF-α, giving researchers a direct line from a named bacterium to measurable inflammation in the gut.

Source: Defining Small Intestinal Bacterial Overgrowth by Culture and High Throughput Sequencing

Source: Small Intestine Bacterial Overgrowth Can Form an Indigenous Proinflammatory Environment in the Duodenum

What this means for you

Persistent bloating, discomfort, or altered bowel habits are worth discussing with a doctor, since a breath test can confirm or rule out SIBO specifically, and can also show whether the hydrogen or methane form is present, since they sometimes need different antibiotic combinations. Treatment usually needs a prescribed antibiotic course, not something to self-manage with diet alone. But rebuilding afterwards matters more than people realise. Antibiotics don't just remove the harmful overgrowth, broad-spectrum courses wipe out much of the wider gut microbiome at the same time, both helpful and unhelpful bacteria together. A study of healthy adults given a short course of broad-spectrum antibiotics found their gut bacteria mostly recovered within about six weeks, but nine species present in everyone before treatment were still missing in most people six months later. A separate study of almost 15,000 adults found people who had taken antibiotics at any point in the past eight years still carried fewer bacterial species than people who hadn't.

Source: Nature Microbiology, Recovery of gut microbiota of healthy adults following antibiotic exposure

Source: Scientific American, A single course of antibiotics may reshape the gut microbiome for years

Rebuilding isn't as simple as taking a probiotic supplement, either. One well-known study found that people who took a standard probiotic after antibiotics had their own natural gut bacteria return more slowly than people who did nothing at all, a genuine reminder that more support isn't always better support. Following a low FODMAP diet once antibiotic treatment is finished has been shown to help instead. In one survey of patients who had completed antibiotics before starting the diet, they were about seven times more likely to respond well to it than those who hadn't had antibiotics first. Recurrence is common, at least half of people see SIBO return, which is part of why rebuilding with a varied, plant-rich diet afterwards matters as much as the initial treatment.

Source: Effectiveness of the low FODMAP diet in patients with IBS and SIBO

That's the same idea behind GutLab, everyday gut health starts with regularly feeding the microbiome a broad range of plant-rich ingredients.