The intestinal microbiota and its role in health and disease processes have been the subject of several studies. Changes in the intestinal microbiota occur due to several factors, such as the use of medication, age, lifestyle and diseases, which can modify intestinal homeostasis and lead to excessive growth of bacteria in the small intestine, triggering a clinical condition called small bowel bacterial overgrowth (SIBO). Individuals with SIBO may present gastrointestinal symptoms ranging from nausea, diarrhea and/or constipation, and flatulence to distension and abdominal pain, resulting from poor absorption of nutrients or changes in intestinal permeability. The gold-standard treatment is based on the use of antibiotics to eradicate bacterial overgrowth. Some studies have evaluated diets in the treatment of SIBO; however, the studies are of low methodological quality, making extrapolation of the results to clinical practice unfeasible.
Small intestinal bacterial overgrowth (SIBO) is defined as a clinical condition caused by excessive numbers of small intestinal bacteria (≥ 103 CFU/mL) that include predominantly gram-negative aerobic and anaerobic species[1]. In the physiological state, there are mechanisms to prevent excessive colonization of bacteria in the small intestine, such as an acidic stomach pH, pancreatic enzymes, the intestinal immune system, small intestine peristalsis, the ileocecal valve and the intestinal barrier itself. The main gastrointestinal symptoms are nausea, diarrhea and/or constipation, flatulence, distension and abdominal pain. The noninvasive diagnostic method most commonly used in clinical practice is the measurement of hydrogen gas and/or methane exhaled in the breath after the ingestion of a fixed amount of a carbohydrate substrate. The indication of colonization by methanogens, which are not bacteria but belong to the Archaea domain, led to the proposal of a new term called intestinal overgrowth of methanogens. In terms of treatment, the use of antibiotics is currently the gold standard for eradicating bacterial overgrowth[1]. Rifaximin has been shown to be effective in the treatment of SIBO, despite the heterogeneity found in the studies as well as the lack of a recommendation regarding the dose and duration of treatment[8]. The antibiotics used are based on whether SIBO is associated with methane production (M-SIBO) or hydrogen production (H-SIBO). M-SIBO is associated with delayed small bowel and colon motility and is produced under anaerobic conditions. The treatment of M-SIBO tends to be easier than that of H-SIBO and is often associated with constipation. H-SIBO is associated with an overgrowth of gram-positive bacteria in the small intestine and usually manifests with diarrheal symptoms[9]. Regarding diet, studies have focused on diets with a reduction in fermentable products, involving an approach with few fibers and no gluten. A recent systematic review included studies that evaluated the use of probiotics, an elemental diet, and herbal therapy for the treatment of SIBO[11]. It was observed that in randomized clinical trials that evaluated the use of probiotics, there was heterogeneity between the strains used and the duration of treatment, and regarding the methodological quality, most studies were of moderate quality. Although it may seem effective, an elemental diet is difficult to follow, and the literature lacks further studies for the clinical applicability of these diets. Dietary strategies for the treatment of SIBO are based on a reduction in the consumption of fermentable products, which involves a diet low in fiber, sugar alcohols and other fermentable sweeteners such as sucralose. However, it is not clear whether the clinical improvement resulting from dietary changes is the result of a modification of the intestinal microbiota or is simply due to a reduction in fermentation and gas production. It is important to highlight that the type and amount of bacteria found in the gastrointestinal tract depend on an individual's diet[12]. Thus, changes in the intestine lead to a significant impairment of nutrient absorption, including that of macronutrients and some vitamins[10]. A recent meta-analysis in which most articles included were from Western countries, with only one Asian study, assessed the association between SIBO and obesity. It was observed that the risk for SIBO was three times higher among individuals with obesity than among individuals without obesity when evaluated only in the Western population[15]. Another meta-analysis with cohort studies evaluated the relationship of a usual diet, intestinal microbiota and intestinal inflammation, comparing patients with intestinal diseases with the general population. Although diets for the treatment of SIBO seem promising, studies are still scarce and of low quality, limiting their clinical applicability. Therefore, it is important to be careful when prescribing restrictive diets, since the most severe cases of SIBO can cause malabsorption syndrome, which can lead to nutritional risk, and a healthy diet rich in vegetables and whole foods seems the best option to obtain a balanced microbiota.
These days it seems like there’s a diet for everything. Advertisements, articles, and stories about various diets have dominated social media, magazines, and every news outlet for decades. This is made even more difficult for those who have been diagnosed with, or suspect they may have, a gastrointestinal condition like SIBO (Small Intestinal Bacterial Overgrowth), IMO (Intestinal Methanogen Overgrowth) or ISO (Intestinal Sulfide Overproduction). The goal of this article is to explore the most common dietary approaches people try when managing microbial overgrowths like SIBO, IMO, and ISO, explain what each one is designed to do, and place them in the larger context of your gut health. As is usually the case when addressing medical conditions, there is no “one size fits all” solution that can be universally applied to all patients in a population. It is vital for you to consult with your healthcare provider(s) to assess your condition, investigate possible causes, and explore which approaches to treatment and management will be most effective for you.
Did you know that some Arctic populations have survived for generations on almost entirely animal-based diets? The carnivore diet seeks to replicate this way of eating, but is it truly sustainable? The carnivore diet is a highly restrictive dietary regimen that eliminates all plant-based foods, relying exclusively on animal products such as meat, fish, eggs, and dairy. The carnivore diet claims to provide several health benefits. Some supporters of the carnivore diet suggest that eliminating plant-based foods may benefit individuals with autoimmune conditions by reducing exposure to potential dietary triggers, such as lectins and oxalates.
The carnivore diet is an extreme elimination diet that removes all plant-based foods and focuses exclusively on animal-based products such as meat, fish, eggs, and some dairy. Although not created for people with SIBO or IBS, it has gained some popularity among people experimenting with ways to reduce bloating, gas, or other gut symptoms. The idea is simple: if fermentable carbohydrates are the main fuel for gut microbes, removing them entirely should reduce fermentation and gas. With only animal proteins and fats on the menu, there’s less fuel left for bacteria or archaea to break down. Some anecdotal reports indicate symptom relief when adopting this approach.
Read also: The Carnivore Diet: An Autoimmune Solution?
Given the limited long-term research, individuals considering this diet should exercise caution and consult healthcare professionals to ensure adequate nutrient intake.
Understanding SIBO
SIBO, or Small Intestinal Bacterial Overgrowth, is a condition where bacteria normally found in the large intestine overgrow in the small intestine. This can lead to a range of uncomfortable symptoms like bloating, gas, diarrhea, constipation, and abdominal pain.
SIBO is bacterial overgrowth in the small intestine. And small intestinal bacterial overgrowth occurs when there’s an abnormal increase in the overall bacterial population in the small intestine. The small intestine should be largely sterile there’s it’s not going to be completely sterile. There are actual bacteria that are in the small intestine. The large intestine, also known as your colon, is where most of your bacteria is. You have trillions and trillions of bacteria in and on your body and the biggest concentration of them are in your colon. So we want lots To have good bacteria, or probiotics or microbes, whatever you want to call them in your large intestine, and when you get SIBO bacteria ends up in the small intestine, where it’s not supposed to be. And these are unwanted types of organisms. So there are three types of SIBO. Most people only know of the two types that are on standard SIBO testing, which are intestinal myth, antigen overgrowth, or methane dominant SIBO, and then hydrogen SIBO, or hydrogen dominant SIBO. Those are the two that if you go to the GI doctor, and they order a SIBO test, most likely you will get those two tested. There’s a new or newer, known type of SIBO, called hydrogen sulfide SIBO.
Risk factors for developing SIBO include taking proton pump inhibitors or opioids, gastric surgery, nerve damage to the small intestine, or a failure of the ileocecal valve.
Left untreated, SIBO can cause symptoms including pain, diarrhea, and malnutrition (due to the loss of the body’s main nutrients). In rare cases, a serious neurological condition called D-lactic acidosis can occur.
Read also: The Carnivore Diet's Impact on Sleep
The Carnivore Diet: A Detailed Overview
The carnivore diet is a highly restrictive eating plan that eliminates all plant-based foods, including fruits, vegetables, grains, legumes, nuts, seeds, and sometimes dairy (depending on how strict you decide to be). It focuses solely on animal-based foods, such as:
- Meat: Beef, pork, lamb, chicken, turkey, and organ meats
- Fish: All types of fish and seafood
- Eggs: Chicken, duck, quail, and other types of eggs
- Animal-Based Products: Butter, ghee, bone broth, gelatin and sometimes milk, yogurt and cheese
Purported Benefits of the Carnivore Diet for SIBO
Proponents argue that this dietary approach can help manage SIBO by:
- Reducing Fermentable Carbohydrates: Many plant-based foods contain fermentable carbohydrates (FODMAPs), which can fuel bacterial growth in the small intestine. By eliminating these foods, the carnivore diet aims to starve the bacteria contributing to SIBO.*Improving Gut Health: The high protein and nutrient density of animal-based foods can support gut health and immune function.
Addressing the Root Cause of SIBO
While the carnivore diet may offer temporary relief from SIBO symptoms by reducing FODMAPs, it does not address the underlying root cause of the condition. SIBO is often caused by a combination of factors, including:
- Reduced Stomach Acid: Low stomach acid can allow bacteria to overgrow in the small intestine. A positive effect of the carnivore diet is that by eating more meat and high protein diet, it can actually dial up the stomach acid production if you do not have other factors that could impede this production for example a lack of minerals and/or an H. Pylori infection.
- Slowed Gastric Emptying: Delayed stomach emptying can also contribute to bacterial overgrowth. Some popular drugs such as Ozempic (or other GLP-1 agonists) can actually cause gastroparesis.
- Gut Motility Issues: Disruptions in gut motility can prevent bacteria from being cleared from the small intestine. Usually, this is due to a dysfunction of the migrating motor complex (MMC).
The Carnivore Diet: A Short-Term Strategy?
The carnivore diet can be a viable option for short-term symptom management of SIBO, especially when combined with other strategies like addressing low stomach acid or improving gut motility. However, long-term adherence to this restrictive diet raises concerns:
- Nutritional Deficiencies: The carnivore diet can lead to deficiencies in essential nutrients found in fruits and vegetables, such as fiber, vitamins, and minerals.
- Gut Microbiome Diversity: A lack of dietary diversity can negatively impact gut microbiome diversity, ultimately hindering overall health. A growing body of research suggests a strong association between dietary diversity and the diversity of bacteria in the gut microbiome. This is logical: different foods provide different types of prebiotics (food for gut bacteria), which in turn support the growth of a wider range of beneficial bacteria.
The Importance of a Diverse Microbiome
A diverse gut microbiome is crucial for all aspects of health (mental, emotional, physical). Think of it as a bustling ecosystem of beneficial bacteria working together to keep you healthy. A diverse microbiome helps train your immune system, improving its ability to fight off harmful pathogens and reducing the risk of allergies and autoimmune diseases. It also aids in digestion, ensuring efficient breakdown of food and absorption of vital nutrients. A diverse microbiome has been linked to better metabolic health, potentially lowering your risk of obesity, type 2 diabetes, and heart disease. Emerging research even suggests a connection between gut microbiome diversity and mental health, including depression and anxiety. In short, a diverse microbiome is essential for a strong immune system, efficient digestion, reduced risk of chronic diseases, and overall resilience.
Read also: Troubleshooting Carnivore Diet Diarrhea
For these reasons, I recommend gradually transitioning out of a full carnivore diet once symptoms are under control. Working with a practitioner can help you determine the right duration for the carnivore diet, ensuring it aligns with your specific health goals and needs.
Reintroducing Foods After Doing the Carnivore Diet
After a period of following the carnivore diet, I recommend a gradual reintroduction of fruits and vegetables to avoid deficiencies and lack of microbiome diversity. This gradual reintroduction should be done under the guidance of a qualified healthcare professional, such as a nutritionist, dietician, or functional medicine practitioner.
Important Considerations Before Starting a Carnivore Diet
The carnivore diet may not be suitable for everyone, and individual responses can vary. The carnivore diet is a highly restrictive approach that may be difficult to maintain long-term. It's essential to consider the potential downsides and whether it aligns with your lifestyle and preferences.
Alternative Dietary Approaches for SIBO
- Low FODMAP Diet: The Low FODMAP diet, developed by researchers at Monash University, is often tried by patients with SIBO, IBS (Irritable Bowel Syndrome), and other related conditions. The idea behind the Low FODMAP diet is straightforward: if you eliminate your intake of FODMAP carbs, you will reduce the amount of fermentation and gas production happening in your intestines, making symptoms more manageable. The Low-FODMAP diet is usually recommended in conjunction with other treatments like antibiotics, and it is not generally intended to be a permanent solution. Long-term restriction of FODMAPs can negatively impact the gut microbiome, limiting its diversity and effectiveness, while also leading to a potential for nutrient deficiencies.
- Low Fermentation Eating (LFE): LFE focuses on reducing fermentable foods while emphasizing consistent meal timing and limiting problematic foods to minimize bacterial overgrowth. LFE reduces fermentable substrates for gut microbes, while also focusing on maximizing healthy spacing between meals. Spacing meals four to five hours apart allows your Migrating Motor Complex (MMC) to more thoroughly and rhythmically sweep bacteria out of the small intestine between meals.
- Elemental Diet: The Elemental Diet isn’t a typical “diet”. Think of it as more of a medical nutrition therapy-a powerful gut reset-which can be especially useful for those with severe or recurrent SIBO, IMO, or ISO. Since it aims to bring your gut back in balance using a heavily nutrition-focused approach, doctors sometimes recommend the Elemental Diet in cases where antibiotics aren’t effective or well-tolerated. With the Elemental Diet, patients consume a liquid-only formula that provides fully broken-down nutrients (such as amino acids, simple carbs, and fats) in forms that are easily absorbed in the gut without requiring fermentation. By depriving bacteria of their food source, the diet essentially starves out your bacterial overgrowth while still providing essential nutrition. Studies show that the elemental diet has a high success rate, with some reports indicating that up to 80% of individuals experience a significant reduction in bacterial overgrowth after following the diet for two to three weeks. However, because it requires strict adherence to a specific liquid diet, it can be challenging for some people due to issues like taste, cost, lifestyle challenges, and calorie restrictions.
- SIBO Biphasic Diet: The SIBO Biphasic Diet is a structured eating plan developed by Dr. Nirala Jacobi, ND, focused specifically on people diagnosed with SIBO. It’s a phased dietary protocol designed to limit foods that are more likely to ferment in the small intestine, such as certain fibers, legumes, and high-FODMAP fruits. The “Biphasic” part of the name refers to the diet being structured into two phases. In the first phase, restricted foods are reduced or eliminated to help minimize bloating, gas, and abdominal discomfort. The phased design is intended to both address the symptoms in the short term and make the diet more sustainable over time. By removing fermentable carbohydrates during phase 1, the diet reduces the fuel needed for bacterial overgrowth. Phase 2 then broadens the Foods to Choose categories by gradually reintroducing foods, with adjustments dependent on individual tolerance and symptom response. Because of the complex nature of the SIBO Biphasic Diet, it is generally not recommended without the supervision and guidance of an appropriate healthcare provider.
- Anti-Inflammatory Diet: An Anti-Inflammatory Diet isn’t a single, rigid plan, but rather a way of eating that emphasizes foods believed to calm inflammation in the body. It sometimes resembles the Mediterranean diet, which highlights fruits, vegetables, olive oil, fish, legumes, and whole grains. Some people also try variations which remove gluten or dairy from their diets as well, since these have also been linked to inflammation and gut distress in some people. The theory here is that reducing chronic inflammation can help soothe the gut environment and improve overall health. While these diets don’t target microbial overgrowth directly, they may decrease gut irritation, improve nutrient intake, and support a broader approach to digestive wellness.
Conventional Treatment for SIBO
Antibiotics are the first line of treatment for SIBO. These medications get rid of the bacteria that’s overgrowing in the small intestine. For some people, successfully treating the bacterial overgrowth does not eliminate digestive symptoms. If your symptoms continue after treating SIBO, you may have another digestive condition that requires treatment or management. For example, lactose intolerance can cause symptoms similar to SIBO, such as bloating, gas, and diarrhea. If a food intolerance is causing digestive symptoms, you may need to make changes to your diet. These changes should be guided by your doctor or a registered dietitian. In other cases, treating SIBO provides temporary relief, but not a long-term solution. In about 44% of cases, SIBO symptoms come back within 9 months after the first treatment. When antibiotics alone do not help, the elemental diet is the only diet proven to treat SIBO. It is a predigested liquid diet prescribed by a doctor.
Hydrogen Sulfide SIBO
There’s a new or newer, known type of SIBO, called hydrogen sulfide SIBO. The only test that you can have for hydrogen sulfide is something called the trios test. And the trio test is only available in the US. The way that testing works for SIBO. Or the way, the mechanism behind like how they’re measuring these gases, is the hydrogen sulfide gas diffuses across membranes in your body, it makes its way to blood vessels, which then makes its way to your lungs, and you breathe it out. So the breath test is measuring the amount of hydrogen sulfide gas that you are off putting and determining if you have this hydrogen sulfide overgrowth. There’s lots of conflicting opinions on like how to actually interpret a positive test. But you have to evaluate based on a baseline test or a baseline number. Because the gas actually could be coming from the colon from the small bowel, it could be coming from the mouth actually could be coming from the stomach from the bladder. There’s tons of it’s not just the small intestine that can have this gas, it can be everywhere, or not everywhere, many, many places. And there’s there’s some practitioners that have different opinions on this. There is a rule of thought or a school of thought that says that if you have a flatlined SIBO test, the standard test, not the trio test. It could be hydrogen sulfide, because essentially hydrogen gas is being produced is being gobbled up and it’s producing hydrogen sulfide.
You cannot diagnose SIBO based on stool testing. However, we do know now that there are specific bacteria that can contribute to SIBO. And specifically hydrogen sulfide SIBO. So the two bacteria that contribute to hydrogen sulfide SIBO are below phyla, and the sulfa, Vibrio, these are on some stool tests, not all stool tests, like for example, I know a lot of practitioners use the GI map. desulfovibrio is now actually on the GI map. Whereas below phyla is not. Biome FX has these markers. That’s the microbiome labs stool test, there’s a stool test called Andre that has it. Gi effects has some of these markers. So depending on what stool tests you do, you can’t diagnose hydrogen sulfide SIBO from it, but there these two bacteria being present does potentially indicate that maybe that could be consistent with the symptoms that you’re having. There are other Proteobacteria that can potentially contribute. But it doesn’t mean again that just because you have these on a stool test, you have hydrogen sulfide SIBO. For example, E coli, certain strains of E. coli, can contribute to hydrogen sulfide, Pseudomonas Klebsiella, Citrobacter, and Proteus are also bacteria that can contribute to hydrogen sulfide.
Hydrogen sulfide gas can be produced in the mouth, the small bowel, the colon. But the two most common areas for this bacteria are the small bowel and the colon. So in the small bowel, that’s where we’re dying. That’s where we’re taking the the trio smart test, and we are diagnosing it with the breath test. And that’s the standard way that you’re going to test for these.
Some of the main signs are bloating, distension, bowel changes. A lot of the research shows constipation, but there are now some research studies that show diarrhea and I know Dr. Pimentel talks about this a bit as well. Some of the other more significant or unique symptoms that you could have are hypersensitivity to light or sound, bladder irritation, you see this quite a bit with interstitial cystitis. Brain fog is a big one. Another symptom that we often see is egg smelling gas. Visceral hypersensitivity specifically, is a pretty common symptom of IBS, SIBO, but more common with those that have hydrogen sulfide SIBO. And essentially, when someone has visceral hypersensitivity, what’s happening is related to mast cells and histamine. So there’s too many mast cells, and these mast cells are causing too much histamine in the gut, which is causing some of these symptoms. So if you have histamine issues, if you have mast cell or suspected mast cell issues, potentially this could be a driving underlying cause. And I guess that’s something also to keep in mind as well is your SIBO is not a it’s a symptom. It’s not a root cause.
Hydrogen sulfide itself, as a gas is very irritating, irritating to the colonic sites, which are the cells of the colon. And these cells absorb water, they absorb minerals, they absorb so many things. And they regulate our microbiome. And when these cells are irritated, it is very hard for them to do their job. And this has an impact on the mucus layer of the gut, the mucus layer is going nuts. And the microbiome is going nuts. And there’s just tons of irritation and tons of inflammation. It can also degrade the lining of the gut, which can lead to tons of symptoms. There’s also some really interesting research about colitis, and how colitis, and in the connection between colitis and hydrogen sulfide SIBO. Hydrogen sulfide is extremely toxic to your mitochondria. And if you go back to like eighth grade biology, you probably remember learning about mitochondria, and mitochondria and ATP production, we need ATP production for energy production. And so that’s why brain fog is such a common symptom with hydrogen sulfide SIBO, because it’s directly impacting the mitochondria, which is directly impacting energy production. You need strong, healthy mitochondria for so many things. But specifically for muscle function, contraction, energy neuron firing. And so this is where like some of the muscle pain…
Is the Carnivore Diet Right for You?
The carnivore diet may offer temporary relief from SIBO symptoms, but it does not address the root cause of the condition for most people. It's important to work with a SIBO practitioner to determine if this diet is appropriate for you, and to develop a personalized plan that addresses the underlying causes of your SIBO.