Your Gut And You, Part II – The Gut Microbiome

Gut Microbiome2

Time to look at the Gut Microbiome!

IN Part I of this gutsy series, I discussed how what we eat determines levels of inflammation and disease. But there’s another chapter in the story, which plays an equally important role. If you thought the fact that 80% of the immune system is in the gut was crazy, consider this: about 90% of your cells are bacteria, not actually you! That’s right… there are billions of bacteria living in you (over 25,000 species!), and they affect your digestive system, immunity, and health in more ways than you may realize.


Like any good story (for that’s what life is, in retrospect) there are the good guys, and there are the bad guys. The good bacteria live in symbiosis with your system. Humans get their first major blast of these fellows at birth, as the infant travels through the birth canal and is exposed to the mother’s gut bacteria. After birth, bacteria are continually introduced to the growing baby through the natural environment, as well as from the saliva of other humans: there’s a reason we kiss babies! (And lovers! A 2014 Microbiome Journal study entitled Shaping the oral macrobiota through intimate kissing, found “an average total bacterial transfer of 80 million bacteria per intimate kiss of 10 seconds.”)

A person’s unique gut microbiome stabilizes around 1 year of age.

These good bacteria set up shop in the body’s system, colonizing real estate in the 200 m² that is your gut. You feed them stuff like fiber and butter, and in return, they help you digest your food, produce butyrate (a form of energy), and support your immune system. They also crowd out the bad, nasty bacteria, which produce toxins, drain your energy, and make you sick.


The ancestral, Paleolithic diet encouraged an abundance of good guy bacteria, obtained from natural births and soil covered food. Yep, eating a little dirt here and there was a good thing! As a result, the healthy gut microbiome thrived, promoting health for the host (that’s you!). The overuse of sanitation today, however, means less exposure to good bacteria, while encouraging resistant strains of bad bacteria. It makes the body’s digestive system weak, sterile, and less adept at dealing with pathogens. The prevalence of C-sections also means babies are often not inoculated with the necessary good bacteria in the first place. Talk about starting off on the wrong foot! Perhaps worse, the constant use of systemic antibiotics today wreaks havoc on the gut microbiome, wiping out populations of good bacteria which keep us healthy. How often do you go to the doctor, sick from a virus, and are prescribed an antibiotic? Not only does the antibiotic do nothing for the virus, it also wipes out the guys which were helping your immune system in the first place! Say hello to gut dysbiosis! (This is not a good thing.)


Furthermore, gut bacteria may also play a prominent role in weight gain and weight loss. Two major sources of gut bacteria include Bacteroides  and Firmicutes. Bacteroides may be the “thin people” bacteria, while firmicutes may be the “fat people” bacteria. Obese people tend to have more firmicutes, and less bacteroides. The weight gain could be due, in part, to the fact that firmicutes are able to extract more energy (calories) from food. In scientific studies, researchers have taken gut bacteria from sets of twins in which one is fat, the other thin. When they transplant the different gut bacteria into mice, the rodents who get bacteria from the thin twin lose weight, while the rodents who get bacteria from the fat twin gain weight!


  • Antibiotics
  • Antibacterials
  • C-sections
  • Environmental Toxins, Pesticides
  • Stress


  • You have digestive problems.
  • You burp after meals.
  • You have bouts of constipation or diarrhea.
  • You are not regular in regards to elimination.
  • You have skin issues.
  • Your have erratic energy levels.
  • And basically… anything else wrong with you.


In order to foster a good bacteria community inside yourself, you need to welcome some bacteria into your life! Surprise!

Soil Based Bacteria (“HSOs”): Some probiotic bacteria are transient – they do not set up permament residence in your gut, and thus you may need to regularly ingest them for beneficial effects. This includes the bacteria we get from “dirty” food. To get these little buggers, consider eating fresh, organic, unwashed fruit and veggies. You can also supplement with soil-based probiotic products such as Prescript Assist, which I recently started taking. (Note: There is some debate as to whether these soil-based organisms can too easily become “opportunistic” and take-over your system in a negative way. The jury is still out.)

Non-HSOs: Other types of bacteria, like those found in fermented foods, do colonize, and set up more permanent neighborhood in your gut. While there are an estimated 3.3 million different types of bacteria, here are a few of the biggies, at least when it comes to YOU (Let’s be selfish!):

Lactobacillus: This is one of the most common bacteria found in probiotics, and includes the good guy lactobacilluss acidophilus. Lactobacillus acidophilus helps you digest your food, and produces hydrogen peroxide and lactic acid in the process, which can stop bad bacteria from taking over. Lactobacillus also supports the immune system, and antibody production. It’s good for people with lactose intolerance, because it produces lactase, which digests lactose. It also may help with food allergies, skin conditions, IBS, as well as many other health problems. Lactobacillus is commonly found in yogurt with live active cultures, and also in probiotic supplements.

Bifidobacteria: These guys are one of the major players in the gut biome, and make up about 6% of your stool (and I’m not talking about the wooden chair thing). Bifidobacteria support the gut, break down lactose, and help with vitamin and nutrient absorption. Different strains of bifidobacteria can help your immune system, keep you regular, digest carbohydrates, and help resolve IBS.

Streptococcus: When you think streptococcus, you may think strep throat. Granted, while some strains of streptococcus may go rogue, the main strains are largely beneficial, and support good gut health, dairy digestion, and reduce inflammation.

Saccharomyces Boulardii: This probiotic can be particularly helpful in treating traveler’s diarrhea, and may help combat C. difficile infection. It is only found naturally in high quantities in populations consuming lots of lychee fruit. I just thought that was kinda interesting.


  • Raw, Unpasteurized Sauerkraut (My new obsession is the Rejuvenative Foods brand)
  • Raw, Unpasteurized Kimchi
  • Raw, Unpasteurized Miso
  • Raw, Unpasteurized Tempeh
  • Raw, Unpasteurized Kefir
  • Raw, Unpasteurized Yogurt
  • Red Wine (oh hey!)

In addition to introducing the actual guys themselves (the probiotics), you want to keep them well fed. That’s where prebiotics come into play: indigestible bits of food (like inulin and resistant starch) which support and feed your gut microbes. Common Paleo-friendly foods featuring prebiotics include asparagus, bananas, chicory, garlic, onion, and Jerusalem artichokeResistant starches include cooked and then cooled sweet potatoes, green bananas, potato starch, and plantains. 

Note: Do not go crazy and consume large amounts of prebiotics at once, as this may result in digestive distress. It also may encourage probiotics to go oppurtunitistc, yielding or exacerbating conditions like SIBO (small intestinal bacteria overgrowth). Instead, try implementing smaller amounts here and there into your meals, and see how you react.


The gut microbiome affects our daily lives on a profound level, and is easily disrupted in today’s sanitized, toxic, antibiotic-fueled society. Since the microbiome is diverse, varied, and barely understood, there’s not one probiotic which will magically work for everyone. (Sad day.) I suggest trying out different probiotics, until you find one that suits your system. Even more important, make an effort to regularly consume non-pasteurized, raw fermented foods (with live cultures), as well as fibrous prebiotics. Avoid things which negatively impact the gut microbiome, such as stress, environmental toxins, pesticides, and especially antibiotics. (In PART III of this series, I’ll discuss specific supplements to foster a healthy gut microbiome, as well as natural alternatives to antibiotics.)

Now go kiss some healthy people, get a little dirty, and support that microbiome!

For a super intense and awesome overview of how gut bacteria affects your life, and especially your brain, I recommend Dr. David Perlmutter’s Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain – for Life!


Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain – for Life (David Perlmutter)
Fix Your Gut: A Book Dedicated to “Fixing” All Your Digestive Ailments and Concerns (John Brisson)
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