Chronic Diarrhea in Pets

The premier topic for this blog is also the one most frequently asked about – chronic diarrhea. Whether the pet is a cat or a dog, at least 80% of the requests for help revolve around this issue. Chronic diarrhea is usually diagnosed as irritable bowel syndrome or disease by veterinarians. First, please ask yourself (and answer honestly) these questions:

1. Has the pet’s diet changed recently?

2. Has anything changed in the pet’s home in the last three months? This includes:

  • Change in locationChronic diarrhea in pets

  • Change in household residents, either pet or human, in or out

  • Change in owner’s emotional or health status in the last three months

Why is this important?

1. Change in diet

It takes the microorganisms of the gastrointestinal tract (GIT) at least two weeks to adapt to any change in diet. This is especially true when changing from kibble to raw. Ideally, this change is done gradually, over a two week period. However, that is often not the case.

    The GIT microorganisms of a healthy, non-stressed pet present an impenetrable barrier to opportunistic pathogens that are always passing through. As a consequence, these pathogens are not permitted to establish or proliferate. In short, they pass harmlessly down the GIT and out with the feces.

    A new diet, especially as significant a change as from kibble (dominated by carbohydrates) to raw (dominated by protein) totally shakes up the resident microflora. Many beneficial microbes that depend on carbohydrates perish and leave gaps in the protective barrier. These gaps can easily be established by passing opportunistic pathogens.

    Once a pathogen gets a toehold, it can start utilizing dietary nutrients and proliferate. Many such pathogens secrete toxins and can make the animal ill.

    It also means food that may have been utilized before, is now able to pass to the colon. In most cases, very little carbohydrate gets to the colon. It is readily absorbed by the host. When it gets past the area of enzymatic absorption (the small intestine), carbohydrates are fermented by microorganisms usually kept in check in the colon. Their feeding frenzy results in a shift is colon residents, usually followed by diarrhea.

    In addition, shifting from a carbohydrate-based diet to one high in protein requires a metabolic shift as well. Normally, enzymes digest carbohydrates to generate energy. In the case of a raw-fed animal, energy is derived from the digestion of protein, via a cycle known as gluconeogenesis (literally “glucose from a new source”). This cycle is always “on” in cats, which makes them requisite carnivores. Dogs and humans can turn it on and off. BUT, it takes a few days before the cycle turns on in these animals.

    Gluconeogenesis is a failsafe method of generating energy in non-requisite carnivores. It comes on after about three days when a person or pet has exhausted all the glycogen, or animal sugar, stored in the muscles. Usually this only happens when an animal is starving.

The point is, there are three days when the newly-raw fed pet does not have a good source of energy. The digestive tract is in upheaval from the switch from carbs to protein, and the animal is low on glucose. Glucose is the gasoline that runs the animal engine, and it is the only carb used by the brain.

By the way, raw feeding is analogous to a human on low-carb or “Atkins” style diets. In both cases, gluconeogenesis must be engaged to generate energy.

2. Changes in household occupants, emotional, and health status

    Pets do not like change, they feel threatened by it. Perceived threat (stress) activates the “flight or fight” mechanism, which is automatic in all mammals. This reaction, which involves a rapid-fire secretion of hormones, prepares the animal to either flee or fight for its life.

    Metabolically speaking, the hormones redirect energy away from the GIT, an energy hog, to the muscles. This means that peristaltic movement of digesta through the GIT ceases. Since many beneficial bacteria are either attached or non-motile, they starve to death. Gaps open in the protective barrier, as in the scenario above. The amount of flow disruption depends on the severity and length of time the animal is stressed.

    The longer the animal is stressed, the greater the extent of damage to the protective barrier, and more likely that the animal will become infected.

    Although peristalsis may have ceased, undigested food continues to (slowly) move toward the colon. Also as with change of diet, this allows pathogens to proliferate and toxins to be secreted. It also usually results in diarrhea. Changes occur in the appearance of the lining of the GIT due to this change in microbial population and the toxins they secrete. These changes can be seen with a colostomy of abdominal surgery, and usually result in the diagnosis of IBS or IBD.


Stress is part of life, owners and pets will experience it throughout their lives. Chronic diarrhea in pets can be prevented, even under these circumstances. All it takes is awareness and the use of a concentrated probiotic such as MSE Paste or Liquid Rescue. Ideally, the probiotic should be used before a planned stressful activity such as a change in diet or a vet visit. However, since it takes time for pathogens to establish and proliferate, treatment after the fact is also effective, and can at the very least, minimize damage.

Treating chronic diarrhea

Unfortunately, it takes so long for the changes in the GIT to occur that it is easy to disassociate the causes from the disorders. Every person I have counseled over the last two years who came to me with a pet with chronic diarrhea has always been able to recall at least one of the stressful situations outlined above. And within three months of the pet developing the problem.

Many pets are taken to veterinarians, who then diagnose them with IBS or IBD and prescribe antibiotics and other drugs. Antibiotics actually exacerbate the situation. They kill gastrointestinal microflora indiscriminately, which can weaken the animal’s defenses even further. They also treat this as a lifetime ordeal.

The good news is, if the endogenous beneficial bacteria can be re-established, the damage to the GIT will heal. The GIT has an amazing ability for self-renewal. It completely replaces itself every three days (normally). This is necessary because of corrosive stomach acid and physically damaging food particles.

The first step is to start feeding MSE Natural Defense. Natural Defense contains pectin, which forms a matrix as it absorbs water. This water is only freed after microbial action in the colon. This helps stop diarrhea, but it must be fed daily. Pectin does not have any residual effect, it only works while it is in the body.

Natural Defense also contains several beneficial microorganisms that combat pathogenic interlopers. They help the endogenous beneficial microorganisms re-establish and get the GIT back in order.

The re-establishment of endogenous beneficial bacteria takes time, at least two weeks, and sometimes as long as a month. Assuming no further stresses. The damaged tissue may take longer to replace. I recommend that MSE Natural Defense be fed for at least two months.

Natural Defense should be fed dry to dogs. It can be mixed into canned food for cats, or sprinkled on dry food. Pets with asthma should not be given Natural Defense. In these cases, MSE Microbial Paste should be used instead. It also contains pectin, but at a lower level, and it is trapped in a thick paste.

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