The Three Types of SIBO: Hydrogen, Methane and Hydrogen Sulphide

Written by Karly Raven, BHSc - Naturopath and SIBO Specialist, Nourished Gut Clinic
Last updated: August 2026

Most people are told they have SIBO. Very few are told which of the three types of SIBO they actually have.

That distinction is not academic. It is the single most useful piece of information on your breath test, because the three subtypes are driven by different organisms, produce different symptoms, and respond to different treatment. Treating methane the way you treat hydrogen is one of the most common reasons a course of treatment fails.

As a naturopath specialising in complex gut conditions at the Nourished Gut Clinic, I have spent over six years working with people who have been through two or three rounds of SIBO treatment already. In a large number of those cases, the protocol was reasonable. It was simply aimed at the wrong gas.

I set out the full evidence base for the three types of SIBO in a literature review published in the ACNEM Journal in June 2026: Hydrogen, Methane and Hydrogen Sulfide SIBO: A Literature Review of Pathophysiology, Diagnostic Approaches and Phenotype-Specific Treatment Strategies (Vol 45, No 2). This article is the plain English version of that work.

Jump to a section

1. What SIBO actually is
2. Type 1: Hydrogen dominant SIBO
3. Type 2: Methane, now called IMO
4. Type 3: Hydrogen sulphide, or ISO
5. Can you have more than one type of SIBO?
6. Why the types of SIBO change your treatment
7. Frequently Asked Questions

What SIBO actually is

The usual explanation is that bacteria from the colon migrate upward into the small intestine. That is part of the story, and it is the part most articles stop at. It is not the whole picture, and the missing half changes how you treat it.

Your small intestine is not sterile. It has its own resident microbial community, smaller and less diverse than the colon's, adapted to a fast moving environment with more oxygen and more bile. SIBO is a disruption of that community, not simply an invasion from below.

Two things go wrong at once. The total microbial load rises beyond what the small intestine is built to handle, and the composition shifts, with a particular group of organisms expanding while overall diversity falls away.

Leite and colleagues, publishing in PLOS ONE in 2020, sampled duodenal fluid directly rather than inferring what was happening from a breath test. People with SIBO showed a 4.31-fold higher relative abundance of Proteobacteria, driven largely by Enterobacteriaceae such as Klebsiella and Escherichia, which were increased 7.35-fold. Microbial diversity fell as those organisms expanded.

That matters clinically for two reasons.

• These are residents, not invaders. Klebsiella and Escherichia live in the small intestine ordinarily, in small numbers. In SIBO they have been allowed to overgrow. You are dealing with an ecosystem that has lost its balance, not a contamination event.
• The diversity loss is a finding in its own right. You are not only dealing with too many of the wrong organisms. You are dealing with the loss of a functioning community, and that has to be rebuilt rather than simply cleared.

This is the single biggest reason I treat eradication as roughly a third of the job. Killing addresses the overgrowth. It does nothing for the diversity that went with it.

Whatever their origin, those organisms ferment carbohydrate before you have finished absorbing it. Fermentation produces gas. The gas produces the bloating, distension, pain and altered bowel habit that bring most people to a clinic in the first place.

This is closely tied to IBS. A 2026 systematic review and meta-analysis in Frontiers in Microbiology, pooling 25 studies, found people with IBS were significantly more likely to have SIBO than healthy controls, with a pooled odds ratio of 5.71 (95% CI 3.45 to 9.45). Given that IBS affects around one in five people according to healthdirect Australia, that overlap matters.

The type of gas produced tells us which organisms are involved. That is the whole basis of subtyping.

Type 1: Hydrogen dominant SIBO

Hydrogen is the most common presentation, accounting for roughly 60% of the cases I see in clinic.

It is produced by fermenting bacteria, typically Proteobacteria such as E. coli and Klebsiella species, sitting in the small intestine and feeding on carbohydrate.

What it tends to look like:

• Bloating that builds through the day, often worst by evening
• Looser stools or diarrhoea, or a mixed pattern
• Reacting to onion, garlic, legumes, wheat and stone fruit
• Symptoms that arrive within an hour or two of eating

Hydrogen SIBO usually responds well to a well constructed antimicrobial round, provided the reason it developed is also addressed. The gas is the easy part. The terrain that allowed it is the work.

Type 2: Methane, now called IMO

Methane is the second most common picture, at roughly 30% of cases.

The terminology changed for a good reason. The ACG Clinical Guideline on SIBO (Pimentel et al., American Journal of Gastroenterology, 2020) proposed the term intestinal methanogen overgrowth, or IMO, because the organism responsible is not a bacterium at all. Methanobrevibacter smithii is an archaeon, a separate domain of life. Calling it bacterial overgrowth was never accurate, and more importantly, it is why antibacterial treatment so often fails to shift it.

Methanogens also are not confined to the small intestine. They can colonise the large bowel as well, which is why the diagnostic threshold applies at any point during the test rather than within a set window.

What it tends to look like:

• Constipation, often long standing and often the dominant complaint
• Bloating that is constant rather than fluctuating
• A feeling of fullness or heaviness that does not resolve overnight
• Poor response to fibre, where more fibre makes things worse rather than better

Methane actively slows gut transit. That creates a loop, because slow transit gives methanogens more time to do what they do. Breaking that loop is a treatment priority, not an afterthought.

Type 3: Hydrogen sulphide, or ISO

Hydrogen sulphide is the newest of the three and the one most often missed, at around 10% of cases. It is sometimes called intestinal sulphide overproduction, or ISO.

For years it was invisible, because standard two gas breath testing measures hydrogen and methane only. A patient could have a genuinely flat test and significant symptoms.

Research published in the American Journal of Gastroenterology in 2022 by Villanueva-Millan and colleagues found that methanogens and hydrogen sulphide producing bacteria map to distinct microbial profiles and distinct IBS subtypes. Clinically, hydrogen sulphide skews toward diarrhoea where methane skews toward constipation.

What it tends to look like:

• Diarrhoea or urgency, sometimes severe
• A sulphurous or rotten egg quality to gas
• Reactions to garlic, onion, eggs, cruciferous vegetables and sometimes protein
• Bladder symptoms, joint aches or a general sense of being unwell alongside the gut symptoms
• A flat breath test that does not match how the person feels

The organisms involved include Desulfovibrio, Bilophila and Fusobacterium. This subtype is more likely to involve biofilm, which is why I start biofilm work in the first round for these cases rather than holding it back.

Hydrogen sulphide is the subtype I gave the most attention to in my ACNEM Journal literature review, because it is where the evidence has moved fastest and where clinical practice is still catching up.

Can you have more than one type of SIBO?

Single subtype cases are the exception in a clinic like mine, because most people arriving have already been treated at least once.

Hydrogen combined with methane is the most frequent mixed picture. When that happens, methane is usually the limiting factor. I treat it as the anchor and build hydrogen coverage around it, because clearing hydrogen while leaving methanogens in place tends to produce a short lived improvement and then a return.

Where hydrogen sulphide sits alongside hydrogen, I lead with the sulphide side, because biofilm disruption is difficult to sequence in later.

Why the types of SIBO change your treatment

Here is the practical consequence, and it is the reason this article exists.

• Hydrogen responds to a combination antimicrobial approach aimed at fermenting bacteria.
• IMO requires agents that work on archaea. Standard antibacterials do not reliably touch methanogens, which is why so many methane dominant patients have a history of treatment that did not seem to do anything.
• ISO requires broad coverage plus biofilm disruption, and the sulphur load in both diet and supplements has to be managed carefully.

Dietary staging shifts too. Fermentable fibres such as inulin and FOS, which are genuinely useful in some presentations, feed methane production and are not appropriate during active IMO.

At the Nourished Gut Clinic, subtype determines the cornerstone of the protocol, the length of the round, and the order we do things in. Everything else is built around that decision. We work this way with clients right across Australia by telehealth, which you can read about on our online SIBO naturopath page.

Once you know which subtype you are dealing with, the next question is how confident you can be in that result. That is what SIBO breath testing covers. From there, SIBO treatment sets out what a complete protocol looks like.

Frequently Asked Questions

Can you have more than one type of SIBO at once?

Yes, and it is common. Hydrogen combined with methane is the mixed picture I see most often. Hydrogen sulphide can sit alongside either. Mixed presentations are not a complication so much as a sequencing problem, because you need to decide which subtype anchors the protocol. In practice, methane usually anchors when it is present, because it is the harder of the two to shift.

Is SIBO just bacteria from the colon moving up into the small intestine?

That is the common explanation and it is only half right. Your small intestine has its own resident microbial community, and SIBO is a disruption of that community rather than purely an invasion from below. Duodenal sampling published in PLOS ONE in 2020 found Proteobacteria such as Klebsiella and Escherichia markedly expanded in people with SIBO, alongside a measurable drop in microbial diversity. These are organisms that belong there in small numbers and have overgrown. That is why rebuilding diversity matters as much as reducing the overgrowth.

Why did my SIBO treatment not work?

The most common reason I see is a mismatch between the treatment and the subtype, particularly methane dominant cases treated with agents aimed at bacteria. The second most common reason is that the overgrowth was treated but the reason it developed was not, so it returned. If you have relapsed more than once, the question worth asking is not which antimicrobial to try next, but what has not been addressed. I have written about this in why does my SIBO keep coming back.

Is methane SIBO worse than hydrogen SIBO?

Not worse, but generally slower to treat. Methanogens are archaea rather than bacteria, they are less susceptible to standard antimicrobials, and the methane itself slows transit, which sustains the overgrowth. IMO usually needs longer rounds and sustained attention to motility. Constipation dominant patients often need a longer runway before they see meaningful change, and knowing that upfront makes the process much easier to stay with.

How do I find out which type of SIBO I have?

A breath test measuring hydrogen and methane will identify the first two subtypes. Hydrogen sulphide cannot currently be measured by breath testing in Australia, and the diagnostic criteria for it have not been validated. If your symptoms strongly suggest sulphide, a flat two gas test does not rule it out. At the Nourished Gut Clinic we look at the whole curve rather than a single number, alongside your history and bowel pattern, and we recognise and treat the sulphide pattern clinically where it fits.

Ready to find out which type of SIBO you have?

If you have been treated for SIBO without lasting change, the subtype question is worth revisiting before you try another protocol. Knowing which gas you are dealing with often explains a treatment history that has felt inexplicable.

If you want a practical starting point while you think about it, the free 3-Day Bloat Fix is a short plan you can begin this week. It will not resolve an overgrowth, and I will not pretend it can, but it will show you how quickly digestion responds to the right conditions.

If you want to see how we work with SIBO specifically, our online SIBO naturopath page walks through testing, treatment and what working together by telehealth actually looks like.

If you are ready for a proper clinical answer, the Nourished Gut Program is our six month process for rebuilding digestive function. It is application only and we take five new clients each month. You can also book a free Digestive Strategy Session to talk it through first.

Karly Raven, BHSc is a naturopath, microbiome restoration specialist, and SIBO expert. She is the founder of the Nourished Gut Clinic and creator of the Feed Forward methodology. Karly works with people with IBS, SIBO, IBD and chronic gut conditions, and mentors health practitioners through karlyraven.com.

This blog is for educational purposes only and does not constitute medical advice. Please consult a qualified health practitioner before making changes to your treatment plan.