Hydrogen Sulfide Bacteria – Implications for IBD and Leaky Gut

hydrogen sulfide bacteria in inflammatory bowel disease and leaky gut byron bay herbalist naturopath gut health specialist gut health expert digestive health professional

Hydrogen sulfide producing bacteria could be playing a role in your leaky gut and inflammatory bowel disease. Today we will explore which bacteria, often found in your large bowel, produce hydrogen sulfide and how they may be driving increased intestinal permeability (aka leaky gut) and inflammatory bowel disease. 

What Is Hydrogen Sulfide and Why is it a problem

There are a range of hydrogen sulfide producing bacteria commonly found in your gastrointestinal microbiome. The problem emerges when, as with most bacterial overgrowths, these select bugs have been given a chance to grow and exceed a ‘healthy’ level. 

First of hydrogen sulfide is present in low – think non-toxic levels – in the brain, heart, vasculature system, GI tract and even in the urinary tract. When levels exceed a certain threshold (increased by these hydrogen sulfide producing bacteria) a number of things happen. 

  1. Animal studies have shown intestinal ulceration (think IBD!)
  2. Butyrate oxidation is shut down – This is the main fuel source for cells that line the large bowel (colonocytes). I have written about butyrate sooo many times before but it really deserves its own article – coming shortly!

So here we have an ulcer causing compound that also inhibits the main energy source for the large intestine (1). 

When hydrogen sulfide reaches a certain level it can have widespread implications. It is toxic to different organs in the body, can damage your DNA and stimulate the inflammatory process which is seen in many autoimmune diseases. This isn’t to say that hydrogen sulfide doesn’t have a positive role to play in the body. Only that excessive levels pose serious problems (2).

Below we can see that hydrogen sulfide is produced in the transsulfuration pathway (ie not by bacteria in our gut) and has beneficial roles to play in our physiology.

hydrogen sulfide producing bacteria  byron herbalist gut health expert
Image taken from: Hydrogen Sulfide in Physiology and Diseases of the Digestive Tract

Which bugs produce hydrogen sulfide?

So let’s get down to brass tax. 

Which bugs in my gut produce hydrogen sulfide? 

The list includes a number of bugs that we have covered before. Almost every one of them is considered an issue when allowed to overgrow (I like to think of these as bacterial overgrowths). Some are even problematic when present in the smallest numbers (I consider these bacterial infections). 

Major players in hydrogen sulfide production include Desulfovibrio and Bilophila species. Others include 

A full list along with the sulfur substrates has been included below just to be thorough. 

hydrogen sulfide producing bacteria  byron herbalist gut health expert australia
Image taken from: Microbial pathways in colonic sulfur metabolism and links with health and disease

But back to the two major players in hydrogen sulfide. 

Desulfovibrio and Bilophila receive almost no attention, even in the functional medicine community. I think that this is due to the fact that it isn’t screened for in most of the advanced functional gut testing options. Even the GI MAP, considered by many to be the rolls royce of stool testing doesn’t screen for these two bugs! 

While this isn’t the place to do a deep dive into the complicated details of these two bugs it is worth noting that they can and do grow to alarming numbers in people’s gut microbiome and contribute to a range of gut issues that we will be covering shorly. 

But first, how to test for these bugs. 

Testing for hydrogen sulfide producing bacteria

The new stool tests on the block are all DNA based. And thank goodness for that! Many of the bacteria that live in our large intestine are obligate anaerobes, meaning that they can’t live in the presence of oxygen. Old technology, seen in a comprehensive digestive stool analysis, or CDSAs, won’t be able to screen for many of the microbes in our gut. 

New DNA based technology including the 16 S rRNA technology, can screen for and report back on the presence of bacteria that can’t be found using culture and microscopy technology. Our stool testing is getting so darn advanced that we are finding bacteria that have never been found before! Exciting times.

The number one stool test for screening for hydrogen sulfide producers, listed above, is the Ubiome explorer. You will want to venture into the advanced section of the report and look for the two main hydrogen sulfide producing bacteria (again they are mainly represented by the genera Desulfovibrio and Bilophila. 

testing your gut microbiome for hydrogen sulfide producers
Image taken from: Ubiome

Implications in Leaky Gut and Inflammatory Bowel Disease

A very interesting and comprehensive review, published in CellPress covered the details of hydrogen sulfide in the progression of leaky gut and inflammatory bowel disease. I found it so interesting and relevant that I thought it would be worth sharing with you folks. 

For a deeper dive you can have a read of it yourself – Sulfide as a Mucus Barrier-Breaker in Inflammatory Bowel Disease?

For the cliffnotes read on. 

Intestinal permeability aka leaky gut and inflammatory bowel disease

First off it is worth covering what a healthy functioning gut wall looks like and what happens when it is compromised. For more information on leaky gut head over here and read to your heart’s content!  

Below we see a diagram of a healthy functioning gut wall (this is the large bowel). Here we can see the two layers of gel-like layers made up from a glycoprotein called mucin. The top layer in the image is where the bacteria that reside in our large bowel like to live. I think of this mucus layer as high density living for bacteria. Almost like highrises specifically designed for them. 

The second layer in the image seen in the ‘tight MUC2’ section is sterile and bacteria are unable to take up residence. This is a healthy gut wall. The epithelial cells seen on the left of the image are protected from the contents of the gut. Happy cells.

hydrogen sulfide producing bacteria  byron herbalist gut health expert
Image taken from: Sulfide as a Mucus Barrier-Breaker in Inflammatory Bowel Disease?

When the protective layer of the gut breaks down issues arise

The same review paper covered some interesting new thoughts on how excessive hydrogen sulfide, produced by bacterial overgrowths and infections could drive leaky gut and even inflammatory bowel disease states.

We have another great image (below) to help describe this process. 

Basically the thinking goes that hydrogen sulfide can break down the mucus barrier in the intestines. This allows the contents of your gut – think bacteria and food particles – to directly contact the cells that line your gut which further damages the gut wall and stimulates the immune system to respond. 

hydrogen sulfide producing bacteria  byron herbalist gut health expert intestinal permeability leaky gut
Image taken from: Sulfide as a Mucus Barrier-Breaker in Inflammatory Bowel Disease?

This thinking is so revolutionary and progressive that the authors commented on how reducing hydrogen sulfide producing bacteria may improve IBD. 

Based on the existing literature that IBD is associated with impaired mucus barrier function, and with high concentrations of sulfide-producing bacteria and sulfide itself in the gut of both human and animal IBD models, we argue that this novel mechanism of sulfide-mediated mucus barrier-breakage could contribute to the pathogenesis of IBD. Lowering sulfide concentrations in the gut lumen is therefore an exciting new therapeutic target for IBD. 

Sulfide as a Mucus Barrier-Breaker in Inflammatory Bowel Disease?

Focusing on Healing and Reducing

In the past we have focused on dysbiosis, or an imbalanced gut flora, marking inflammatory bowel disease. Here I commented on the decrease of major beneficial bacteria such as Faecalibacterium prausnitzii a superstar of the gut and increases in less friendly members from the Bacteroidetes phylum. Even pathobionts such as Klebsiella, Escherichia coli and Shigella have been observed in IBD patients. 

But we didn’t really know if this was the results from having inflammatory bowel disease or if it was a main driver or even the cause of IBD. Here we can see a microbiome imbalance characterised by hydrogen sulfide producing bacteria driving the body towards states of inflammation and immune dysregulation by damaging the gut wall. 

Sounds a heck of a lot like IBD doesn’t it?  

Most of the treatments that help to resolve inflammatory bowel disease focus on healing and sealing the gut wall. If, by chance, you are suffering from one form of IBD or another it may be worth looking into the possibility of dysbiosis, characterised by a bloom in Desulfovibrio and Bilophila species as one of the drivers of leaky gut and inflammatory bowel disease. 

Now over to you.

Do you have any experiences with leaky gut, inflammatory bowel disease or an imbalanced gut biome? Leave a comment below and share your thoughts.

References and Resources

  1. Toxicity of hydrogen sulfide toward sulfate-reducing bacteria Desulfovibrio piger Vib-7
  2. Microbial pathways in colonic sulfur metabolism and links with health and disease
  3. Hydrogen Sulfide in Physiology and Diseases of the Digestive Tract
  4. Microbial pathways in colonic sulfur metabolism and links with health and disease
  5. Ubiome explorer
  6. Sulfide as a Mucus Barrier-Breaker in Inflammatory Bowel Disease?

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  1. Todd, I’m a dietitian/nutritionist in the US. Just got my BiomeFx results with imbalance of bilophila wadsworthia. Would you be able to discuss my case with me? I understand you can’t work with patients outside of Australia. Would you discuss my case with my colleague, Anne, who is helping me figure out a protocol? as a consultant?

  2. Hey Todd,
    an utterly enlightening article!!!

    Is there any natural way to reduce hydrogen sulfide or Desulfovibrio spp. in the gut?


    1. Hi Simone, thanks for your comment. A few strategies really help including targeted prebiotics, reducing high sulphur foods and herbal medicine. I have found uva ursi, juniper, clove, pomegranate husk, thyme and oregano leaf in tincture form to work well. Even polyphenol rich foods and supplements can help. Quercetin has some evidence here.

      Hope that helps!


      1. Hi Todd,

        Which prebiotics would you recommend? From my research GOS based (Bimuno) and potentially PHGG seem to be good choices, are there any others?

  3. Do not overlook the role of sugar in the gut that activates the sulphuric gas. Eating eggs or chicken combined with sugar induced by way of a beverage or desert will produce that gas.

  4. Hi Todd,
    Is agave inulin the targeted prebiotic you were referring to? If not, could you please suggest which prebiotics.

    1. Hi Dan, thanks for the comment. I know Dr Nigh’s work well and don’t believe he considers H2S ‘beneficial’. From my understanding of his view point it is an adaptive role to provide sulphate (aka sulfate) when there are issues or a breakdown in the essential process of sulphur metabolism. If it is adaptive (maybe beneficial compared to the alternative of NO sulphate) it still results in serious symptoms, damage to the gut and dysregulated biochemistry. Hope that helps!

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