(Woodpath is an education site focused exclusively on gut health. Our articles are researched by clinical nutritionists and contain citations at the end of the page.)

Some people seem to struggle more than others to lose weight. Or, it may take you longer to lose the same weight as a friend — despite adhering to the same diet and exercise regimen.

It’s possible SIBO (Small Intestinal Bacterial Overgrowth) might be at the root of your weight gain.

While SIBO has become more recognized as a gastrointestinal condition, most people affected don't know they have it.

They also don't know how to treat it.

Understanding SIBO — and its possible connection to weight gain — might help you get closer to your health goals.

What is SIBO?

SIBO is a digestive condition where the bacteria that is supposed to colonize your large intestine finds its way into the small intestine, where it doesn't belong.

SIBO is a form of gut dysbiosis — meaning there's an overgrowth or imbalance of growth in the gut bacteria.

While there are a number of potential root causes of SIBO, they all involve some malfunction along the digestive tract.

Possible Causes

Low Stomach Acid (Hypochlorhydria)

Bacteria sneaks past the stomach due to inadequate stomach acid and multiplies in the small intestine. Low stomach acid can occur due to chronic stress or the overuse of proton pump inhibitors (PPIs) like Prilosec for acid reflux. (Dukowicz,Lacy & Levine 2007)

Slow Motility

The time it takes for the partially digested food to move from the small intestine to the large intestine through the ileocecal valve slows down, leaving it to putrefy in the small intestine.

Physical Obstruction or hange

While less common, surgical intervention such as gastric bypass or other change in the digestive tract disrupts the balance of bacteria or creates a slight obstruction that allows bacteria overgrowth to take place.

Diagnosing SIBO

Commonly, a lactulose breath test or a glucose breath test is given to the patient, but the temporarily restricted diet that goes along with this test is difficult to follow. Patients can end up with inconclusive results.

That is why many GI specialists and doctors of functional medicine will observe your symptoms and make a diagnosis based on these observations.

Unfortunately, the symptoms can vary based on the type of bacteria that's colonized your small intestine, and include a number of overlapping symptoms with IBS (irritable bowel syndrome) which can complicate the diagnosis.


Symptoms of SIBO may include:

  • IBS-like digestive symptoms (constipation, diarrhea, feelings of incomplete bowel movements, gas, bloating, and abdominal pain)
  • Nutrient deficiencies that lead to weight loss and malnutrition
  • Unexplained weight gain or weight loss resistance, regardless of diet and exercise (Conlon & Bird 2015) (Mathur, Kim, Morales, Sung, Rooks, Pokkunuri, Weitsman, Barlow, Chang & Pimentel 2013)
  • Chronic fatigue syndrome/adrenal fatigue/feelings of sluggishness (Rao, Bested, Beaulne, Katzman, Lorio, Berardi & Logan 2009)
  • Skin conditions (rosacea, acne, eczema, psoriasis) (Weinstock & Steinhoff 2013)
  • Autoimmune diseases like Celiacs, Hashimoto's, and Crohn's disease (Dukowicz, Lacy & Levine 2007)
  • Food sensitivities and food allergies
  • Leaky gut syndrome (intestinal permeability, which leads to inflammation and a number of the above symptoms as well)

Weight Loss or Weight Gain, Which is it?

The symptoms of SIBO can be directly contradictory. Both constipation and diarrhea (along with a combination of both) can be symptoms of SIBO.

Both weight loss and weight gain can be symptoms. So which is it? How do you know? And what can you do?

There are tens of thousands of microbes living in your digestive system, all of which make up the complex human microbiome. Your microbiome is as unique as your fingerprint, but it's ever-changing based on your diet, stress levels, physical activity, and exposure to environmental stressors and pollutants.

The more variable and diverse your diet, the more diverse and healthy your microbiome will be, which contributes to your overall health.

The two main types of microbes that can colonize in the small intestine and cause SIBO create either methane gas or hydrogen gas as they grow and digest your food. The lactulose and glucose breath tests are designed to spark the bacteria into producing those gasses so that the breath can then be analyzed and for each type of bacteria. 

The type of digestive issues you are experiencing correlates to the type of bacteria that has overgrown in your system.

Put simply:

  • Hydrogen-producing bacteria causes diarrhea, malabsorption, and, possibly, weight loss
  • Methane-producing bacteria causes constipation, slow motility, and, possibly, weight gain

Knowing this simple distinction will help you understand your own symptoms and what to do next.

SIBO and Weight Gain

Methane-producing bacteria may be the cause of your particular case of SIBO. As a result, you may not eliminate your food intake efficiently. The interloping bacteria is slowing down your overall food transit time, creating a back up in the system and causing weight gain.

But this isn't an issue of body fat — it's just an issue of clogged pipes. What about body fat?

A 2013 study on rats showed that an abundance of M. smithii bacteria resulted in weight gain. (Mathur et al., 2013)

M. smithii is considered healthy bacteria — in normal doses. It is extremely efficient at breaking down the food you eat into calories your body will absorb in excess.

The rats who were inoculated with this bacteria and fed the same diet as the control rats gained substantially more weight. This phenomenon might help us to understand why certain people have a much harder time losing weight than others. It could be an abundance of M. smithii bacteria.

Understanding Leaky Gut

Leaky gut is often correlated with SIBO.

A leaky gut can allow bacteria into places in the body where it doesn't belong, setting off a cascade of inflammatory responses that can damage the gut lining and the immune system.

A damaged immune system can become either hypoactive or hyperactive and create the same allergies and autoimmune issues that SIBO can.

Foods that feed the bacteria living in your small intestine (whether they're good bacteria or bad) can lead to further inflammation and end up causing leaky gut and weight gain, even if you didn't have those problems in the first place. (Conlon & Bird 2015)

Chronic inflammation is also directly correlated to excess middle body weight, chronic stress, and metabolic diseases like type II diabetes. (Dr. Hyman Inflammation 2012)

While healing a leaky gut typically involves diet and lifestyle changes, those changes alone won't clear up SIBO. And unfortunately, some of the recommendations to heal leaky gut may exacerbate SIBO.

Diversifying your diet by adding various fruits, vegetables, fermented foods, herbs, and spices, can help rebalance your gut flora and start the process of healing a leaky gut. But a number of foods that we'd ordinarily consider healthy (broccoli, cauliflower, garlic, and onions, to name a few) may make SIBO symptoms worse.

These foods are part of a category of plant-based foods called FODMAPs (Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols). Part of treating SIBO is temporarily reducing or eliminating FODMAPs to get your symptoms under control by starving out the offending bacteria.

Additionally, antibiotic treatment is typically required to treat SIBO adequately.

Treating SIBO

There are three main steps that holistically-minded medical professionals will recommend to help you treat SIBO:

  1. Low-FODMAP diet (meant to be temporary, but may help you reach specific health goals)
  2. A course of targeted antibiotics (can be a conventional prescription or an herbal protocol)
  3. Maintenance plan (ideally to prevent SIBO from recurring and keep the weight off)

All three of these steps should be taken under the care of your practitioner.

1. Low-FODMAP Diet

A low-FODMAP diet eliminates or dramatically reduces all foods that feed the bacteria in your small intestine. This list of foods is extensive but includes things you'd typically avoid if you were trying to lose weight: grains, bread, pasta, potatoes, sugars, alcohol.

By cutting these items, not only can you reduce your overall inflammatory food intake — you may also starve out the bacteria causing SIBO.

Monash University has created a handy FODMAP chart worth referencing.

2. Antibiotics

Antibiotic treatment might seem counterintuitive if you know that it's linked to weight gain. (Cox et al., 2014)

But when treating SIBO, the only way to ensure that the bacteria are gone is to use some form of antibiotic to kill them. Luckily, there are targeted antibiotics like Rifaximin that only kill the interloping bacteria and spare the rest, preventing many of the adverse side effects of antibiotic use. (Bures et al., 2010)

Unfortunately, this antibiotic can be a challenge to get, as it's quite pricy. Many insurance companies will ask you to try a less expensive (and less targeted) alternative before agreeing to pay for Rifaximin. Only you and your trained medical provider will know the right steps to take should this obstacle present itself in the course of your SIBO treatment.

Another option is herbal antibiotics. You’ll likely want to work with a Naturopathic Doctor or functional medicine practitioner if you prefer this line of treatment.

Herbal antimicrobials have been shown to be just as effective as conventional antibiotics, but they require a longer course and will not be covered by insurance. They're also less likely to have side effects than conventional antibiotics. (UHN Digestive Health, 2018)

3. Maintenance Plan

After you’ve eliminated FODMAPs and have undergone a course of antibiotics, it's important to prevent recurrence.

In some cases, you might need to give your stomach a boost: supplementing with HCl and/or digestive enzymes. In other cases, it might mean taking a supplement to improve motility from the small to large intestine.

In all cases, it means reducing stress, chewing your food very thoroughly, keeping sugar and starchy food intake low, and filling up on nutrient-dense, anti-inflammatory foods.

You may eventually begin adding fermented foods into your diet to repopulate your large bowel with healthy bacteria. But that should be the very last step, taken only after your medical provider gives you the go-ahead. That’s because adding bacteria back into your system could cause a recurrence.

And, as always, you can get gut updates and stunning nature imagery from our popular Facebook page. Also, scroll down for our best gut articles.

Research Citations

Reveal all citations