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Gut Health (Part 2): Bacteria In Pet Food

Updated: Oct 6, 2022

Last week, we discussed the role of the bacteria in the environment and the body. We learned that bacteria are essential for the health and well-being of our pets and ourselves. Without them, we can fall victim to a number of serious diseases which usually involve failures in immune and digestive function (1)(2)(3).

Gut Health 4 Part Series

Food Safety, Microbes and Over-Sterilization

Food safety is a top concern for veterinary professionals and pet owners. We agree, which is why this week, we are going to tackle the topic of bacteria and food safety how this relates to health and wellness in our pets. Recent research into probiotics has helped us understand that microbes are an essential part of the body's overall health and resilience and function to assist in homeostatic balance (4). Often, when the conversation turns to pathogenic bacteria, we revert to our conditioned response to “sterilize” and eliminate bacteria. So what does BALANCE really mean? How does it apply to food safety?

The Role of Beneficial Bacteria

First, we must remember that NOTHING is sterile. There are literal cities of beneficial and pathogenic bacteria on every surface that surrounds us, as well as in our bodies. We just can’t see them. The pathogenic bacteria do not usually cause any illness, unless they are allowed to grow unchecked. What typically keeps them in check is the beneficial bacterial. Specifically, many lactic acid bacteria produce metabolites that inhibit the growth of specific pathogenic bacteria (5). In many countries, probiotics are actually used to manage the balance of pathogenic bacteria in livestock to ensure a safer food chain (6).

Basically, nature’s approach to food safety is to keep a balance of microbes in the environment, the source of the food (protein and vegetable) and in the intestine. In a balanced ecosystem, all bacteria, including pathogenic bacteria actually play role in health and wellness. Let’s take E.coli for example. Escherichia coli is usually labelled as a “bad” or pathogenic bacteria but it’s important to note E.coli is commonly found in the environment and gut of most animals and is completely normal in balanced amounts. There are many strains of E.coli and not all of them are harmful. Some of them have even been shown to be useful as probiotics by reducing harmful strains of e. coli. (7) Another study showed that certain strains were even able to inhibit the growth of malignant skin and bowel cancers! (8) (9)

So How Does This Apply to our Pets?

When a pet becomes ill, doctors often blame food for the illness, especially if you are feeding raw food. However, the reality is that bacteria don’t only come into the body via food but also through environmental debris trapped in the mucoidal linings (air particles) and through interaction and physical contact with other animals (e.g. grooming or playing) and inanimate objects. These factors all need to be considered to address the growing concerns being voiced by pet health care professionals about pathogens in food.

Pet Food Science vs Real Food Science

Pet Food Science

Raw food is dangerous and loaded with bacteria and processed pet foods are safe, sterile and pathogen-free.

Real Science

ALL FOOD – processed and raw can contain pathogenic bacteria so just because you feed processed food doesn’t mean you’re avoiding them. Want proof? Just check out the Food and Drug Administration Veterinary food recalls page to confirm this:

The difference is, when you feed fresh food and probiotics, the food contains beneficial bacteria and is supporting your pets gut health so that the pathogenic bacteria doesn’t become a problem. I cannot say this enough - it’s about BALANCE, not sterility.

Reality is that dogs and cats did not evolve in a bubble – they evolved with a natural ability to handle the bacteria in their environment and food. Animals are even more equipped for it than we are with their short and highly acidic digestive tract. It is imperative to our immune function that our pets harbor a healthy microbe population (4). When animals are unable to deal with every-day amounts of pathogenic bacteria, it’s likely not a problem with the pathogens around them. It is often an indicator that there’s a problem with the animal’s immune system and gut health. Pets with sensitive guts that frequently suffer from diarrhea, vomiting, intestinal infections or skin inflammation (which resemble allergies) or infections are textbook examples of what can happen when the microbiome has been disturbed.

One of the most common places to find e. coli and other bacteria is actually in poop (exiting the gut) which we all know is a guilty pleasure for some dogs! Dogs and cats groom themselves, lick surfaces and other animals. They interact with, so unless you wrap your pet in bubble wrap, they are going to get exposure to a high amount of bacteria. What you can realistically do is make sure they have the nutritional support to maintain a healthy gut microbiome i.e. fresh, quality diet, probiotics and prebiotics!

Factors that may disturb the microbiome include poor diet, the use of antibiotics and other medications, underlying metabolic diseases, exposure to environmental toxins and even emotional stress. Animals that fall into one or all of these categories are good candidates for probiotic support along with any corrections that their diet may need. Additionally, when we destroy the microbes in our homes through rigorous sanitation and don’t include foods with microbes in our diets, we are compromising our ability to populate our internal microbiome. This results in an increased risk of becoming ill from pathogenic bacteria, which now can run rampant in the absence of healthy bacteria.

Food Safety in Commercial Diets and At Home

Just to be clear. While bacteria may be an avoidable reality when it comes to real food, it does not mean that food safety and hygiene should be ignored when handling food. For commercial manufacturers, they must put in place food safety systems to ensure that they are not contributing to bacterial contamination or promoting it and increasing bacterial loads.

When feeding food at home, we also have to be mindful of how it’s handled to ensure that food remains fresh until served. We’ve compiled a list below of the most important factors of food safety when it comes to your pet and potential pathogenic bacteria:

  1. Make sure you know where your food is coming from, how it’s being handled from start to finish. Pathogenic bacterial strains cannot contaminate carefully handled food. At Red Dog Blue Kat, our raw foods are processed in a closed facility that gets sanitized on a daily basis, has rigorous handling procedures and is processed in a 6000 square-foot refrigerator which does not allow for harmful bacteria to grow. Our meat is also sourced from human-grade facilities only with rigorous inspection and food safety practices.

  2. Raw foods should be thawed and served fresh. Any leftovers should be stored in the fridge promptly and used within 48 hours.

  3. Food bowls, counters, containers and your fridge should be kept clean by wiping any raw debris with a warm, soapy cloth.

  4. Bones should be fed in areas that can be easily cleaned such as a rubber mat, in a designated area outside or in a crate with a plastic tray.

It’s that easy! Stay tuned for Part 3 coming up next week on how to choose the best probiotic supplements for your pet!

Check out the studies below for some great developments in the understanding of probiotics and health:

  1. Application of Probiotics to Control Foodborne Pathogens from Farm to Fork:

  2. The Hygiene Hypothesis:

  3. Probiotics to Prevent the Need For, and Augment the Use Of, Antibiotics:

  4. Role of Probiotics in health improvement, infection control and disease treatment and management:

  5. Use of probiotics in gastrointestinal disorders: what to recommend?

  6. Insights from 100 Years of Research with Probiotic E. Coli:

  7. Probiotics and E. coli infections in man:

  8. Beneficial Properties of Probiotics:



(1) The gut flora as a forgotten organ.

(2) The ‘hygiene hypothesis’ for autoimmune and allergic diseases: an update

(3) The effect of infections on susceptibility to autoimmune and allergic diseases.

(5) Use of Bacteriocin Producing Lactococcal lactis subsp. lactis LABW4 to Prevent Listeria monocytogenes Induced Spoilage of Meat

(6) Feeding beneficial bacteria: A natural solution for increasing efficiency and decreasing pathogens in animal agriculture

(7) Inhibition of growth of Shiga toxin-producing Escherichia coli by nonpathogenic Escherichia coli.

(8) Mast Cell Degranulation Induced by Type 1 Fimbriated Escherichia coli in Mice

(9) Probiotics and Medical Nutrition Therapy


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