SIBO Weight Gain: The Surprising Connection Between Your Gut & Metabolism

Small intestinal bacterial overgrowth, or SIBO, is a digestive condition that is commonly associated with symptoms like boating, food sensitivities, abdominal pain, fatigue, and bowel movement irregularities (diarrhea and/or constipation).

However, SIBO can also have health implications beyond digestive symptoms, including effects on the metabolism.

In this article, we’ll discuss SIBO weight gain, how to heal SIBO naturally, and steps to take to lose unwanted weight with SIBO.

Let’s dive in!

What is SIBO?

SIBO is an overgrowth of bacteria in the small intestine, which is the portion of the digestive tract where most nutrients are absorbed (1).

In healthy people, there should be a relatively low number of bacteria in the small intestine. When bacteria overgrows in the small intestine, those bacteria start to ferment certain carbohydrates from the diet, causing uncomfortable symptoms like gas and bloating.

SIBO also causes inflammation in the digestive tract and decreases the gut’s ability to absorb important nutrients.

It is estimated that up to 78% of IBS (irritable bowel syndrome) cases are actually caused by SIBO, and many of these cases go undiagnosed (2)


There are a few possible ways for SIBO to be diagnosed.

Breath Test

The most common method of testing for SIBO is a breath test. This test measures the amount of hydrogen and methane in the breath after drinking a carbohydrate solution (either lactulose or glucose) (3).

High levels of either hydrogen or methane gasses in the breath indicate bacterial overgrowth in the small intestine.

Small Bowel Aspirate

The second method of testing for SIBO, which is actually the gold standard for diagnosis, is a small bowel aspirate (4).

In this test, a small tube is inserted into the nose, through the stomach and into the small intestine. A small amount of fluid is aspirated (removed) from the small intestine and is cultured for bacteria.

This method is less popular because it is more invasive than the breath test.

Types of SIBO

There are 3 main types of SIBO, depending on the variety of bacteria that is overgrown in the gut.

The 3 types are methane-dominant, hydrogen-dominant, and hydrogen-sulfide dominant SIBO.

In general, methane-dominant SIBO tends to be associated with constipation, while hydrogen-dominant and hydrogen sulfide dominant SIBO are more often associated with diarrhea (5)

Can SIBO Cause Weight Gain?

While SIBO is mostly known for its digestive symptoms, like bloating and abdominal pain, it can also have a significant impact on metabolism.

The bacteria in your gut impact how your body digests food, absorbs nutrients, and uses energy. Imbalances in gut bacteria can significantly impact metabolic rate.

The truth is that SIBO can lead to either weight loss OR weight gain. SIBO often causes malabsorption (poor absorption) of nutrients, which can lead to weight loss.

However, many individuals with SIBO report weight gain and a struggle to lose weight (6). There are several reasons why SIBO could contribute to weight gain.


One of the side effects of SIBO is inflammation in the gut, which causes a breakdown of the gut lining. This is also known as “leaky gut” or increased intestinal permeability.

When the gut lining becomes impaired, proteins, bacteria, and toxins are able to pass through the gut barrier and enter the bloodstream, causing inflammation throughout the body.

This chronic inflammation causes imbalances in the hormones that regulate appetite, making it easier to overeat and gain weight (7).

Slower Gut Motility

Certain types of SIBO bacteria (methane-producing bacteria) have been shown to slow down motility in the gut, which means that it takes longer for food to pass through the digestive tract (8).

Slow motility can result in constipation, but it also means that food is in the digestive system for longer, allowing more calories to be extracted from food. This can contribute to weight gain.

Insulin Resistance

Some studies have shown that people with SIBO have a higher incidence of insulin resistance (9,10).

Insulin resistance is a condition where the cells become resistant to the hormone, insulin. When this happens, the body has to start producing more insulin in order to control blood sugar levels in the body (11).

High levels of insulin due to insulin resistance signal the body to store fat and make it much more difficult to lose weight.

Nutrient Deficiencies

SIBO is known to impair absorption of nutrients, which can lead to deficiencies of important vitamins and minerals (12).

While poor absorption of macronutrients like carbohydrate, fats, and proteins can lead to weight loss, vitamin and mineral deficiencies can also contribute to weight gain in some cases.

The metabolism requires several important nutrients to run efficiently. Without adequate levels of nutrients, the metabolism compensates and slows down, making it more difficult to maintain a healthy weight.

Increased Calorie Intake From Food

Bacteria in the gut play a role in digesting food and helping the body convert food into energy.

When certain bacteria in the gut are overgrown, particularly methane-producing bacteria, they can actually extract more calories from food.

This means that individuals with methane-dominant SIBO may have a higher calorie intake than someone without SIBO eating the exact same amount of food (13,14).

Is it Belly Fat or Bloating?

One of the classic symptoms of SIBO is abdominal bloating, and depending on the severity of SIBO, this symptom can be quite significant.

Many individuals with SIBO note that their abdomen looks large, and may feel like they look pregnant.

It can be difficult to determine if this distended belly is actual belly fat, or just bloating associated with SIBO. The truth is that SIBO can contribute to unwanted weight gain, and it can also cause a bloated and distended belly, without actual weight gain.

Healing SIBO Naturally

The standard treatment for SIBO is an antibiotic that specifically targets the bacteria in the intestinal tract.

However, there are several natural treatments for SIBO that are just as effective as antibiotic treatment (15)

Natural Treatments

Natural treatment for SIBO involves using herbs that have natural antibacterial properties rather than using antibiotics.

What’s important to note about SIBO treatment, whether you go the natural or conventional route, is that relapse is very common if you don’t treat the root cause and rebalance the gut bacteria (16).

The 5R Protocol

A natural and comprehensive approach to treating SIBO involves a step-by-step protocol, commonly referred to as a 5R Protocol in functional medicine. The steps of a 5R Protocol for SIBO that I use in my practice are:

1. Remove: Remove foods that irritate the gut and contribute to symptoms, as well as remove the bacterial overgrowth with antibacterial herbs.

2. Replace: Replace digestive enzymes and stomach acid, which are common root causes of SIBO.

3. Repair: Repair the gut lining to restore the barrier function of the gut.

4. Reinoculate: Reintroduce beneficial bacteria to the gut to promote balance and healthy digestion.

5. Rebalance: Rebalance the gut and address lifestyle factors, like unmanaged stress, that contribute to the development of SIBO.

How to Lose Weight With SIBO

In order to successfully lose weight with SIBO, it’s important to first address the imbalances in the gut that are negatively impacting your metabolism.

Traditional dieting and calorie restriction typically is not very effective with a positive SIBO diagnosis, because of the alterations in metabolism tha SIBO causes.

Additionally, low calorie diets can be a form of stress to the body and can make it more difficult to heal from SIBO.

Start with Treatment

Treating SIBO and getting rid of excess bacteria that are promoting weight gain is going to make it much easier to reach your weight loss goal.

Whole Foods Diet With Diversity

Many people who have SIBO avoid foods because they cause bloating or other symptoms.

However, your beneficial gut bacteria thrive on diversity in the diet. Adding more diversity into your diet and eating more whole foods can rebalance your microbiome after SIBO and improve your metabolism.

As you recover from SIBO, it’s important to slowly add any foods you eliminated back into your diet, particularly foods that are high in fiber.

Prebiotic and Probiotics

Prebiotic fibers are what feed the beneficial bacteria in your gut. These fibers can improve the balance in your gut and increase the specific strains of bacteria that increase metabolism and help your body maintain a healthy weight.

Foods that are high in prebiotic fibers are:

  • Oats

  • Bananas

  • Flaxseed

  • Artichokes

  • Garlic

  • Onions

  • Berries

  • Cocoa

  • Apples

  • Legumes

  • Quinoa

  • Asparagus

Adding a probiotic supplement after SIBO treatment can also add beneficial bacteria to your gut that can improve your metabolism and help with weight loss (17).

My favorite probiotics for SIBO are spore-based probiotics, like MegaSporeBiotic, because they tend to be well tolerated and have shown to be more effective at increasing beneficial bacteria in the gut.

You can purchase MegaSporeBiotic at a 10% discount through my online supplement dispensary, Fullscript.

Final Thoughts

In summary, SIBO is an overgrowth of bacteria in the small intestine, which causes symptoms like bloating, abdominal pain, diarrhea and/or constipation, and food sensitivities.

SIBO also causes significant alterations in the metabolism, and can contribute to unwanted weight gain.

Treating SIBO and rebalancing the gut microbiome can make weight loss much easier and more effective.

SIBO is a complicated condition and working with a skilled practitioner to find relief and prevent relapse is important.

If you need help getting rid of SIBO naturally, rebalancing your gut microbiome, and losing weight, click here to schedule a free 30 minute consultation with me and learn about how I can help.

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