Addressing SIBO in Dogs and Cats

by | Feb 18, 2023 | Health Conditions

I have been lecturing and educating the public and veterinarians about gut health for many, many years. I worked on the gut microbiome in my veterinary hospital for 25 years. But 5 years ago I gave a lecture at a Dogs Naturally Summit about a disease of the gut that was not well researched nor understood in the veterinary realm called SIBO (Small Intestinal Bacterial Overgrowth). And since that time I’ve found that we are learning more and more about it. 

Today I want to explain in detail what SIBO is and how we can try and navigate your pet to a healthier, happier, and longer life. I am thrilled that it is much more recognized and accepted now because I know first hand it can be the underlying issue for many animals that suffer with chronic disease. 

SIBO is defined as an increase in the number of bacteria, and/or changes in the types of bacteria present in the small bowel. In most patients, SIBO in dogs and cats is not caused by a single type of bacteria, but is an overgrowth of various types, especially e.coli, but the balance of flora changes to a predominantly anaerobic one, resembling that of the colon.

The function of the top part of the small intense is to continue the digestion of food as it leaves the stomach and absorb nutrients into the bloodstream. These then circulate within the body.

But when digestion is impaired for whatever reason (many of these we will address below), the food that should have been absorbed remains in the small intestine and is then eaten by the bacteria. This in turn creates a population explosion! This is SIBO.

Signs and Symptoms of SIBO in Dogs and Cats

Symptoms of SIBO in dogs and cats closely mirror those of leaky gut and IBS – and for good reason – researchers are now looking at SIBO as being a cause of IBS.

Here are some of the things to watch for that may signal SIBO is present:

  • Chronic or intermittent diarrhea – can sometimes appear to have a large volume with little straining and or constipation
  • Some animals may appear inordinately hungry and may even eat stool or other indigestible items
  • Non-regulated EPI (exocrine pancreatic insufficiency), when diarrhea persists but is alleviated by antibiotics
  • Bloating or GI pain after eating
  • Reflux after meals
  • Foul smelling gas
  • Stomach gurgling and discomfort or cramping
  • Histamine intolerance due to the overgrowth of bacteria, producing excess histamine from undigested food = itchy animals (“allergy symptoms” – food and environmental) intolerances
  • Skin disease
  • Multiple food sensitivities/intolerances
  • Respiratory symptoms such as asthma
  • Joint pain
  • Mood changes
  • Weight gain or loss
  • Malabsorption and malnutrition
  • Chronic illnesses, eg. diabetes, neuromuscular disorders and autoimmune diseases

Overgrowth of bacteria causes a number of systemic conditions. SIBO not only affects the digestive system, but it also has far-reaching consequences. Bacterial overgrowth damages the lining of the small intestine, resulting in poor digestion, poor nutrient absorption, and inflammation.

SIBO in dogs and cats has been associated with conditions such as (but not limited to):

  • Decreased T4 to T3 conversion/hypothyroidism
  • Increased inflammation in the GI tract,
  • Damage to intestinal wall including leaky gut
  • Constipation due to production of methane gas
  • Malabsorption of nutrients, malnutrition
  • Anemia
  • Acid reflux or changes in stomach acid
  • Bone diseases

What Causes SIBO?

What causes this bacterial overgrowth? The gut relies on nerves, muscles, enzymes, and neurotransmitters to properly digest food. While enzymes mainly break down food, the nerves, muscles, and neurotransmitters physically move the food through the digestive tract from the stomach to the small intestine and then to the colon. When this happens in a healthy gut, bacteria gets passed through the digestive tract along with the food to its final destination in the colon. 

However, problems arise when something interferes with this process.

The body has a number of positive mechanisms to prevent SIBO from occurring:

  • Stomach Acid Secretion – maintains an acidic environment for killing off bad bacteria before they enter the small intestine
  • Bile Secretion – produced in the liver, stored in the gallbladder and released into the small intestine, bile protects against bad bacteria within the small intestine
  • Migrating Motor Complex (MMC) – waves of small intestinal wall muscular activity that move waste and unwanted bacteria through the digestive tract and to the colon. The MMC is not the same as peristalsis that happens in the large intestines
  • Immune System – the fluid in the small intestine contains immunoglobulins that act as antibodies to fight bacteria and other pathogens 
  • Ileocecal Valve – this is a one-way valve that allows the flow of contents into the large intestine but prevents them from refluxing back into the small intestine

Basically, to get SIBO, one or more of these protective mechanisms needs to fail.

There are many causes of SIBO, most of which are complex and affect more than one of the protective mechanisms discussed above. However, they can be grouped into three main categories:

  • MMC (Migrating Motor Complex )Damage
  • Structural
  • Functional

1. Damage To The Migrating Motor Complex

This is where bacteria are not cleared or swept away from the small intestine correctly. Conditions that increase the risk of impaired MMC function include:

  • Gastroenteritis
  • Lyme Disease
  • IBD
  • Medications, including antibiotics, proton pump inhibitors (decrease gastric acidity used for everything from acid reflux, IBD, nausea, GI upset) and pain relievers like any opioids, tramadol
  • Diabetes
  • Hypothyroidism
  • Surgical drugs or sedations – ketamine is often used in a cocktail for premeds, sedation or hypothyroid-dentals, nail clips, ear cleaning, etc. Think about how often animals are sedated compared to us.

2. Altered Anatomy/Structural Abnormalities

Anatomical changes can result in bacterial clearance being blocked within the small intestine or allow migration of bacteria from the large intestine back up into the small intestine. 

These include conditions such as:

  • Adhesions – spay or abdominal surgery
  • Obstructions
  • Cancer
  • IBD stricture
  • Ileocecal valve impairment

3. Altered Physiology (Functional)

In this situation, the function of the body has been altered and bacteria are not killed off in the stomach or small intestine as they should be, often as a result of:

  • Diets high in sugar, refined carbohydrates
  • Processed Dry Foods!
  • Raw food without added digestive enzymes
  • Lack of sex hormones
  • GERD (Gastroesophageal Reflux Disease)
  • Altered bile flow and or enzyme production, example EPI (exocrine pancreatic insufficiency)
  • Medications such as proton pump inhibitors (PPIs) and antacids
  • Immunodeficiency
  • Leaky gut

Diagnosing SIBO in Dogs and Cats

Diagnosis of primary SIBO is still not narrowed down, but there are several steps you can take to find out more about your animal’s own situation and condition.

First, rule out other potential causes of bacterial overgrowth and diarrhea. 

This can be done in a variety of different ways:

  • X-rays
  • Fecal examination (not cultures, which are notoriously


Next is a serum folate and cobalamin assay, which is a blood test that reveals high folate levels and decreased cobalamin may also lead to the diagnosis.

In dogs with EPI, these values will most likely be abnormal so they are not indicted. Values below the control range are often seen in patients with EPI and bacterial overgrowth in the upper small intestine (SIBO). 

  • Folate is one of the B-vitamins and is needed to make red and white blood cells in the bone marrow, convert carbohydrates into energy, and produce DNA and RNA. Values above the control range are consistent with bacterial overgrowth in the upper small intestine
  • Cobalamin – also called vitamin B12 – is absorbed in the distal small intestine (specifically in the ileum). A vitamin important for the normal formation of red blood cells and for the health of the nerve tissues. Undetected and untreated vitamin B12 deficiency can lead to anemia and permanent nerve and brain damage.

As folate is synthesized by the bacteria, and cobalamin is bound by them, this test is a good place to start because its easy to do.

The gold standard is breath hydrogen testing but it’s hard to find. This breath tests measure the breath excretion hydrogen (H2). The test measures how the amount of hydrogen present in your pet’s breath changes after he consumes a sugar solution. There’s usually very little hydrogen in the breath. Having a higher level of it indicates bacterial overgrowth in the small intestine

A positive breath H2 test is very suggestive of SIBO to the point that I would not feel any other tests would be required If the test is negative a culture of duodenal juice may be recommended but this is where I would draw the line and go more on symptomatology and treat with natural modalities or really conservative conventional meds ie: antibiotics but be sure to rule out the above mentioned.

There is also a methane breath test but I don’t know anyone who does it for pets.

Idiopathic SIBO

If your veterinarian can not find the cause, it could be idiopathic SIBO. In these cases you’ll find that antibiotics are very helpful to “manage clinical signs.”

This type of SIBO is often referred to as antibiotic-responsive diarrhea (ARD). It’s often seen in younger dogs and some possible theories to its cause are immune dysregulation, possibly associated with abnormal CD4+ T cells (immune cells), IgA plasma cells (antibodies), and cytokine (a chemical messenger) expression. This, to me, makes total sense because my take on so many “idiopathic diseases” would equally hold true with this. Over vaccination, dry processed food, medication, post surgery negative complexities… in fact I have seen more “ARD” after puppy vaccinations than you could possibly imagine.

SIBO Diagnosis: Now What?

Don’t freak out!!! This is the approach that I most often take with SIBO in dogs and cats.

1- You want to try and support your dog’s body to eradicate some of the overwhelming bacteria by starving them and using some antibacterial herbs. 

2- Stimulate the action of normal motility and digestion to help move and dispel the overgrowth. 

3- Rotate GI protocols for different parts of the gut! Think about how you are taught to rotate food… we can try and incorporate the GI protocols into that to help simplify it.

This is how we’re going to do it. 

1. Starving the Bacteria and Biofilms

An estimated 75% of bacterial infections and fungal infections involve biofilms. Biofilms are colonies of microorganisms that are protected by an extracellular matrix which can be thought of as a protective home for the infection to live in. This protective home makes the infection up to 1000 times more resistant to antibiotic therapies and therefore, more difficult to kill. This is why a comprehensive antimicrobial SIBO treatment protocol should include the use of a biofilm disrupting agent. Enzymes serve a dual purpose as they will decompose the biofilm and attack the cell structure of fungi and help to break down and digest food.

I use Yeasty Beast Protocol!

It’s so cool how nature again led me to develop this product. It has enzymes, cellulase and hemicellulase, Saccharomyces Boulardii (the only transient probiotic non-pathogenic yeast that survives gastric acidity, produces B vitamins which are compromised with SIBO), as well as Pau D’Arco and caprylic acid which are antibacterial and anti-fungal.

All = biofilm busters!

2. Stimulating Motility Prokinetics

Prokinetics are a class of drugs used to stimulate the cleaning wave or migrating motor complex (MMC), the “housekeeper” of the small intestine, sweeping away debris and bacteria. This mechanism is often not working in people with SIBO; in fact, its malfunctioning is a primary underlying cause. Some examples used in veterinary medicine are cisapride and metoclopramide. 

This is especially important because methane gas (which is produced from bacterial overgrowth) slows down and almost paralyzes the GI tract. Prokinetics are also very important to promote bowel movements because every bowel movement causes elimination of excess bacterial load in the form of stool.

A key underlying cause of SIBO in dogs and cats is thought to be deficient activity of the migrating motor complex (MMC). An intact MMC moves debris and bacteria down into the large intestine during fasting at night and between meals. Prokinetics stimulate the MMC, symptomatically correcting this underlying cause.

I have always used natural prokinetics here are some examples: 

1. Probiotics

Restoring a proper balance of good bacteria is a critical part of re-establishing a healthy microbiome after the SIBO is eradicated. Many practitioners do not recommend using prebiotics or probiotics on SIBO until it is known if the migrating motor complex works. For several years now, there has been much said about the benefits of probiotics in restoring gut health. This has mainly been attributed to topping up certain bacteria in an effort of overwhelm bacteria which have become pathogenic. 

However, recent research suggests that certain bacteria are influential in restoring effective motility of cleaning waves and that this could be a reason to incorporate certain species of bacteria. 

These studies look at how probiotics enhance gastrointestinal motility by increasing the frequency or strength of contractions, but without disrupting their rhythm. Effects of probiotics have actually been tested on humans and, depending on the symptom, have been shown to reduce the effects of constipation. 

These include:

  • Lactobacillus reuteri
  • Lactobacillus casei
  • Bifidobacterium breve

Certain probiotic strains are of benefit to people suffering from SIBO. These microflora have specifically identified, but only in studies on rats. These are the specific species that have shown to be really helpful with SIBO:

  • Bifidobacterium lactis
  • Bifidobacterium bifidum
  • Lactobacillus rhamnosus
  • Lactobacillus acidophilus

So, if you know that motility is an issue, these can be helpful.

However, unless you know for sure the reason why your dog or cat has SIBO I stay away from any bacteria that is not soil-based! 

No matter the reason for SIBO, I still always, always start with soil-based first. That’s because these help to colonize the bacteria that should be in the small intestine and suppress the potential bacteria that has colonized incorrectly from the large intestine. 

My all time favourite and ones I have had great success with are soil based probiotics – Bacillus subtilis, Bacillus pumilus, Bacillus coagulans, and Bacillus lichenformis.

2. Prebiotics

Probiotics need prebiotics to grow and thrive, so we can’t leave these off the list. However, a key point for the use of probiotic supplements for SIBO in dogs and cats is to avoid prebiotics that are not functional or those that are sugar-based. These can exacerbate symptoms during active SIBO and encourage bacterial growth post SIBO. 

Common prebiotics found in probiotic supplements include FOS (fructooligosaccharide), inulin, arabinogalactan (larch), MOS (mannose-oligosaccharide) and GOS (galactooligosaccharide). Prebiotics may be tolerated in small amounts with some cases but this is very individual and I personally would not recommend them! 

Instead, I recommend functional ones that have been researched and developed – ones made from turkey tail mushrooms and chlorella are perfect to use! Once the symptoms have resolved, rotating all different probiotics is my choice. This is why I developed a pre and probiotic line to do just that, to rotate through diverse strains and systems of the body.

[RELATED] Research shows that ancient minerals can help with symptoms of SIBO. Read more here.

3. Melatonin

Melatonin has been studied as a co-adjuvant treatment in several gastrointestinal diseases including IBS, constipation-predominant IBS, diarrhea-predominant IBS, Crohn’s disease, ulcerative colitis and necrotizing enterocolitis. It plays an important part in gastrointestinal physiology which includes regulation of gastrointestinal motility, local anti-inflammatory reaction as well as moderation of visceral sensation.

Melatonin, an important mediator of the brain gut axis, has been shown to exhibit important protective effects against stress-induced lesions in the gastrointestinal tract and helps with free radical scavenging and diminishing inflammation. Be aware that melatonin can contain xylitol which is poisonous to dogs so read carefully and is contraindicated with diabetes so make sure you speak with your vet before trying it with your pet!

Doses for dogs:

  • 1mg for dogs under 10lbs
  • 1.5-2mg for dogs 10-25lbs
  • 3mg for dogs 25-100lbs

Cats are very different from dogs, so speak with your trusted veterinarian about doses for kitties.

There are many others like ginger, curcumin, and Native, Chinese and Japanese herbs. Our friend, canine herbalist Rita Hogan, recommends willow phytoembryonic therapy, ginger, cilantro, Oregon grape root, and garlic. These are highly effective with SIBO. Willow phytoembryonic therapy works to heal the gut and bring down inflammation and pain. Cilantro is excellent at bringing down bacteria levels. Limit Oregon Grape root to two weeks on two weeks on. 

To better understand how and when to use these natural prokinetics, speak to your trusted canine or feline herbalist.

4. Mind-Gut Connection 

Many clinicians have observed that emotional conflicts appear to provoke exacerbation of colitis and IBS. A brain-mast cell connection is the most likely mechanism of symptom exacerbation by stress in patients with IBS. Gut sensitivity seems to be increased by stress and decreased by relaxation. The gut affects the HPA (hypothalamic-pituitary-adrenal) axis directly. Research shows stress induced in early life leads to dysbiosis in germ-free mice – which causes abnormal behaviour, and anxiety and aggression.

These behaviours can be transferred by fecal transplant, therefore supporting the link of this connection. For example, the mice that were not stressed didn’t have dysbiosis. But when researchers gave the stressed transplants to the unstressed mice, they then became stressed. (Read that study here for more information.)

The integrated microbiota-gut-brain-axis, which links the microbiota with the central nervous system (CNS), the autonomic and enteric nervous system and the hypothalamic-pituitary-adrenal (HPA) axis via immune, neural and endocrine pathways, may allow bacteria to affect cognitive function and behaviour. Stress affects this by reducing the MMC (migrating motor complex) which affects the movements, secretions, and permeability of the gut.

5. Enzymes

This is an important step! I feel the exclusion of enzymes are a large cause of SIBO (and many, many other diseases). Enzymes are extremely helpful in supporting the body to combat SIBO and Leaky Gut.

We are all doing our best with our animals. That said, we need to recognize that dry processed food is void of the essential enzymes the body needs. This lack simply creates an extra step in the digestive process. Now, the body needs hydration first in order to even start the process, which in turn slows down digestion and creates the perfect storm for bacteria to overfeed. Then we see the explosion of even good bacteria leading to SIBO.

Raw, species-oriented food doesn’t create this need for the extra, unnatural step in digestion!!

Yet, we are still so far away from providing a species-prey diet. Even great raw food diets are majorly lacking in the correct digestive enzymes. These would be provided by the brain, glands, sex organs, etc, which are not typically included in commercially prepared raw food diets. Enzyme-deficient foods, or even not the correct enzymes, can lead to poor digestion and malnutrition. Even if you are feeding amazing food, the lack of enzymes can be moving your pup right along into chronic disease!

When it comes to gut health, and SIBO in dogs and cats, it’s important to look at it from as high a level as possible. Rotate different high-quality ethical proteins, feed a variety of organic or pesticide-free vegetables, provide whole food supplements, incorporate in many diverse strains of scientifically-backed probiotics, accompanied by functional prebiotics, and shower your pet with as much love and fresh air as possible. All of these components help provide a healthy ecosystem of the gut hopefully leading to the vibrant health and longevity we all want for our beloved companions. 

Julie Anne Lee, DCH RCSHom

Julie Anne Lee, DCH, RcsHOM, has been the owner and practitioner of some of the busiest and long standing holistic veterinary hospitals and clinics in North America. This includes founding the first licensed strictly holistic veterinary clinic in Canada. She developed and taught a three year post-graduate program for veterinarians at the College of Animal Homeopathic Medicine. She also presented lectures for the American Homeopathic Veterinary Association on homeopathy and functional pathology, the British Homeopathic Veterinary Surgeons Association on treating chronic disease, the Canadian Society of Homeopaths on clinical comparisons of the treatment of human to animals, P.E.I Veterinary University on the gut microbiome, and many more over the last 20 years.

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