A Deep Dive on Hydrogen Sulfide SIBO: Symptoms, Testing and Treatment

A Deep Dive on Hydrogen Sulfide SIBO: Symptoms, Testing and Treatment

Adapted from episode 114 of The Perfect Stool podcast and edited for readability.

I’ve done multiple other podcasts on SIBO and IBS, so do see episode 36: IBS Treatment: Addressing an Irritable Bowel Naturally and Episode 83: Recurrent SIBO: Symptoms, Causes, Testing and Treatment for an in-depth treatment of all types of SIBO and IBS, but today, I’m going to focus on hydrogen sulfide SIBO (H2S SIBO).

You know how when you learn a new word, all of a sudden you hear it being used all the time? That’s kind of going on right now with me and hydrogen sulfide SIBO. It kind of feels like everyone I’ve seen lately has suspected or diagnosed hydrogen sulfide SIBO. And it’s funny because before now, it wasn’t that common in my experience.

But I’m starting to recognize the type, and if I had to say one thing that tells me that someone might have hydrogen sulfide SIBO, other than a positive breath test or a stool test showing elevated levels of hydrogen sulfide producers or what are called sulfate reducing bacteria, it’s how miserable they are. From a painful, gurgling gut, known as increased visceral sensitivity, to bloating and distension, to excessive burping, to urinary urgency, a burning bladder or interstitial cystitis, to systemic inflammation, rampant food intolerances and often histamine reactions, my hydrogen sulfide clients are just some of the worst suffering. Other symptoms you might see include weight loss, post-prandial hypotension, meaning low blood pressure after meals, weight loss, an elevated heart rate, exercise intolerance, brain fog or insomnia.

Hydrogen sulfide overgrowth is also associated with ulcerative colitis, Crohn’s Disease, colorectal cancer and Parkinson’s Disease, so definitely not something you want to let fester.

And what I’m finding, surprisingly, is that some of my toughest cases of what I though was an overgrowth of methanogens, is in fact an overgrowth of hydrogen sulfide alone or in combination with methanogens. This is because while the overwhelmingly common presentation of hydrogen sulfide is diarrhea or loose stool, it can also present with constipation if there’s an overgrowth in the large intestine or if you have a simultaneous overgrowth of methanogens, which pretty much always causes constipation. The classic example of this is someone with a mixed type IBS where constipation is the usual presentation, but then occasionally there will be bouts of attacks where they have diarrhea and often all-over body pain or extreme abdominal pain, often requiring a trip to the emergency room.

And what a lot of these clients have had in common, if they have constipation, is that they have slowly but surely stopped eating everything besides meat or meat and a limited number of vegetables and maybe a very limited quantity of rice. And they often have histamine intolerance or signs of sulfur intolerance, like the inability to stand cruciferous vegetables or alliums, like onions, garlic, shallots, chives and leaks, which have sulfur. A few have noticed they don’t tolerate red meat, which is particularly high in sulfur. Ironically, all of this may actually stem from a deficit of sulfur, which is a new theory I’m testing out, so I’ll get back to you on that, but this is theorized because of the impact of glyphosate on food, which impairs a pathway in gut microbes called the shikimate pathway. This pathway produces the very important amino acids l-tryptophan, our serotonin precursor, and l-phenylalanine and l-tyrosine, our dopamine precursors, as well as other nutrients. And it’s been shown that glyphosate also impedes sulfur production by causing a deficiency in molybdenum, a cofactor for the enzyme sulfite oxidase, which produces sulfate. Then if you have homozygous copies of the CBS (cystathionine beta-synthase) enzyme, which drives the recycling of sulfur-containing compounds, you may have too much unusable sulfur in your body, which can lead to sensitivities, while simultaneously having a deficiency.

But suffice it to say that hydrogen sulfide is very important in the human body, playing roles in inflammatory, neuromodulatory, immune, endocrine, vascular and respiratory actions. However, at high levels it becomes toxic to cells, inhibiting cytochrome oxidase, a hemeprotein which an important enzyme in the electron transport chain in our mitochondria, which is the way we produce energy in the cells. It also damages the intestinal mucosa and inhibits the oxidation or use of butyrate to feed the colonocytes or cells lining the colon. So upregulating hydrogen sulfide production in the gut may be a compensatory mechanism, but I’ll have to get back to you on my experiments with that.

Which bacteria produce hydrogen sulfide?

So lots of common genuses of gut bacteria produce hydrogen sulfide it turns out, including Escherichia as in E coli, which is not just the pathogenic E coli you’ve heard of, but also includes many commensal species, klebsiella, which is known as the big histamine producer, proteus species and Citrobacter freundii (but not all citrobacters), all of which are part of the family Enterobacteriaceae, some of which are hydrogen sulfide producers. Also the genuses streptococcus and staphylococcus, which I see elevated on virtually every GI Map I see, pseudomonas, H pylori, salmonella, some Clostridium, and Yersinia Enterocolitica. But the two that have been most highlighted as potentially overgrown and relevant to the hydrogen sulfide SIBO picture are Desulfovibrio species and Bilophila wadsworthia.

The interesting thing is that hydrogen sulfide producers come from a number of different phyla, including Deltaproteobacteria, Proteobacteria, Pseudomonadota, Thermodesulfobacteriota, Fusobacteriota and one genus from the phylum Euryarchaeota called Archaeoglubus. And while most are gram negative, one genus, Desulfotomaculum is gram positive and is a spore former. But the majority of the sulfate reducing bacteria are from the genus Desulfovibrio, around 66%, hence why you see those species listed separately on the new version of the GI Map under the heading Commensal Overgrowth Microbes, right above Methanobacteriaceae, the methanogens responsible for intestinal methanogen overgrowth (IMO). And then Bilophila Wadsworthia is in the class Desulfovibrionia and the order Desulfovibrionales but a different genus. And can I just say, bacteria nomenclature is really confusing, even for me? And then finally, Fusobacteria, which is from the phylum Fusobacteriota and the family Fusobacteriaceae, is another one that’s well known to be a problematic one in hydrogen sulfide SIBO, including Fusobacterium nucleatum, known to be responsible for periodontal disease and all sort of other mischief.

What do hydrogen sulfide producers eat?

So the next thing you might want to know about H2S producers is that most of them use hydrogen (H2) as a fuel source, through a process called oxidation. The hydrogen is coming from other gut bacteria that produce hydrogen, which you will certainly be familiar with as the more common type of SIBO. And while hydrogen gas is odorless, hydrogen sulfide gas is smelly like rotten eggs. But again, one of the difficulties in recognizing hydrogen sulfide overgrowth is that many people with it will not say they have gas, smelly gas, or gas that smells like rotten eggs. Or they’ll only occasionally have gas like that, like after they’ve had a meal heavy in animal fat.

But other sulfate reducers use different fuel sources or multiple fuel sources. So for example, Bilophila wadsworthia metabolizes the amino acid taurine. Fusobacterium, Desulfovibrio, E coli and Klebsiella metabolize the amino acids cysteine and methionine. Which makes finding food to eat much more complicated (e.g., protein), but I’ll get to that in a minute.

The other thing you might want to know is that methanogens also use hydrogen as a fuel source. So although you may be negative in a breath test for hydrogen, if you have methanogens and/or hydrogen sulfide producers overgrown, if you kill them off, you may end up with a hydrogen overgrowth. So don’t think that it’s likely to be a one and done program to get rid of these pathogens; sometimes it requires several rounds of treatment with testing in between to see where you are.

How do you test for Hydrogen Sulfide SIBO?

So there is only one breath test out there that tests for all three possible gases in SIBO/IMO, including hydrogen sulfide, and it’s called the triosmart test or order from my Rupa Health Lab Shop*. But stool tests, like the GI Map or GI Effects, can also point to the presence of H2S SIBO in conjunction with symptoms, when you see elevated bacterial markers for H2S producers. You can find all these tests in my Rupa Health Lab Shop*. Although I have been partial to the GI Map in working with clients, I’m beginning to think that the triosmart might make more sense for clients who are constipated, both because you can differentiate between the rarer H2S overgrowth or find out if it’s present alongside IMO, and because then you can track the level of methanogens and determine exactly how bad the overgrowth of methanogens is and have some sense of how long a treatment protocol someone might need. With the GI Map, you’re just seeing stool levels, which isn’t necessarily indicative of small intestine levels. But if you happen to have taken a SIBO breath test that only included hydrogen and methane, the sign that you might have a hydrogen sulfide issue is that you have a flat line or no growth on either of those gases.

I’ve also heard that you can use sulfite urine testing strips* to test for the presence of free sulfites, which may help you diagnose H2S SIBO, but I don’t know the details of how to use the strips in this way.

How do you treat hydrogen sulfide SIBO?

So the bad news for those of you who are on a paleo or carnivore type diet is that the diet for hydrogen sulfide SIBO is actually a plant-based diet. To start with, you want to reduce your animal fat completely, and ideally your animal protein as well, other than fermented dairy, which seems to be helpful in reducing levels of Bilophila wadsworthia, per two studies, one on probiotic yogurt consumption and the other on consumption of a fermented milk product. There may also be benefits for yogurt and kefir consumption in the reduction of Fusobacteria, as an in vitro study found they inhibited its growth. But no animal foods ideally for 3-4 weeks, then you can start reintroducing those foods one by one, starting with the lowest fat types.

But otherwise, you’ll want to decrease fat entirely for 2-3 weeks, definitely avoiding butter and tallow and lard and fatty cuts of meat. Coconut oil and coconut milk in moderation are okay after your initial low fat period. And small amounts of olive oil or omega 3’s are the best choice for fat throughout. MCT oil may also be okay in that initial period and after as it doesn’t require bile for absorption. You also want to avoid simple sugars or high fructose and focus on whole foods with lots of fiber. And then avoid animal protein as much as possible. So basically, you’ll have to incorporate sources of protein that are not animal based, but not including soybeans or quinoa if you have overgrowths of Fusobacterium, Desulfovibrio, E. coli or Klebsiella, as those two foods are high in cysteine. You’ll want to sustain this diet until such time as you are feeling better.

And if the sulfur-containing vegetables like garlic, leeks, onions, scallions, and shallots and cruciferous vegetables bother you, you should limit those as well.

Now if you are one of the unlucky ones who has both a hydrogen sulfide overgrowth and a methane overgrowth and a high level of constipation, you may be asking, what can I eat, especially if that coincides with histamine issues and food intolerances. In those circumstances, I tend to recommend a diet that’s more in between, with a limited quantity of low-fat sources of animal protein like skinless chicken breasts, white fish and shrimp, with low-fat, fermented dairy, nuts, seeds, and any high fiber carbohydrate foods you don’t react to, like lentils, chick peas or beans, starting with small quantities and working your way up, as well as fruits and veggies you can tolerate. Another option of course is doing an elemental diet, which consists of just a liquid diet for 2-3 weeks, which mostly likely you’d want to combine with antimicrobial supplements in order to help it along. I did a podcast on elemental diets, which is episode 100, called Give Your Gut a Break.

This may seem like a scary idea if you have had trouble keeping on weight, but in fact, my guests from that episode, Debbie and Roy Steinbock, maintained that people maintain or gain weight if they have had trouble putting on weight while on the diet. But people wanting to lose weight simultaneously lost weight. So it’s good for any weight circumstances. Or you may just use the elemental diet “shakes” as a supplement to the food you’re eating in order to make sure you’re not losing weight, or to replace 1-2 meals a day. You can find the Physicians Elemental Diet* powder in my Fullscript Dispensary.

What supplements to avoid with hydrogen sulfide SIBO?

So as you’re decreasing sulfur in your diet, you’re also going to want to avoid supplements with sulfur or bile. This includes ox bile, bitters, bile stimulating herbs, carrageenan and additives with sulfur, glucosamine and chondroitin sulfate. You should avoid protein powders with high levels of sulfur amino acids like taurine, cysteine and methionine, although collagen is okay.  And then of course avoid NAC (n-acetyl cysteine), glutathione and anything with a -thiol or sulfur group, including alpha lipoic acid. Thiamin or B1 and Biotin also have sulfur, so avoiding high doses of those might be a good idea. Also, certain probiotics are known to produce hydrogen sulfide, so best to avoid those, including Lactobacillus reuteri BR11, Lactobacillus delbeueckii ATC4797 and possibly Bacillus subtilis. There are a couple of others that produce H2S, L plantarum 299v and L rhamnosus GG, but I’ve heard recommendations and studies in which foods or supplements with those strains were helpful in H2S SIBO, so the jury may be out on that.

What supplements are helpful for H2S SIBO?

So what is helpful to take for H2S SIBO? First, there are several herbs that are helpful, including gymnostemma, codonopsis and Korean ginseng, which is panax ginseng*. Then minerals may be deficient that are necessary for repairing bodily processes that aren’t working properly, in particular molybdenum*, 50-150 mcg per dose but no more than 500 mcg/day, or a multi-mineral supplement. I like the Jigsaw Essential Blend Multimineral* as it has zinc, copper, selenium and molybdenum in it at good doses, all of which are recommended for H2S SIBO. Hydroxocobalamin*, a form of B12, is also recommended, as opposed to methylcobalamin, a form I recommend to most clients because of the prevalence of MTHFR SNPs. Then beyond that, butyrate is important (although go easy on it if there’s constipation, only taking one 300-500 mg pill every 3 days if you’re constipated to start). If you’re not constipated, you could use my Tributryin-Max, 1-3 daily, decreasing if you get constipated, or any other tributyrin or CoreBiome based product, although you’ll need more of a lower-dosed butyrate supplement.

Then the prebiotic FOS* is also helpful, 2 grams a day with meals if you don’t react to that. Be careful not to choose one with inulin though as many people with SIBO are reactive to that. And finally, something I’m recommending to most people these days, serum bovine immunoglobulins*, which help bind to and remove gut pathogens without impacting commensal bacteria. The dose that’s been studied is 5 grams a day, which is recommend in two doses of 2.5 grams on an empty stomach, usually first thing in the morning and last thing before bed.

And let me not fail to mention good old Pepto Bismol* or a generic equivalent* or a supplement containing bismuth. MDs will use 500 mg of bismuth three to four times a day with H2S SIBO in addition to Rifaximin, the antibiotic for SIBO. There’s only one product in Fullscript with bismuth that isn’t full of dyes and additives you might want to avoid, which is called Biofilm Phase-2 Advanced*, and has 200 mg of bismuth in two of them, along with some other stuff though that may not be great in H2S SIBO, like alpha lipoic acid. I’m just beginning to experiment with this product, so I’ll let you know how it works out in a subsequent podcast.

And also, I shouldn’t fail to mention that exercise and stress management are also important in managing H2S SIBO.

Well I hope this helps some of you get to the bottom of your gut health or all over body suffering and find a way out.

If you are struggling with bloating, gas, burping, nausea, constipation, diarrhea, soft stool, acid reflux, IBS, IBD, SIBO, candida overgrowth, fatigue or migraines and want to get to the bottom of it, that’s what I help my clients with. You’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my 3- and 5- appointment health coaching programs in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me. 

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