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What Are the Signs of SIBO?

Written by Dr. Michael Ruscio, DC on November 27, 2023

Written by Dr. Michael Ruscio, DC on November 27, 2023 — Reviewed by Dr. Hannah Hamlin

Telltale Symptoms Can Guide Your Actions to Get Rid of SIBO for Good

• What is SIBO?|
• What Causes SIBO|
• Treating SIBO Simply and Safely|
• Support Your Gut Health to Resist SIBO|

It’s common in functional medicine to focus heavily on gut health. When most people think about poor gut health, the first symptoms they think of are directly related to the gastrointestinal tract. And it makes sense that imagining gut issues would elicit thoughts of digestive disorders like abdominal pain, gas, cramping, diarrhea, nausea, or indigestion. 

While it’s true that poor gut health often shows up as gastrointestinal symptoms, other areas of the body can suffer from it as well. And it’s not always easy to see the connection between poor gut health and non-digestive symptoms.

What I’ve come to understand through my clinical experience and studying research is that one gut condition in particular is strongly associated with non-digestive issues like brain fog, depression, and even skin eruptions [1, 2]. Small intestinal bacterial overgrowth, or SIBO for short, is the name of a type of microbial imbalance (dysbiosis) in the small intestine that can lead to inflammation, malabsorption, and a cascade of symptoms in the GI tract and elsewhere.

If you’ve been experiencing gut challenges as well as skin issues, difficulty concentrating, mood problems, or hypothyroidism, there’s a good chance you’d benefit from a protocol to treat SIBO.

Let’s break down what we know about SIBO, including what’s behind it, how it can go beyond the digestive tract, and if testing is really worth it, as well as the research-backed treatments I typically recommend for my patients.

What is SIBO?

SIBO stands for small intestinal bacterial overgrowth. Although we don’t know for sure, its prevalence may range from 2.5% to 22% of adults [3]. As the name SIBO suggests, having too many bacteria in the small intestine is not a good thing. 

The vast majority of gut bacteria reside in the large intestine, but a healthy small intestine also contains a small amount of beneficial bacteria. Certain digestive issues, and perhaps especially chronic inflammation, can increase the numbers of good and bad bacteria in the small intestine [4]. Too much microbial activity in the small intestine can cause gut dysbiosis (an imbalance of the microbiome), and your health may suffer on a number of levels [4].

Understanding the various ways SIBO may manifest is a useful tool for helping you decide how to address an array of symptoms. In general terms, we know that the digestive system is connected to other systems of the body and that these systems talk to each other. When there’s a problem in the gut, it might also show up on the skin via the gut-skin connection, in the brain via the gut-brain connection, as joint pain via the gut-joint connection, and as thyroid issues via the gut-thyroid connection.When it comes to SIBO in particular, specific digestive disorders and and non-digestive symptoms tend to point to it as an underlying cause. For example, about 30–40% of people with a combination of bloating, reflux, constipation, joint pain, and brain fog most likely have SIBO at the root of their symptoms.

Clearly, SIBO isn’t always the root cause of these symptoms, but it’s worth considering a SIBO treatment protocol if a lot of these symptoms apply to you.

Digestive symptoms of SIBO include those common in IBS:

• Abdominal distention or bloating [5]
• Reflux or indigestion [6, 7]
• Cramping [5]
• Flatulence and burping [5]
• Diarrhea [5]
• Constipation [5]
• Combination of diarrhea and constipation (mixed type) [5]

You might recognize these symptoms as signs of irritable bowel syndrome (IBS). That’s not a coincidence: several meta-analyses have found that SIBO is common in people with IBS [8, 9, 10]. Other conditions that are highly associated with SIBO include hypothyroidism [11] and celiac disease and non-celiac gluten sensitivity [12].

Non-digestive symptoms of SIBO:

• Fatigue [13]
• Mood (depression, anxiety) [14]
• Brain fog
• Rosacea [2]
• Restless leg syndrome [15, 16]
• Joint pain [17, 18, 19]
• Headache [20]

If anything in that second list of symptoms surprises you, you’re not alone. It’s not intuitive to connect SIBO with joint pain or brain fog. But the science connecting these conditions is there. 

In fact, the science showing that SIBO treatments can improve all the conditions above provides us with a roadmap to potential relief, especially if other interventions aren’t helping.

What About the Different Types of SIBO?

There are four different types of SIBO, but the type you have doesn’t change the treatment approach. 

SIBO is categorized by the type (or types) of gas the excessive bacteria emit when they’re active. The four types and the symptoms they correlate with are [21] in the following table [3].

Regardless of the SIBO type you have, it can exert damage to the small intestine that contributes to inflammation, malabsorption, vitamin deficiencies (such as vitamin B12 [21]), and potential malnutrition [3]. 

Although each different SIBO variation might give you different symptoms, the good news is we don’t need to adjust treatment according to the type you have. But before we get into treatment, you may be wondering how to tell if you even have SIBO. 

Is SIBO Testing Necessary?

The standard way to find out if you have SIBO is to use a breath test, and I’ll explain why testing may not be necessary. 

There are two types of breath tests for SIBO: lactulose and glucose [22]. In both cases, you drink a sugary liquid (containing one or the other) and, at prescribed intervals throughout the day, you breathe into a device that captures the gas from your lungs in a test tube. You then send the multiple tubes of air from your lungs to a lab for analysis and wait for the results. Although both tests are similarly accurate, the glucose test appears to have fewer false positives than lactulose [23].

Although I used to have my patients take SIBO breath tests, I’ve since learned that only treating people with positive SIBO results excludes many who might also benefit from treatment. So, at this point, I don’t recommend testing because it’s expensive and not always accurate. Instead, I let the patient’s symptoms guide my treatment. If they match those I listed above, I move forward with SIBO treatment.

If you’re experiencing SIBO symptoms but test negative for it, that doesn’t mean you should do nothing. Far more people will respond to therapies for SIBO than those who will test positive for it. That’s because SIBO overlaps with many other conditions that start in the gut, and SIBO treatment consists of gut-supportive interventions that work for a variety of digestive and non-digestive symptoms. 

The bottom line here is that you shouldn’t let an expensive and potentially inaccurate test stand in the way of safe, largely natural therapies that can help heal your gut.

The only reason I think you should test for SIBO is if your insurance requires the results to cover the antibiotic prescription (rifaximin) that might be important for your treatment. It’s expensive, and many insurance companies will resist covering it. Luckily, for those with stubborn SIBO who need antimicrobials, there’s an herbal workaround, which I’ll describe in the treatment section below.

But I’m going to hold off on treatments just a little longer to take a look at what we think causes SIBO.

What Causes SIBO?

The answer to this question is complicated and multifactorial. In other words, a number of potential risk factors, both internal and external, could lead to excess bacteria in the small intestine. The most probable causes include:

• Bacterial movement from the mouth to the small intestine (top-down) 
• Bacterial movement from the colon to the small intestine (bottom-up)
• Surgical complications causing food to sit and ferment in the small intestine
• Certain medications

When considering possible causes of SIBO, it’s important to remember that every gut microbiome is unique, and an input that could lead to SIBO in one person might be harmless in another.

Top-Down Hypothesis

In the case of SIBO that comes from the top-down, the issue likely originates in the stomach. In an informative conversation I had with Dr. Richard McCallum about his top-down hypothesis, he posited that some cases of SIBO may arise as a result of low hydrochloric acid (HCl) in the stomach allowing bacteria from the mouth to enter the small intestine [5, 24] . 

In a healthy digestive system, the stomach releases HCl as part of the normal digestive process to kill the majority of living microorganisms in food and help break down the food. This process protects you from foodborne illnesses and bacterial growth in the small intestine, where it doesn’t belong.

But when you have low stomach acid, some bacteria may slip through the stomach alive and travel into the small intestine, where they can colonize. The more this happens, and if partially digested food is available in the small intestine, the more likely you’ll end up with an overgrowth.

How does partially digested food get into the small intestine? In addition to HCl, your digestive tract produces enzymes to help digest your food. When your digestive system is running well, your mouth and stomach produce enzymes as you chew and swallow to start breaking down food before it reaches your small intestine. Your pancreas produces more enzymes to continue the digestive process as food leaves your stomach and enters your duodenum (the first part of your small intestine). The liver also produces bile, which the gallbladder releases into the duodenum to help you digest fats. 

All these enzymes and bile serve to break food down into nutrients that are easy for the small intestine to absorb. But if your body doesn’t release enough HCl, enzymes, or bile, partially undigested food particles can reach the small intestine. Those particles provide food for any bacteria there to eat, or ferment, and make a lot of gas in the process. 

The more undigested food in your small intestine, the more bacteria will move in on it and ferment it to make the fuel they need to reproduce. Normally, fermentation should only occur in the large intestine, where bacteria break down fiber and prebiotics that should pass through the small intestine undigested. In the colon, it’s normal to have gas produced during fermentation. But when too many bacteria produce gas in the small intestine, the result is bloating, pain, unpleasant bowel movements, and eventual inflammation, malabsorption, and malnutrition [25].

Bottom-Up Hypothesis

The bottom-up hypothesis starts with the large intestine rather than the stomach. When motility is slow—meaning food doesn’t move through the system at a fast enough pace—what’s in the large intestine (where the vast majority of the bacteria in your gut should live) can begin to migrate into the small intestine. When this bottom-up movement occurs, the bacteria in your large intestine seed the small intestine with bacteria that shouldn’t be there [26].

Interestingly, this type of bottom-up activity can happen after a rapid bowel purge caused by something like foodborne illness or traveler’s diarrhea. Your body usually clears these infections on its own, but sometimes a temporary autoimmune response afterward disrupts the motility apparatus. Disrupted motility can cause contents from the large intestine to reflux into the small one or slow way down, creating the right conditions for a small bowel bacterial overgrowth.

Abdominal Surgery

Some abdominal surgeries, like gastric bypass or colectomy, may lead to SIBO as a result of [27]:

• Intentionally shortening the intestine 
• Adhesions, or areas of scar tissue that bind parts of organs to each other abnormally 

Both of these can create pockets in the small intestine where food particles can get stuck. Bacteria in the small intestine can then land on those pockets and ferment the contents. Just like with stagnant water in a puddle, bacteria can thrive on stagnant food particles in the gut. 

Medications

Certain medications can disrupt your intestinal bacteria and contribute to SIBO. These medications include nonsteroidal anti-inflammatory drugs (NSAIDs) and acid-lowering medications like proton-pump inhibitors (PPIs) [5]. Using these—and in my experience, possibly decongestants—on a regular basis may damage the small intestine in ways that contribute to and support SIBO.

Treating SIBO Simply and Safely

The primary treatment protocol for SIBO includes temporary dietary changes and probiotics, and in some cases antibiotics or antimicrobials. 

Once your symptoms have cleared, you can re-introduce foods into your diet and experiment with reducing or stopping probiotics. In that process, you may find that you should continue to limit or eliminate certain foods, and that you want to continue taking probiotics. 

On the other hand, if your symptoms don’t improve, you and your healthcare provider can consider antibiotics or herbal antimicrobials. The ongoing work of maintaining your gut health will depend on your individual needs. I always recommend undergoing this process with the help of a healthcare professional so that you can best understand your unique needs. 

Now, let’s take a closer look at how we treat SIBO in the clinic.

Removing SIBO’s Food Sources With Diet

Much like with any other gut-related ailment, dietary adjustments tend to come first. The most effective diet for treating SIBO is a low-FODMAP diet, with or without an elemental diet.

Low-FODMAP Diet

A low-FODMAP diet significantly reduces specific carbohydrates (Fermentable Oligosaccharides, Disaccharides, Monosaccharides, And Polyols) that you should avoid until your symptoms subside. These foods not only feed the bacteria you’re trying to eradicate, but they often cause gas and discomfort. The idea behind temporarily eliminating these foods is to stop providing the bacteria in your small intestine with foodstuffs they can ferment and use to reproduce. Ideally under the guidance of a knowledgeable healthcare provider, you’ll usually be on this diet for four to eight weeks.

It’s probably a little confusing to see so many healthy foods missing from this list. Normally, vegetables like garlic, onion, and broccoli are beneficial in a healthy, whole-foods diet, and I recommend them to help feed your gut flora. Unfortunately, in the case of SIBO, they’re also feeding the flora we’re trying to get rid of. Luckily, this diet is a temporary intervention, so you won’t have to avoid higher-FODMAP foods forever.

You can also consult Monash University’s FODMAP Diet app. Monash has pioneered FODMAP diets, and their app lets you see the FODMAP content of a huge database of foods so you can choose how much or how little of even higher-FODMAP foods you can eat at each meal. For example, most general low-FODMAP diet food lists put broccoli squarely in the restricted list, but the Monash app specifies that you may be able to eat 2.65 ounces (a decent-sized crown) of it per meal without issue.However you choose to go about it, limited science supports the low-FODMAP diet for treating SIBO and improving non-digestive symptoms. Although we don’t have much research looking directly at using the low-FODMAP diet to treat SIBO, one recent randomized pilot study (a small study that sets the stage for further research) found that a low-FODMAP diet reduced SIBO by 30%. I’ll talk more about probiotics soon, but in volunteers who took a probiotic with their low-FODMAP diet, SIBO dropped by another 10% [28].

Without much specific research on the low-FODMAP diet for SIBO, we turn to the next best thing: studies examining the diet’s effects on similar gut issues that go hand-in-hand with SIBO. It’s not 100% clear yet that what works for IBS necessarily works for SIBO. However, many IBS patients also have SIBO, and solid research shows the low-FODMAP diet has been widely helpful for IBS patients [29]. 

For example, a 2017 meta-analysis looking at the effects of a low-FODMAP diet on IBS patients found that this diet alleviated digestive symptoms like pain and bloating in about 70% of IBS patients [30]. As we wait for more scientific evidence to support the use of a low-FODMAP diet for SIBO, I’ll continue to let my clinical experience guide me to recommend that SIBO sufferers reduce their FODMAPs.

Elemental Diet

An elemental diet is a simpler, yet more restrictive option that can eradicate SIBO [31]. If you’re experiencing especially painful or extreme symptoms, starting with this easy-to-digest option might be good for a short period. 

The elemental diet is a hypoallergenic meal replacement that’s free of prebiotics and fiber to provide you with the nutrients you need while starving the bacteria in your small intestine and giving your gut a rest. This temporary diet is a good reset, but once your symptoms have calmed down, it’s a good idea to transition to a low-FODMAP diet for the remainder of your treatment.

Some people find the best benefit if they use an elemental diet exclusively every day for a week or two, but it can also be helpful for shorter gut resets, say a few days long. Even just replacing one or two meals a day with an elemental diet can give your gut the extra boost it needs to eradicate SIBO when you’re eating a low-FODMAP diet and, as I’ll discuss next, taking probiotics.

Supporting Your Gut with Probiotics

It might seem counterintuitive to take probiotics when you’re trying to kill the bacteria in your small intestine, but probiotics can improve outcomes in SIBO patients. A meta-analysis showed that probiotics alone eradicated SIBO in 53% of patients [32], which rivals the efficacy of antibiotics [33]. Even more compelling is the evidence showing that combining probiotics with antibiotics can raise the eradication rate to 86% [32].

Probiotics help reduce inflammation and rebalance the microbiota, which improves the gut lining and can help reduce the malabsorption that sometimes accompanies SIBO [34, 35, 36, 37, 38, 39]. Probiotics are also good to take during courses of antibiotics to reduce their negative side effects, like diarrhea [40].

Not only that, but probiotics can help relieve non-digestive symptoms, whether or not they arise from SIBO. For example:

• Probiotics can effectively treat depression and anxiety [41, 42].
• A Bifidobacterium strain of probiotics can improve cognitive function in older adults with mild cognitive impairment [43].
• Probiotics may reduce fatigue by improving thyroid function in people with hypothyroidism [44].

I recommend that my patients use a triple-therapy approach to probiotics, especially when healing from SIBO or other common gut conditions. The triple therapy probiotic we use in the clinic combines all three categories of probiotics (Lactobacillus and Bifidobacterium species, Saccharomyces boulardii, and soil-based probiotics) into one formula to give you the most comprehensive approach to refortifying your gut microbiome. You can try this formula for four weeks and then reevaluate your symptoms.

Some SIBO patients experience resolution with diet changes and probiotics. If this is you, you can continue with probiotics, and you shouldn’t need to consider an antibiotic. However, if you’ve hardly noticed the needle moving toward improvement after eating a low-FODMAP diet while taking probiotics for a month, it’s probably time to consider antibiotics or herbal antimicrobials with your healthcare provider.

Evicting the Squatters With Antibiotics or Herbal Antimicrobials

Once you’ve tried diet changes and probiotics for about a month, it’s time to evaluate your improvements. If you’re not satisfied, your next step may be to ask your healthcare provider about a course of antibiotics, or herbal antimicrobials if you don’t have access to or prefer not to use antibiotics.

The antibiotic most recommended for the treatment of SIBO is rifaximin, brand name Xifaxan. I mentioned above that this drug is expensive and some insurance companies don’t cover it. You’ll have to find out what your coverage allows, but the science on its efficacy is solid. Much like probiotics, rifaximin can eradicate SIBO in about 50% to 60% of infected patients [33, 45]. And there’s likely no need to stop taking your probiotics. As I mentioned above, combining probiotics with antibiotics can raise the eradication rate to about 86% [32] and prevent antibiotic-related diarrhea [40].

If you don’t have access to rifaximin or you’d prefer to avoid antibiotics, another option is to try an herbal antimicrobial. One highly beneficial constituent of herbal antimicrobials for SIBO is oil of oregano. Oil of oregano is a broad-spectrum antimicrobial, meaning it will likely help rebalance your gut, even if you don’t know what type of microbe—bacterial, fungal, or parasitic—you’re dealing with [46, 47]. Some other effective herbs you may see in an herbal antimicrobial formula are berberine [48, 49] and sweet wormwood [50, 51]. 

In a small clinical trial our team conducted, herbal antimicrobials, with or without enzymes that dissolve biofilms (which are like tiny bacterial fortresses), eradicated SIBO in about 40% of patients. That’s not too far off from the eradication rate of antibiotics. Combined with probiotics, herbal antimicrobials may be almost as effective as antibiotics plus probiotics.

The main difference, then, between herbal antimicrobials and rifaximin, is that herbals tend to take longer to work. Whereas you typically take rifaximin for 10–14 days, herbal antimicrobials need at least a month to show benefits [52]. That said, they’re gentler on the system and don’t seem to contribute to bacterial resistance, such as methicillin-resistant Staphylococcus aureus, aka MRSA [53].

Support Your Gut Health to Resist SIBO

SIBO is a type of gut dysbiosis that can lead to many different symptoms, both digestive and non-digestive. The most common gut-related symptoms—constipation, diarrhea, gas, and abdominal cramping—may not be surprising, and if you’re familiar with IBS, you’ll see how much the symptoms of SIBO overlap. However, small intestinal bacterial overgrowth may also cause non-digestive symptoms like depression, rosacea, fatigue, and brain fog, so don’t discount SIBO as a possible cause of these, especially if you also have gut issues. 

Our clinic has found that a simple approach, including a low-FODMAP diet with or without a temporary elemental diet probiotics, and possibly an antibiotic or herbal antimicrobial, is the best protocol for eliminating an overgrowth of bacteria in your small intestine. I hope after reading this, you feel empowered, knowing that you can identify when you’re likely to have a SIBO infection, and that you can talk to your healthcare provider about trying these simple steps to get your gut health back on track.

If you’re looking for someone to guide you on your SIBO recovery, we’d love to help you. Please feel free to reach out to our clinic to become a new patient.

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