ANW Apprenticeship Guide # 3
Introduction to the Microbiome
In this Guide, we will get acquainted with the body's most important source of pathogenic defense, known as the Forgotten Organ, and begin delving into the myriad of ways bacteria is not only beneficial to our health but necessary for life to exist as we know it. Become friends with bacteria and learn how to feed it to help your pet stay happy, healthy, and regular.
The vast majority of bacteria are good.
No, really!
Bacteria is beneficial and friendly more often than it is harmful or pathogenic. And thank goodness for that, because the microorganisms in our bodies number in the trillions. In fact, they nearly match or sometimes outnumber human cells in the body, according to researchers at the Weizmann Institute of Science.
Wizard's Note: It was previously thought, according to an estimate made in 1972 by a microbiologist, that bacteria outnumbered our own human cells by ten to one. This is the ratio you are likely to encounter if you search for this yourself. However, in 2016 that was determined to be more myth than reality. But even with that being the case, the contributions to human and other animal health by our bacterial colonies mustn't be overestimated, nor overlooked.
If the trillions of bacteria in our bodies weren't generally good, none of us would survive. We have clearly evolved to work synergistically with most bacteria, which form Microbiomes in and on our bodies. A Microbiome is, simply put, a cooperative colony of groups of different bacteria. And it's not just bacteria, either. The vast colonies of friendly microorganisms in our bodies consist of viruses, fungi, parasites, bacteria, and other microbes. It's only when the balance of this microbiota is disrupted that we begin to have problems.
And this is similarly true for our dogs and cats. Not only do both humans and our pets have bodies loaded with beneficial bacteria (inside and out), but we also routinely carry around bacteria, fungi, and other microbiota that is generally considered pathogenic or known to cause illness. Some examples include Candida albicans (the devilish fungi that is the culprit behind most yeast infections), Staphylococcus aureus (also called Staph), Clostridiodes difficile (or C. Diff, which can cause digestive upset including diarrhea), and Escherichia coli (usually abbreviated as E. coli).
All of these microorganisms live in our guts and on our skin pretty much all the time - and are generally harmless. But when our Microbiomes are affected by stress, antibiotics, illness, or poor nutrition, opportunistic microbes can begin to wreak havoc.
So, let's take a brief look at why we have such a close relationship with the microbial world, what benefits we receive from hosting trillions of the little guys, and how we can avoid disrupting this bacterial balance that protects and nourishes us and our pets. Because, while there are numerous approaches to improving and maintaining health if bacteria are not part of the plan, you're likely to struggle. Just as we focus on vitamins, minerals, fats, proteins, and other nutrients in our pets' diets, we also need to focus on their beneficial bacteria!
Our Connection to the Microbial World
The oldest known fossils are of cyanobacteria, from Archean rocks in Western Australia. They date as far back as 3.5 billion years, which is incredible considering the oldest rocks only date back around 3.8 billion years. The oldest known dinosaur dates back around 243 million years ago, making bacteria roughly 14 times older than the dinosaurs - and they're still going strong.
Bacteria are the oldest inhabitants of Mother Earth. Scientists believe that bacteria are the common ancestor of all life on the planet. This means that every plant and every animal ultimately descended from bacteria. It makes sense we would maintain a symbiotic relationship with them.
In the early 1800s, scientists began to ask how single-celled organisms like bacteria could evolve into all of the plants and species of animals that have existed and now exist today. The answer came when Charles Darwin developed his Theory of Evolution in 1859. And, due to insurmountable evidence and continuous, correct predictions for evolution, it is accepted as fact by scientists the world over. Now, the Theory of Evolution refers to the mechanism (how evolution works).
Darwin essentially speculated that there was once a small body of water, warmed by sunlight, which contained simple organic compounds. These combined to form a protein and eventually became more and more complex. The RNA World hypothesis suggests that life on Earth began with a simple RNA molecule that could copy itself without help from other molecules. This hypothesis is debated among scientists.
Wizard's Note: DNA, RNA, and proteins are central to life on Earth. RNA, which stands for Ribonucleic Acid, is a specialized messenger protein that carries instructions from DNA to create proteins. Protein is critical to cellular life, division, and growth. DNA uses a process of copying information on RNA and then RNA creating proteins using the information, all of which takes place in Ribosomes. Ribosomes are a molecule consisting of RNA and proteins which exist in large numbers in the cytoplasm of all living cells. They bind messenger RNA and transfer RNA to synthesize polypeptides and proteins. Ribosomes link amino acids together, using the order specified by the codons of messenger RNA, in order to form polypeptide chains (proteins). This process happens repeatedly in every single living cell - including the simplest bacterium and is one theory to explain the origin of all living things on Earth.
An experiment by Harold Urey and Stanley Miller in the 1950s brought Darwin's speculation to the lab. To start they filled a flask with the gases believed to be present in the atmosphere of ancient Earth. They then suspended it over a small pool of water and applied electrical sparks. What they observed was that complex organic compounds, including amino acids, formed abundantly in the water. And amino acids (proteins) are the most basic components of life. The experiment showed us that the beginnings of life could indeed have formed in much the way Darwin theorized.
Scientists have since found more compelling evidence that Darwin's 'little warm pond' explanation is viable, such as investigating regions near volcanic rifts in the ocean floor, where we find microorganisms capable of surviving at very high temperatures. These conditions likely characterized the surface of ancient Earth where life was thought to begin.
Now, whether it was really a 'little pond sitting in the sun', or some other combination of water, energy, and atmospheric chemicals, and whether the resulting organic compounds evolved into RNA or some other complex proteins, the fundamental suggestion that this type of environment produced simple organic compounds that ultimately gave rise to complex life remains a central idea to the origin of life.
All in all, bacteria is what gave life its initial foothold, and this is why living beings all have such a close relationship with it.
The Benefits of Bacteria
Besides bestowing Earth with the first source of life, bacteria play other important roles for the creatures of this planet. Most of this planet's life is microbial. Microbes such as bacteria provide crucial services for our ecosystems and are also nature's decomposers. Humans use bacteria as tools, too. We utilize their natural abilities to keep pests off of our plants, ferment our foods, make all sorts of drugs, antibiotics, vaccines, and much more. Bacteria are plentiful and useful. They are found in the soil, in the sea, and in freshwater, too. Bacteria live and survive everywhere.
And everywhere includes on, and inside of, us and our pets.
Microbiomes within the soil and sea are affected by pesticides, pollution, climate change, and other toxic disruptions, which result in the plants inhabiting these areas also becoming susceptible to diseases and nutrient deficiencies. Similarly, the microbiomes of animals can be affected by these things, and ultimately decrease the health of the animal hosting them.
Microbiomes are found in the ear, nose, mouth, throat, and airways, as well as on the skin. And they are also in the intestines, the caecum, and the colon. From the upper intestinal lumens to the crypts of the lower intestines, to the end of the line of the digestive system, they're found on nearly every internal surface in our guts.
Sometimes referred to as the Forgotten Organ, the Microbiome is an integral part of the both the immune system and the digestive system - and, recently discovered - our mental health. Microbiomes work to stabilize the body's surface and barriers. They also modulate (meaning exert a modifying or controlling influence on) the immune system. The immune system is continuously exposed to pathogenic bacteria and other harmful microorganisms, so we can thank our beneficial bacteria for protecting us from these harsh, external influences. The Microbiomes also ensure proper maturation of the cells making up our intestinal lining (called Enterocytes), and they assist the Endocrine (or hormonal) system. It's because of this inter-organ communication with our bacteria that many researchers are looking at the microbes in the gut for their therapeutic purposes. The Microbiome can be considered somewhat of a chemical factory, as well; it produces molecules with antibiotic, antiviral, and antifungal properties, all of which are used in the daily battles to protect its host from harmful pathogens. It also competes with pathogenic bacteria for nutrients, as well as attachment sites - as both good and bad bacteria require such things to colonize and grow in our intestines.
Suffice it to say, without our Microbiome's protection, our health is compromised.
The trillions of microorganisms consisting of bacteria, yeast, protozoa, and viruses make up populations that can vary greatly from host to host, and are influenced by the genetics of the host, as well as the environment the host lives in, and its diet. For each species, and for each member of each species, the Microbiome is different. Even better than a fingerprint, no two Microbiomes are exactly alike. The Microbiome is probably the most metabolically adaptable, and rapidly renewable, organ in our bodies - which is good considering the vital role it plays in our normal, nutritional, physiological, immunological, and even psychological functions.
To start, the GIT (Gastrointestinal Tract) becomes populated with bacteria soon after birth. Beneficial microorganisms will cover the entirety of the mucosal surface within the digestive tract, providing a defensive barrier for our guts. The Microbiome then starts its lifelong work of training and supporting our immune systems. It combines with the GALT (or Gut Associated Lymphoid Tissue) to make up about 90% of the body's immune capacity. And without the Microbiome in the GIT, the immune cannot function healthily, and the body's microbiota becomes unbalanced. Yes, nearly 90% of an animal's immune system is in its gut! And it is assisted and partly made up by the very bacteria we work so hard to kill and avoid.
Additionally, the Microbiome is an important barrier from carcinogens (cancer-causing compounds), drugs, heavy metals, toxins, and even potential allergens (by either holding onto them until they both pass from the body, pulling a sort of suicide squad move like other parts of our bodies, or destroying them outright).
Our Microbiomes also transport nutrients within the body, reduce lipids in the blood, act as neurotransmitters, convert nitrogen compounds, and possibly even work to alleviate symptoms of lactose intolerance.
On the digestive side, our Intestinal Microbiomes ferment Carbohydrates within the diet, creating SCFAs (or short chain fatty acids) that the body needs in order to properly absorb some nutrients, such as Calcium, Magnesium, and Iron. In fact, as we understand it, the only way our bodies can make these vital SCFAs are through our Microbiomes. These are not nutrients you can simply incorporate into your diet - you must have a healthy, functional Microbiome. The role of the short-chain fatty acids created by the fermentation of fiber in our diets by our gut microbiota is also thought to be responsible for reducing the risks of CVD (Cardiovascular Disease). This is yet another reason for the very active research into the links between diet and our gut microbiota and their significance to our health. More and more emerging evidence shows us that changes in diet impact the diversity of our Microbiomes, and shift the SCFA variations in our bodies, as well.
In short, our beneficial bacteria does no less than protect us, feed us, and keep our minds and bodies healthy. So let's look at how we begin to make friends with our Microbiomes; or, more specifically, our pet's Microbiomes!
Making Friends with our Microbiomes
In 2015, a review published in Cell Reports found that the people who live in high-income countries have less diverse and less resilient Microbiomes than those of third-world countries like Papua New Guinea. The difference? Our reliance on antibiotics, drugs, and our starch-filled diets, as well as our birthing practices (the overused Caesarian sections) and formula-feeding.
As mentioned above, the Microbiome is damaged and disrupted by man's use of certain chemicals and poor nutrition. This includes large amounts of starch (Carbohydrates) in the diet, overly processed and sterilized foods, as well as chronic stress and infections, and the use of antibiotics.
The damage caused by the above factors is called Dysbiosis. Dysbiosis occurs when the balance of pathogenic to beneficial bacteria is disrupted, allowing the pathogenic bacteria to outgrow our beneficial bacteria. This causes the tissue of our guts to become inflamed, and the enterocytes to separate. And it's the dysbiosis that leads to what most dog owners know as 'Leaky Gut Syndrome'; or, the separation of enterocytes that allows pathogens, and undigested proteins, to enter the bloodstream.
The immune system often views the protein matter as foreign and dangerous, and 'ramps up’ to attack. Sometimes the protein mimics closely some of the body's own tissues, causing the body to then create antibodies against itself - otherwise known as autoimmune disease. Many immune experts believe that dysbiosis and leaky gut are the precursors to autoimmune disorders, which, in dogs, include skin disease, heart disease, spinal cord disease, IBD, and pancreatic disorders, to list a few.
An imbalanced Microbiome may also lead to the notorious yeast infections that many a dog owner and their pet have had to suffer through. Yeast is a type of fungus, and this particular type of fungus thrives on sugar. When the microbiome is disrupted, particularly on the skin, an opportunistic yeast called Candida Albicans can overgrow and take control. Normally, Candida lives in harmony with other microbiota on your dog's skin (and in their guts), but when it grows out of control, and especially when it enters the bloodstream through a 'leaky gut', it can cause all kinds of unhappy results. Systemic yeast, which is the fungi that have traveled through the bloodstream, is often misdiagnosed as allergies - because of the skin issues it can cause. This overgrowth of Candida essentially means that a part of your pet's natural microbiome has become so excessive as to turn pathogenic.
Overbathing, unhealthy skin, antibiotics, and a sugary diet can all contribute to this common problem in dogs. The best way to combat yeast infections is to:
Ensure your pet is moved to a low carbohydrate diet
Avoid any unnecessary antibiotic use
Supplement with a natural source of probiotics
Supplement with sources of fiber (prebiotics)
Now, you may find conflicting resolutions regarding yeast overgrowth, with some parties stating a low-sugar diet will not combat yeast. This viewpoint is pretty limited since it's generally focused solely on blood sugar levels as opposed to the effect high sugar diets have on the Microbiome and the body at large.
While it's true that more study is needed in this area, and we have very little to go off in terms of gold standard evidence of such a diet on Candida, we do have other studies that show the dietary link and overall benefits of lowering sugar, as well as utilizing fructose (natural, fruit-based sugars) over glucose (the most common sugar found in our diets and which metabolizes much quicker than fructose) does indeed slow Candida growth.
And we do have anecdotal evidence for utilizing a low-sugar diet to deal with yeast.
We also know that yeast growth is absolutely associated with available nutrients and that Candida Albicans is fond of sugar. It is also an 'opportunistic yeast' - meaning it will take advantage of weakness in your Microbiome and in your skin and gut. Regulation of nutrients which such yeasts thrive on therefore only makes logical (and biological sense), especially as there are many, many other very good reasons for reducing the sugar in your pet's diet.
All that to say, there is no downside to following the advice to lower your pet's sugar intake, and based on what evidence we do have, it's very likely it could reduce their yeast problem.
Now, another common issue in our pet's diets that lead to dysbiosis is the lack of 'living foods' being consumed. Foods that contain natural sources of prebiotics (indigestible fiber) and probiotics (the very beneficial bacteria we've been talking about this whole time) are generally not included in the bowls of our dogs and cats. Instead, their bowls are filled with high-carbohydrate, ultra-processed (sterilized) kibble.
Sterilizing food means what?
You guessed it; destroying any and all bacteria within the food. And if there's one thing you should take away from this article, it's that bacteria are our friends.
The good bacteria in our guts need to be replenished - our bodies do not contain an infinite source of these guys, and they can be depleted. Especially after infection, the use of antibiotics, or illness. Normally, both pets and ourselves would easily replenish our Microbiomes by eating. Fresh and fermented fruits, veggies, and water found in the soil are all natural ways to do this. But for both pets and people eating a mainly sterilized, ultra-processed diet, this becomes harder and harder to do.
A dog or cat eating kibble their entire lives can only hope to be supplemented with a decent synbiotic (prebiotic and probiotic supplement in one), or have some chances at eating some table scraps - or even vegetation and dirt when they are outside. But probiotic supplements have their flaws, too. Not all probiotics are the same, and it's not easy to learn which are worth buying. Even within the same species of probiotics, there can be different strains that provide differing levels of efficacy, or even safety. The vast number of bacteria and their different strains, along with the low probability of those bacteria still being viable by the time your pet can ingest them, has led to conflict in the world of science.
Whether or not probiotics are beneficial, whether they're safe, and whether anyone should be taking them are topics of debate between different researchers. And it's little wonder - considering the market is absolutely flooded with probiotic supplements, most of which have not used clinical trials to determine their efficacy, or even confirmed that the bacteria listed is what's inside, much less at the CFU (colony-forming units) indicated. Some probiotics also contain potentially concerning or questionable ingredients that can be outright dangerous, such as 'Animal Digest', which the FDA found to be one of the pet food ingredients most likely to contain pentobarbital (the drugs used for euthanizing animals).
Wizard's Note: Other ingredients included by the FDA on this list of ingredients to avoid are 'Meat and Bone Meal', 'Beef and Bone Meal', 'Animal Fat', and other hydrolyzed ingredients. If you see these ingredients (written exactly as they are here) in your pet's food, treats, or supplements, please reconsider their use.
Ultimately, if you choose to go the route of supplementing with an OTC or vet-purchased probiotic, just ensure you really do your homework. You are also welcome to reach out to me, the Animal Nutrition Wizard, for help in choosing supplements for your particular pet, and their particular needs.
The best way to help keep your pet's Microbiome replenished and doing what it does best - protect your dog or cat from harmful substances - is to provide them with a fresh, whole food diet, that has varied meats, fats, fruits, and veggies, as well as fermented foods. If this is a big leap for you right now, you can also start small!
Adding in a handful or two of fresh fruit (depending on the size of your dog or cat) and a couple of pinches of chopped-up veggies can still have a positive impact on your pet's health.
Now, go make friends with your bacteria, and use that newfound friendship to keep you, and your pets, healthier.
Congratulations! You’ve just completed my guide on the introduction to the microbiome!
You should now be able to
See and understand the link between diet and the microbiome
Plan out ways to replenish and maintain a healthy microbiome
Make friends with bacteria
Thank you for reading, and remember - Nutrition is magic!