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  • Writer's pictureMarissa Mekelburg MS, RDN, CLT, HHP

What is SIBO and how can diet help?

Is there anything more miserable than having digestive problems, gas, cramps, brain fog, and a belly that looks six months pregnant…and you’re not?

If you’ve been struggling to discover what has been going on, or have received a diagnosis of SIBO, you’re in the right spot. Changes to your diet can help you to resolve your SIBO symptoms.

In this article, I’ll cover what SIBO is and how a multipronged approach – including diet – can help to manage symptoms. I’ll also cover possible root causes of SIBO and explain why figuring out your root causes is so critical in the ability to prevent a SIBO relapse.

What is SIBO?

SIBO, which stands for Small Intestine Bacterial Overgrowth is about bacteria being in the wrong place at the wrong time.

We have good bacteria in and around our bodies; we need them to be healthy. In our digestive tract, most of these “good guys” are in the large intestine (aka the colon). These bacteria help us to get more nutrition from our food. They also help to keep our gut healthy by feeding the cells of the gut with short-chain amino acids; kind of like passing out snacks.

But…they’re supposed to stay in the large intestine.

SIBO is when too many of these bacteria are hanging out in your small intestine. Wrong place, wrong time.

Drawing of human digestive tract and SIBO bacteria

Image courtesy of Canva.

How many bacteria are we talking about? We measure the population in terms of how many living bacteria are in one milliliter of fluid. In case you’re curious, 1 milliliter is about the same as 20 drops of water (1).

1 milliliter of fluid from the small intestine has about 10,000 living bacteria inside. And while that sounds like a lot, the large intestine has far more. 1 milliliter of fluid from the large intestine has about 100 billion living organisms - i.e., 10,000,000 times the population of the small intestine.

A common misconception is that SIBO is an infection of a “bad guy” bacteria. Usually, this is not the case. The bacteria that are in your small intestine are normal organisms in your body, they’re just too many of them in the wrong spot. Most often, these bacteria have traveled and set up shop from the large intestine. Rarely, they’ve come all of the way down from your mouth.

So - why does this matter? Turns out there are a lot of things that can go wrong when these bacteria are not where they belong.

Why SIBO is a bad thing

Having SIBO can cause issues in a number of ways. When bacteria overgrow in the small intestine it can affect both the structure and the function. Let’s explore those possibilities right here.

Interrupts normal digestion and absorption

There are three ways that the displaced bacteria can cause trouble for your body.

1. The bacteria can destroy the enzymes that are needed for the regular digestion of carbohydrates. No enzymes breaking down the carbs means that we can’t absorb them.

2. What happens to the carbs? The sneaky bacteria eat them. They’re “stealing” our food – this can cause nutritional deficiencies.

3. And what else? They interrupt fat absorption by deactivating bile, the fluid that we make and require in order to absorb fat. Since we aren’t able to absorb fat, we are left with fatty stools and deficiencies in fat-soluble nutrients, such as vitamins A and D.

And that’s not all. The bacteria can also damage the lining of your small intestine.

Gut damage

There are also three ways in which the bacteria can damage the lining of your gut. This includes:

1. In your small intestine, you have the ability to absorb nutrients from your food in structures called villi. These kind of look like feathers (or a shag rug) with lots of waving strands. In SIBO, the villi may be damaged, which means you are no longer able to digest or absorb nutrients as well.

2. Also in your small intestine, one cell is supposed to be tightly linked to one another, which gives your body the ability to manage what is absorbed and what is kept in the gut. In SIBO, the tight junctions loosen, causing hyperpermeability (which you’ve probably heard of as leaky gut).

3. Leaky gut can lead to food sensitivities, Autoimmune disorders (molecular mimicry, etc.), and contribute to LPS (Lipopolysaccharide), an endotoxin of gram-negative bacteria, getting into the bloodstream.

So, having SIBO is a big deal - that is why it is so important to have an accurate diagnosis and a thoughtful treatment plan to prevent remissions. We’ll talk about treatments further along in this article, so keep reading.

Now that we know what the rogue bacteria can do, this will help us to understand the symptoms more easily.

Symptoms of SIBO

The symptoms of SIBO are pretty diverse; they can also increase and decrease in severity, depending on what you eat and so on, which makes SIBO more difficult to diagnose.

Bacteria produce gas after eating our food leading to symptoms such as belching, flatulence, abdominal pain, bloating, constipation, and diarrhea.

The bacteria also excrete high amounts of acid, which can cause both neurological and cognitive symptoms.

What does this look like? Here are the symptoms that I see most often with my own clients:

Abdominal pain and/or cramps

Bloating and distension (belly looks “pregnant.” This is something I listen for – when people say I can’t button my pants by the end of the day, I have to wear elastic pants, I look 6 months pregnant, this is a BIG clue we are dealing with SIBO.)

Belching (if sulfur-like, rotten egg smelling may be associated with hydrogen sulfide gas production)

Flatulence (if sulfur-like, rotten egg smelling may be associated with hydrogen sulfide gas production)

Constipation (most often associated with methane gas production)

Diarrhea (most often associated with hydrogen gas production)




Skin issues (rosacea, eczema, etc.)

Food sensitivities

Malnutrition (B12 or iron anemia, etc.)

Histamine intolerance



Mood disorders

Joint pain

Restless legs syndrome

So now that we know how SIBO can present and what is happening in your body…where did it come from, to begin with? Let’s explore risk factors.

Risk factors for SIBO

What causes SIBO? There is more than one thing that can make you at greater risk of developing SIBO. This is a long list, so let’s dive right in!

Insufficient migrating motor complex (MMC)

What is the MMC you ask? MMC is the small intestine’s “cleaning action wave” that moves bacteria and debris down into the large intestine in between meals and during fasting at night.

The MMC sweeps the small intestine clean, preventing bacteria from colonizing there.

How often? The MMC usually happens about 11 times per day or about every 90-120 minutes.

But if you have SIBO, it may only happen three times per day, which means that the bacteria have a LOT more time to get settled and reproduce.

The MMC may not function properly if you have:

● Intestinal nerve damage (Diabetes, surgery, GI infection)

● High histamine levels

● Eating too often (the MMC only occurs during periods of fasting)

a tan hand broom and a dust pan hanging on a white wall

Link to image:

Acute gastroenteritis

Montezuma’s revenge? If you’ve ever had food poisoning while traveling your risk of SIBO just went up. (Sorry to pile bad news on a bad situation!)

What’s going on? Certain pathogenic bacteria that cause acute illness secrete a toxin. When the body is working to defend itself and attacking the toxin, the insufficient MMC can be collateral damage.

Anything which slows motility

Remember how we learned that regular movement of food and bacteria along the small intestine is important to keep scooting bacteria along in the MMC section above?

A few other conditions can slow those movements down, paving the way for bacteria to flow backward and colonize. These include:

● Hypothyroidism

● Scleroderma

● Stress

● Heavy metal toxicity

● Neurotransmitter imbalance (low serotonin)

● Opiate medications

Insufficient stomach acid, pancreatic enzymes, and/or bile

A dream team combo of HCL (the acid in your stomach), pancreatic enzymes, and bile acids keep your small intestine mostly sterile. This means that even if you have a pathogen in something you ate, it should be nuked by your body’s acidic defense system.

But if these fluids are out of balance, the bacteria can sneak through and grow.

Low levels can be caused by:

● H. pylori

● Use of medications that lower stomach acid (i.e. PPIs, antacids)

● Pancreatitis

● Gall bladder removal

Parasitic infections

Parasites such as giardia, and cryptosporidium can damage the GI tract and increase susceptibility to SIBO (2).

Alcohol consumption

While a small amount of alcohol is fine for most of us, moderate to heavy alcohol consumption increases the risk of SIBO. In fact, a Swedish study found that 90% of alcoholics had SIBO - yikes (3)!

Ileocecal valve (ICV) dysfunction

The ileocecal valve – or ICV – is the doorway between the small intestine and large intestine. When the ICV is doing its job as it is supposed to, it closes after digested food goes through the door.

But if not, bacteria can creep backward from the large intestine back into the small intestine.

Crohn’s disease many times will cause damage all along the GI tract, including the ileocecal valve. This damage can lead to inflammation that can harm the valve so much that it may have to be surgically removed which means that the natural barrier helping to protect backflow from the colon has been removed.

Vagus nerve compromise or damage

The vagus nerve – which starts in the brain stem – controls the MMC we’ve been speaking about a few times now.

If the captain (in this case, the vagus nerve) of this process is compromised, it can’t send the corrected messages along the MMC and the movements don’t happen as often as they’re supposed to or they aren’t as well coordinated.

Dysfunction can be caused by:

● Misaligned neck vertebrae

● Hiatal hernia

● Bacterial/viral infections

● Heavy metal toxicity

● Pesticide exposure


● Stress

● Parkinson’s disease

● Autism

● Diabetes

● Lyme disease

● Vitamin B1 or Acetylcholine deficiency

Altered anatomy

If there is something different in how your GI tract is formed, bacteria can get stuck and reproduce instead of being swept along.

Altered anatomy/structure possibilities include:

● Non-draining pockets (from a surgical blind loop or diverticulosis - bacteria gets trapped)

● Fistulas (direct “tunnel” from the large intestine to your small intestine)

● Partial obstruction (from a tumor, etc.)

● Adhesions (bands of tissue that form from surgery or injury to your abdomen)

● Endometriosis (tissue can compress the small intestine)

● Kinks in the bowel

● Strictures in the bowel (narrowing of the intestinal wall)

● Ileocecal valve removal (surgical removal as a result of an appendectomy, Crohn’s disease, etc.)

SIBO + other conditions

SIBO might overlap with a few other conditions, including Crohn’s disease, celiac disease, H. pylori infection, and IBS. In fact, SIBO has been shown to exist in up to 84% of IBS patients and is thought to be the underlying cause.

As mentioned above, Crohn’s can be a risk factor and may have many of the same digestive symptoms.

You’re at higher risk of developing SIBO if you have celiac, especially if your symptoms remain after removing gluten (4).

I explained the possible overlap of SIBO and H. pylori in this blog post: H. pylori and SIBO: Can you have both?

Diagnosis of SIBO

The diagnosis of SIBO can involve a few different tests, an examination of your medical history, as well as elimination of other possible diagnoses. As we saw in the previous section, there is a lot of possible overlap between SIBO and other conditions.

Fluid Culture

Remember how we talked about the normal levels of bacteria in the large and small intestine? The most accurate way to diagnose SIBO is to measure the fluid in the small intestine…but this is also quite invasive (5). So most often, SIBO is diagnosed with breath testing and other tests to rule other conditions in or out.

Breath testing

Bacteria are living organisms that use and “exhale” gas, just like we do. We breathe in oxygen and breathe out carbon dioxide as a normal part of our own metabolism.

Different species of bacteria “exhale” hydrogen, methane or hydrogen sulfide.

To do breath testing you’ll breathe into a machine that can measure the gasses present, and then you’ll drink a sugary drink and see what changes. If you have an overgrowth of bacteria in your small intestine, they will chomp down on this sugary snack and exhale hydrogen, methane, or both, letting your doctor know that overgrowth is present. Knowing what kinds of bacteria are present also helps to guide treatment.

So while breath testing isn’t quite as precise as fluid testing, it is far less invasive, and much more common as well.

No matter what, an accurate diagnosis of SIBO requires expert guidance and testing from your doctor or other healthcare professional. I don’t recommend attempting to diagnose this, or any condition on your own. I talk about this a bit more in this recent blog post: Do I Have IBS or Something Else? No Self-diagnosis, Please!

Treatment of SIBO

There is a misconception you may have heard that diet alone can treat SIBO. Unfortunately, friends, this is false.

SIBO treatment will depend upon the predominant gas being produced (hydrogen, methane (or both), or hydrogen sulfide). If hydrogen sulfide is suspected, then a low sulfur diet can be helpful.

Eliminating SIBO requires a multi-faceted approach to eradicate bacterial overgrowth.

This can include:


Common antibiotics used in the treatment of SIBO include Rifaximin/Xifaxan for 14 days. If methane is dominant, the antibiotic will typically be combined with neomycin or metronidazole.

a person holding a few pills in their palm next to a pill dispenser and a glass of water

Link to image:

Herbal supplements

Herbal treatments vary but will typically include products like oil of oregano, berberine, neem, or products specially formulated for SIBO. Methane dominant herbal protocols will have additional herbs such as Atrantil, Allicin, or peppermint oil. Correct dosing is important as some herbs can have side effects such as nausea or diarrhea or may not be safe during breastfeeding or pregnancy.

Pro tip: I do NOT recommend trying to create herbal protocols on your own. Please work with a knowledgeable practitioner with experience in the herbal treatment of SIBO.

Other supplements that may need to be a part of your SIBO treatment protocol are prebiotics during active treatment (such as partially hydrolyzed guar gum). This is usually well tolerated by those folks that are not tolerating FODMAPs since a higher FODMAP diet is encouraged DURING active treatment as it makes bacteria more susceptible to the treatment.

Additional supplements may include biofilm disruptors, spore-based probiotics, and/or additional digestive support such as HCL, enzymes, bile salts, etc. Completing a comprehensive stool panel such as GI MAP in addition to breath testing can provide the information needed to determine what other supplements might be necessary.

Other medications/supplements

You may also find that a prokinetic medication/supplement is helpful. Prokinetics are medications that help with the motility of the GI tract.


While there are different types of “SIBO diets” there isn’t one right solution that will work for everyone and it's important to note that "SIBO diets" are there mainly for the purpose of managing symptoms.

Some of the dietary plans that are used as an intervention for SIBO include:

● The Specific Carbohydrate Diet (SCD)

● The Bi-Phasic Diet

In my experience helping clients to find relief from their digestive symptoms, I find that most clients come to me already restricting their foods. A lot. And as a dietitian, I don’t want to make things more complicated.

Since we’ve been through how many different conditions can lead to SIBO, it makes sense that a treatment protocol, including diet, needs to be personalized in order to work. I find that starting with a Low-FODMAP approach and potentially doing MRT food sensitivity testing helps to find the most effective SIBO diet plan with the fewest restrictions.

It’s also important to note that an elimination diet is not intended to be followed forever; it is meant to help manage GI symptoms and determine which foods are actually problematic. It is possible to follow an elimination diet for too long, and I have seen a lot of clients making this same well-intended mistake.

I cover this in detail in this blog post: Have you been on an elimination diet too long?

Addressing any root causes

And last but not least, it is very important to resolve any issues that may have caused the SIBO to begin with. If you are not able to correct the root cause, your chance of SIBO coming back is much higher.

For a quick review, root causes might include low stomach acid, slow motility, abdominal adhesions, and more.

It may also include healing your gut if you have leaky gut. More on that here: The Best Gut Healing Protocol to Resolve Your Symptoms.

Symptom management vs. root cause treatment

I’ve had clients tell me before how frustrated they are with their recurring issues. It seems like they figured things out with dietary changes or medication…only to have the symptoms come back a few months later.

Symptoms may be managed through diet (primarily low FODMAP) since the bacterial food source is being reduced but SIBO can be very damaging to the GI tract, and cause nutrient deficiencies, etc. so it is important to address the SIBO and the reason why you got SIBO in the first place.

Expected timelines

How I wish I could tell you that treatment –- once you know the root cause – is fast.

Here is what you need to know: fully addressing and eradicating SIBO is a PROCESS.

Unfortunately, this is a long road. But if you can stick it out through the hard work, you have the opportunity to be rewarded with no returning SIBO symptoms.

Sometimes I hear that SIBO has a reputation for being difficult to treat. In my experience, SIBO is treatable, but you have to stick with the full protocol, including follow-ups. I’ve seen this before with many clients: they only get a single round of medications, they don’t retest or have any kind of follow-up and then – bam – SIBO is back.

This makes clients feel like their SIBO keeps coming back, again and again, when in my experience, it was (most likely) never fully eradicated, to begin with.

Most of the time, treatment begins with medications or herbals.

One round of antibiotics is typically two weeks; antimicrobial herbals are typically taken for a month. The number of rounds of either kind of treatment depends on how high your gas levels were during the breath testing.

Treatment timelines include the time after medications, with dietary management and testing to ensure that you’re actually in remission.

Once a negative retest is achieved, post-therapy begins. For all clients, I recommend these things:

  1. Prokinetic medications/supplements (3 months or longer)

  2. Low FODMAP diet (minimum 3 months)

  3. Repairing the damage caused by SIBO. This can include healing leaky gut, identifying and replenishing deficient nutrients as well as addressing food sensitivities.

In addition, depending on your unique SIBO case, there might be more included in your treatment plan. For some clients, I also recommend:

  1. HCL replacement

  2. Enzyme replacement

  3. Vagal nerve stimulation

  4. Ileocecal valve manipulation

  5. Repairing leaky gut

How long altogether?

The full timeline from beginning to end varies but you’re typically looking at about 6 months on the low end to a year or more if fully addressed. As my client, you should be prepared to take retests, investigate and address root causes, and be willing to take necessary supplements and medications.

How I help

Not all doctors or practitioners are the same; in order to actually help clients achieve remission and prevent SIBO relapse, a practitioner needs to have extensive training and experience and be willing to guide their clients through the journey.

That is me in a nutshell!

SIBO is a complicated condition that can overlap with other conditions and can be caused by a myriad of different root causes.

As a Digestive Health Dietitian, I help clients navigate the testing process in case they don’t have a physician willing to order SIBO testing.

I also help navigate all the nutritional nuances from symptom management to nutrient deficiencies to food sensitivities.

I am knowledgeable in herbal protocols and can provide personalized supplement protocols to help support my clients.

I am able to run other tests like a GI MAP so that we have a thorough big picture and can help navigate things brought to light by this testing.

Overall, I am here to support my clients to expertly navigate this complex condition and finally achieve lasting relief.

Key takeaways: SIBO and diet

SIBO is a condition that is becoming better known, better understood, and unfortunately, more common.

Diet is part of a good treatment plan, but as we saw in this article, it is just one piece of the puzzle. Treatment of SIBO should start with an accurate diagnosis, identifying the root cause(s), as well as dietary, pharmaceutical, and herbal treatment.

Without identifying the root cause, you’re only playing a game of symptom management and you’ll not likely win remission long term.

I’d love to help you get there. If you’re ready to work with a knowledgeable guide to support you through your best gut health protocol, get started by scheduling an initial visit. This lets us both feel confident that we’re the right fit to partner together to achieve lasting results. I can’t wait to help you feel so much better.


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