Your Microbiome & You

The microbiome is the genetic material of all the microbes (bacteria, fungi, protozoa and viruses) that live on and inside your body. Trillions of these microbes live inside your body and outnumber your human cells ten to one.

The majority of bacteria and microbes live in your gut, particularly in the large intestine. It turns out that these bacteria greatly influence your health—from obesity to allergies to your sleep, stress management and immune system. Yes, it’s all interconnected!

The gut microbiome (these billions of bacteria that live inside your digestive tract) is the focus of some of today’s most exciting and compelling medical research. The microbiome is a hot topic and its function goes way beyond simply helping your body digest food. Studies have linked microbiome-related imbalances to health conditions ranging from depression and Parkinson’s disease to heart disease. Researchers often refer to the microbiome as a “forgotten organ” because of the indispensable role it plays in human health.

  • Obesity has also been associated with a poor combination of microbes in the gut. 
  • Type I diabetes is an autoimmune disease associated with a less diverse gut.
  • Dust from homes with dogs may reduce the immune response to allergens and other asthma triggers by changing the composition of the gut microbiome. Infants who live in homes with dogs have been found to be less likely to develop childhood allergies.

It has become fairly clear that the foods you eats—or don’t eat—can affect the composition of your microbiome. Research on mice has shown that switching from a fiber-and-antioxidant rich whole-foods based diet to a Western diet heavy in poor quality fats can alter the microbiome’s population within a day. A diet high in refined and processed sugars is able to decrease microbiome diversity within a week. Shifts in the microbiome have been associated with irritable bowel syndrome and diabetes. Furthermore, the rampant use of antibiotics and antibacterial products are able to create disruptions your body’s microflora in ways that could promote disease or illness.

Where Does The Microbiome Come From?

The majority of your microbiome comes from your mother during birth and breastfeeding. However, throughout life, you add, shift and impact your microbiome with the food you eat, from contact with siblings, close contacts with other people and animals, with soil, and anything else you contact within your environment. The impact of environmental factors, including aspects of lifestyle, on the microbiome is still poorly understood.

The species and distribution of microbes within the microbiome vary greatly among individuals. Your microbiome is unique to you and changes continuously throughout your life, depending on your life experiences.

Harming Your Microbiome

Most antibiotics kill beneficial bacteria in your microbiome, sometimes permanently. Sadly, the collateral damage created by their widespread use has been loss of intestinal microbes.

This is one of the reasons why many scientists have suggested and physicians are now practicing a delay in prescribing antibiotics to children. (Note: This is not a statement rejecting antibiotics.)

Antibacterial products such as those we use to clean homes, sterilize food-preparation surfaces, or wash hands and even wash food may also kill off the good bacteria you depend on. Antimicrobials are also found in food-packaging materials, athletic shoes, and clothing.

Researchers now suggest moving away from an over-reliance on these antibacterial products. Get kids exposure to the outdoors and dirt, thus building up the health of the microbiome.

Supporting Your Microbiome

Yes, you are what you eat, and so are the bacteria that live in your gut. Your life is also impacted by what you feed your microbes, meaning, technically, you are what your microbes eat!

When switching from a Standard American Diet, high in processed foods and refined carbohydrates to a whole-foods Paleo diet, your body may not react quickly and may take some time and persistence. As a long-term Paleo adherent, you can still actively support the active bacterial communities living in your gut.

Foods and lifestyle tips to activate and nourish your microbiome:


The fiber in vegetables passes through the digestive system until it reaches the colon. Bacteria in the colon then break down the plant polysaccharides through fermentation into short-chain fatty acids, the largest amount in the form of butyrate. Butyrate is the preferred energy source for cells in the colon and can help prevent colon cancer.

Fermented Foods

Include unpasteurized probiotic and fermented foods, which include live micro-organisms Fermented foods, such as kimchi, sauerkraut, kefir, kombucha and lacto-fermented vegetables all contain beneficial bacteria that can support balancing the bacteria in your gut. Aim for one to two servings of fermented food daily.

Prebiotic-Rich Foods

Prebiotics are non-digestible carbohydrates that get fermented by microbes in your gut. They are the preferred fuel source for your microbiome. Excellent sources of prebiotics include onions, garlic, leeks, artichokes, Jerusalem artichokes, jicama, asparagus, cabbage, root vegetables, green bananas, green banana flour, cooked and cooled potatoes and cooked and cooled rice (if certain grains form a part of your Paleo lifestyle).


Polyphenols are the micronutrients found in red wine, green tea, blueberries, pomegranates, cherries and dark chocolate that act as antioxidants. They decrease inflammation and stimulate the growth of beneficial bacteria while inhibiting the growth of pathogenic bacteria.


Your hair, skin, nails and connective tissues are made of collagen. Collagen also acts as a protective covering for body organs like the kidneys. Unfortunately, aging, genetics, environmental pollutants and nutritional deficiencies deplete collagen. Adding collagen peptides to your diet can help soothe and protect the gut lining and build new tissue.

Bone broth is a great source of collagen and gut supportive nutrients. Pete’s Paleo Bone Broth made with bones from humanely raised, pastured animals as well as organic vegetables and herbs, ensuring the final product is as pure and flavorful as it is packed full of vitamins, minerals and gelatin. Get yours here >>>>>>

Limit Sugar Intake 

Sugar, even Paleo friendly sweeteners, juices and dried fruits, along with artificial sweeteners feed the bad bacteria and can cause gastrointestinal distress in the forms of gas, bloating and diarrhea. Sugar intake, no matter the source, is best limited, for optimal microbiome health.

Probiotic Supplements

Probiotics can be helpful in treating irritable bowel syndrome, diarrhea, colitis, acne, and eczema. The strongest evidence for supplementing with probiotics is related to their use in improving gut health and boosting immune function.

Most probiotics contain various Lactobacillus and Bifidobacterium species. Another class of probiotics are soil-based organisms (SBOs), which have the ability to better survive the trip through the digestive system and reach the intestines intact, in order to “seed” the digestive tract with bacteria that will support a healthy microbiome.

Unfortunately, probiotic supplements don’t always work and many are taking supplements which are useless at best. This is because the vast majority of probiotic bacteria are active and effective in the lower portions of the gastrointestinal tract. In order to reach their destination, these must survive the highly acidic stomach environment.

Research has determined that probiotic bacteria have the highest rates of survival when taken within 30 minutes before or simultaneously with a meal or drink that contained some fat. The food provides a buffer for the bacteria, ensuring that they are able to pass safely through your stomach.

Be Mindful of Antibiotics 

Antibiotics kill bacteria indiscriminately. If you must take antibiotics for a bacterial infection, consider taking Saccharomyces boulardii, an antibiotic-resistant yeast that acts like a probiotic, as well as a multi-strain probiotic or a soil-based probiotic between antibiotic doses. This will help repopulate the beneficial gut bacteria.

Healthy Gut, Happy You

In most cases, supplements aren’t needed to support a healthy gut. They can help, but what you eat is by far the most important factor.

 While your microbiome may change quickly with what you eat, there are no quick fixes or overnight miracles to create a healthy gut. Instead, it’s about being consistent and understanding how your choices impact your bacterial families.

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