The Microbiome: How Healthy Is Your Gut Garden?

Getting to know your bacterial self


Over millions of years, humans have formed intricate relationships that are perhaps the most important relationships known to man. These unions, however, don’t involve another human being.


Just like all other plants and animals, we have formed symbiotic relationships with microbes that live inside our gut and on our skin.  The majority reside in our gut and are collectively referred to as the gut microbiome. We can think of our gut microbiome as a supplementary organ that metabolizes, detoxifies, and activates constituents of our diet that are critical to our health.


Our gut is home to over 400 species of trillions of bacteria. In fact, we are almost equal parts human to microbe, with scientists estimating the ratio between resident microbes and human cells to be about 1:1. This ratio, however, varies from person to person. Although it has been commonly assumed for several decades that microbial cells outnumber human cells in the body by a ratio of around 10:1, a recent 2016 review of more than four decades of research into the human microbiome discovered zero scientific evidence to this and established a more accurate (but still approximate) ratio of 1:1.


Our gut bacteria weigh 3-5 lbs on average and can be categorized as being either beneficial to our health or potentially pathogenic (ie. disease causing) when out of balance. This is because our gut bacteria produce end-products as a result of fermenting our food. Beneficial bacteria yield health-promoting end-products while pathogenic bacteria produce disease-causing end-products.


What exactly do they do in there?


The beneficial bacteria that live in symbiosis with us are critical to our health and are involved in almost every aspect of our health. Think of them as your army of “worker bees”. They train our immune system, help with digestion and nutrient absorption, maintain the health of our intestinal lining, modulate genes, metabolize drugs, produce vitamins, neutralize toxins and carcinogens, make neurotransmitters, and protect us from pathogenic bacteria.


One of the most important functions of our gut bacteria is helping to regulate our immune system. Did you know that 80% of our immune system is located in our gut in order to identify foreign invaders? Our gut bacteria and immune system are in constant communication. Gut bacteria can down-regulate or up-regulate the inflammatory response. Some microbes can degrade the intestinal lining and wreak havoc on the immune system by overstimulating it, while other microbes can help repair the lining.


Maintaining a critical balance


If our gut bacteria become imbalanced and the bad guys (ie. pathogenic bacteria or yeast) are allowed to flourish, their effects can be detrimental to our health.  Pathogenic bacteria can produce carcinogens and other toxins, putrefy protein in our gut, impair digestive function, and cause infections. Therefore, gut bacterial imbalances are closely associated with inflammation, increased body weight, auto immune conditions, diabetes, heart disease, and cancer.


The composition of our gut microbiome is influenced by factors such as stress, smoking, and medication, but the most powerful determinant is our DIET. The food we eat determines what kind of bacteria we foster the growth of, which can increase or decrease our risk of some of our most fatal chronic diseases.


Eating lots of plant fiber helps to create a healthy, balanced microbiome by increasing the prevalence of bacterial species that boost our immune system and help to protect us against disease. Plant-based diets have gained acceptance as an effective dietary strategy for preventing and managing numerous chronic diseases, which may be in part due to their unique gut bacteria compositionthat is, less pathogenic bacteria and more protective bacteria. Fiber-rich plant-based diets can decrease our risk of colon cancer, diverticulosis, gallstones, hemorrhoids, constipation, bloating, acid reflux, irritable bowel syndrome, fatty liver disease, heart disease, and type 2 diabetes. An imbalance in our gut bacteria is linked with numerous other health conditions, such as Crohn’s disease, ulcerative colitis, celiac disease,  autoimmunity, arthritis, skin disorders (eczema, psoriasis, acne), allergies, depression, anxiety, and even chronic pain. Therefore, some of the beneficial health effects of a plant-based eating pattern may be due to its effects on our gut bacteria.


Why do plant-based diets foster the growth of protective bacteria and less pathogenic bacteria? Because our beneficial bacteria are only nourished by one food component– fiber. And fiber is only found in- you guessed it, plants!  Plant foods include vegetables, fruits, whole grains, and legumes. On the contrary, pathogenic bacteria feed on meat, dairy, eggs, processed food, and refined sugars. Therefore, it makes sense that eating a diet high in plant fiber causes our beneficial bacteria to multiply while eating less fiber causes them to starve away.


One of the most important functions of our good bacteria is the production of anti-inflammatory, anti-cancer short chain fatty acids through the fermentation of dietary fiber. The major short chain fatty acids include acetate, butyrate and propionate.


Butyrate appears to be the most important of the short chain fatty acids due to its incredible health benefits.  Our entire gut is made up of 3000 square feet, but only a single cell layer separates our inner world from the outer world. The primary fuel that keeps this single cell layer alive is butyrate. Butyrate not only maintains the integrity of our intestinal lining – it also reduces systemic inflammation, aids in eliminating cancer cells, inhibits the growth of pathogenic bacteria, stimulates appetite-lowering hormones, and promotes fat burning in muscle cells.


Plant-based versus animal-based diets


Studies comparing plant-based diets to animal-based diets have found that just five days on a diet high in animal fat and low in fiber caused an increase in bile-tolerant bacteria, which are linked to inflammatory bowel disease. This diet also resulted the production of more secondary bile acids, which are carcinogenic compounds formed when bacteria metabolize bile, and fewer beneficial fiber-eating bacteria. Moreover, two weeks of switching to a diet high in fiber and complex carbohydrates results in a greater diversity of gut bacteria (a very good thing), increases fiber-eating bacteria, lowers inflammatory markers in the colon, and causes a 70% decrease in the production of secondary bile acids.


Researchers have also  found that certain gut bacteria can take choline and carnitine-rich foods – meat, eggs, and dairy- and convert them into a toxic compound called trimethylamine N-oxide (TMAO).  TMAO may increase our risk of heart disease, stroke, and kidney failure.  People eating more plant-based diets have lower blood concentrations of TMAO.  People who regularly eat meat don’t foster the specific gut microbes that produce TMAO.


Growing a healthy gut garden


In order to establish a healthy and diverse balance of gut bacteria and optimize the production of anti-inflammatory, anti-cancer short chain fatty acids, we must ensure a high intake of plant foods. How else are we going to feed the good guys?


Start by following these guidelines:


  • Consume Healthy Carbs: Plants are rich in fiber and resistant starch, which feed our beneficial microbes. These are called PREBIOTICS. The richest sources of prebiotics are whole grains, beans, asparagus, artichokes, beans, green bananas, sweet potatoes, leeks, onions, and garlic.


  • Include fermented foods in your daily diet: Fermented foods contain live cultures of bacteria and help to repopulate our intestines with good bacteria. These foods are called PROBIOTICS. Probiotic foods include sauerkraut, kimchi, kombucha, non-dairy yogurts, tempeh, raw apple cider vinegar, and miso paste.


  • Take a robust probiotic: Taking probiotics in pill form can be beneficial, however the most important way to increase the population of our resident beneficial microbes is to feed them well by eating a fiber-rich diet!

             How to look for a good probiotic:

  1.    Ensure that it is human-strain
  2.    Look for at least 25 billion CFU (colony forming units)
  3.    Must contain strains lactobacillus and bifidobacteria
  4.    Do your research: Are they ary clinical trials on your condition and the efficacy of probiotics?
  5.    Should have expiration date


  • Manage your animal protein intake


– High-fat/high-sugar/high animal protein diet: Results in less microbial diversity and more species that are           associated with diarrhea, obesity, and allergies

– High-fiber diet: Results in higher levels of short-chain fatty acids that protect against inflammation and more species associated with being lean


  • Avoid Sugar & Artificial Sweeteners


– Can lead to overgrowth of pathogenic bacteria and yeast

– Artificial sweeteners: Cause changes in gut bacteria that promote glucose intolerance and insulin resistance












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Comments 2

  1. Richard Wei MD
    November 28, 2018

    An amazing article on why your gut microbiome is so important in maintaining your health! This is a well researched article that can educate us all on the relationship diet has to your health. Well done Hanna!

    1. November 29, 2018

      Thank you so much for your insight and compliment, Dr. Wei!

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