The Microbiome Explained + What To Eat For It

Microbes are living organisms that are too small to be seen with the naked eye, including bacteria, fungi, yeast, and viruses. A microbiome is a collection of microbes living in a given community, such as the intestines in the human body. These communities are often referred to also as  “flora” or “microbiota”. Our microbiomes start to form the moment we are born. Therefore, the how and where we are born play a major role regarding the types of microbes we acquire. Babies pick up microbes from every person or thing they touch. We continue to pick up microbes throughout our lives. It is important to note that the microbiome is not fixed. It develops over time and changes in response to our environment.

Until recently, bacteria in the gut were thought to only play a major role in regulating bowel movements. However, we know now that gut bacteria affect the ENTIRE body- including the brain. Among other functions, the beneficial bacteria in the gut synthesize some vitamins, aide with digestion, balance our moods, reduce anxiety and protect against infections and certain forms of cancer. The many microbes in our guts have the important role of helping us extract nutrients from food, which we wouldn’t otherwise be able to digest. Strains of good bacteria in the gut are very important , as they are associated with lower rates of obesity, diabetes, and various gastrointestinal diseases.

If there are too many bad bacteria or too few good bacteria in the microbiome (dysbiosis), serious health problems can arise. The population of good bacteria in your body can be inhibited or killed by stress, surgery, illness, trauma, or unhealthy eating habits. Antibiotics is a major culprit at killing off good bacteria. Although it serves its purpose sometimes in killing the bad bacteria that can cause disease, it also kills off many of the beneficial microbes.

So, it is important to be prudent when choosing whether or not to take antibiotics. The foods we eat also have a big influence on our microbiomes. Some foods feed the good bacteria and others encourage the growth of bad bacteria. You can stimulate the good bacteria, known as probiotics, by eating specific foods that the bacteria thrive on. These foods are known as prebiotics.

Tips for Maintaining a Healthy Microbiome
  • Stay hydrated! Every day, you should drink approximately half your body weight in ounces of water.
  • Be sure to consume both prebiotic and probiotic foods.
  • Eat plenty of high-fiber vegetables.
  • Limit or avoid processed foods as well as those high in added sugar, artificial sweeteners and trans fats.
  • Limit or avoid any foods to which you are sensitive, intolerant, or allergic. Common examples are corn, dairy, eggs, fish and shellfish, peanuts, soy, tree nuts, and wheat (gluten)
  • Take antibiotics only when medically necessary. During and after completing a course of antibiotics, eat probiotic foods and take a probiotic supplement. This can help rebuild the population of healthy bacteria in your gut.
Probiotic Foods
  • Fermented meats
  • Fermented vegetables
  • Kimchi
  • Kombucha (be sure it is one that is low in sugar)
  • Miso
  • Natto
  • Pickled vegetables (raw)
  • Sauerkraut
  • Tempeh (fermented soy)
  • Coconut milk yogurt that is plain, with no added sugar and has active cultures.
  • Acidophilus milk
  • Kefir
  • Greek yogurt that is plain and has no added sugar
Prebiotic Foods
  • Asparagus
  • Bananas (limit to 1 per day)
  • Eggplant
  • Endive
  • Garlic
  • Raw honey
  • Jerusalem artichokes (aka sunchokes)
  • Leeks
  • Legumes (black beans, kidney beans, split peas and lentils)
  • Onions
  • Peas
  • Radicchio
  • Whole grains (I recommend gluten-free types such as millet, quinoa, brown or black rice, buckwheat and plain air-popped popcorn)
The main probiotic bacteria that reside in the digestive tract are Lactobacilli and Bifidobacteria. These can be taken in the form of supplements or included in the diet in the form of fermented (or probiotic) foods. The table above lists good examples (but not all) of common probiotic and prebiotic foods. In order to maintain colonization in the digestive tract, probiotics must be taken or eaten on a regular basis. General recommendations call for 1 to 25 billion colony-forming units (CFUs) daily based on the person. To put these guidelines into perspective, most store-bought probiotic yogurt contain about 1 billion CFUs per serving. To get the maximum benefit from fermented foods, it is important to read product labels. Choose only those that contain “active, live cultures” and preferentially raw, unpasteurized, perishable ingredients. Organic foods are the best, as they are not typically heat-treated after fermentation which kills some of the good bacteria. Fermented foods can also be made at home. Though the probiotic content will vary by batch, home fermenting is a safe way to ensure that you are ingesting beneficial bacteria, as various cultures around the world have done for centuries.

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