[THE SEVEN] 5. Take Care of Your (100 Trillion) Gut Bacteria


THE SEVEN: Principles Of Nutrition For Slowing Biological Aging

This series is a distillation of our decades of researching, experimenting and generally obsessing over the question:

What is the ideal way to nourish a human body if the aim is to slow the progression of biological aging?

  1. Identify + Remove Dietary Allergens and Toxins
  2. The Low-Carbohydrate, Metabolic-Flexibility Diet
  3. How To Drink Water... Intelligently
  4. Reducing The Cognitive Overhead Of Eating Well (i.e. Staple Meals)
  5. Take Care Of Your (100 Trillion) Gut Bacteria
  6. Eating Nothing (i.e. Time-Restricted Eating)
  7. The Truly Essential Supplements

When was the last time you took a course of antibiotics?  

If it was inside the last 5 years and you didn’t take well-informed measures to rebuild your gut bacteria afterwards, odds are your bacteria are still out of balance and your health is less than what it could be as a result. 

Even if you’ve been fortunate (and smart?) enough to avoid antibiotics entirely, our modern diet and lifestyle are such that your gut flora are still likely a long way from optimally healthy.

Given the rate at which microbiologists are discovering new ways that the bacteria in our gut impact our health - physiological, mental and emotional - it would not surprise me in the least if this principle becomes the clear, stand-alone Principle #1 in five or ten years. 

This is wild to consider given that, just a few decades ago, microbiologists regarded the bacteria in our gut (known as our gut “microbiome”) as little more than food digesters.

Now we know these bacteria are in constant communication with our immune, endocrine and nervous systems - and ideal functioning of these systems is impossible if our microbiome is unhealthy.

Microbiologists readily admit that they're only at the very beginning of understanding the relationship between our body/brain and our gut microbiome, and we’re virtually assured of discovering even deeper levels of interconnection in the years ahead.

Still even with our limited knowledge of these relationships, this much is absolutely clear: The health of our gut flora is really important to the health of our bodies and brains.

Take Care of Your Gut Flora: The Fundamentals

The Fundamentals: Health Benefits

Stronger, More Resilient Immune System

Improved Digestion + Nutrient Absorption

Balanced Hunger + Appetite

Leaner Body Composition

Improved Insulin Sensitivity

Improved Mood + Cognitive Function


Stronger, More Resilient Immune System

The ways in which immune function is intertwined with gut flora health are wildly complex. What’s clear, though, is that our body’s immune systems interact constantly with our gut and skin microbiota, and that this relationship begins at the very beginning of life.

The exact mechanisms remain unclear, but microbiologists now believe that our gut and skin flora essentially “train” our body’s immune cells to better recognize which viruses and bacteria are genuine threats and which are not.

Looking more holistically at immunity, our gut and skin flora effectively act as our immune system’s “first line of defense”, eliminating pathogenic bacteria and viruses before they have the opportunity to enter the body and potentially create systemic infection. Estimates are that gut and skin flora account for something on the order of 80% of our holistic immune protection. [1]

To illustrate this point, research has shown that unhealthy/unbalanced gut flora is correlated with greater susceptibility to infectious disease, autoimmune disease, and a number of other chronic conditions. [2]

Improved Digestion + Nutrient Absorption

Gut bacteria carry out the critical task of converting indigestible fibers and starches from our foods into a wealth of critical nutrients, including short-chain fatty acids (which serve as high-quality fuel for the brain) and multiple vitamins (particularly B and K vitamins).[3] This means that when you feed and nourish your gut flora, they’ll quite literally do the same for you.

Balanced Hunger + Appetite

It's an unfortunate quirk of the human body that our experience of “hunger” is rarely coincident with the body actually needing fuel or nutrients. If this was the case, there would be a LOT less obesity in the world. Rather, hunger is largely the product of certain hormones circulating in elevated levels, ghrelin (aka the hunger hormone) being the main driver.

Research has shown that the frequency and magnitude of ghrelin release are influenced greatly by the bacteria in our gut. When our gut flora are unhealthy/imbalanced, ghrelin levels can become further decoupled from our body’s need for food, and we end up eating more (and more frequently) than is healthy. Building a healthy gut microbiome reliably balances ghrelin secretion and brings hunger under control. [4]

Leaner Body Composition (+ Improved Insulin Sensitivity)

The connection between ghrelin/hunger and body composition is fairly obvious, but our gut flora also influence the body’s energy storage pathways in other, even more direct ways.

Regulation of insulin - our body’s primary hormone for directing fat/carb storage - also appears to be influenced by the health of our gut flora. In one particularly dramatic study, mice with type 2 diabetes (and thus, very poor insulin sensitivity) received fecal microbiota transplants from healthy mice, upon which, their insulin sensitivity was significantly improved.[5]

The impact of ghrelin, insulin, and associated downstream hormones on body composition is difficult to overstate, and the health of our gut flora is inextricably tied to the proper functioning of these hormones. [6] [7]

Improved Mood + Cognitive Function

Research has demonstrated a dramatic correlation between gut flora imbalance and clinical depression, chronic fatigue, and other mood disorders. The connection is unsurprising, as these disruptions of our mood and energy levels are natural downstream effects of a disrupted endocrine or immune system. Both of these systems are intimately intertwined with gut flora health (as described above).

It's far from intuitive, but research supports the idea that building a healthy gut microbiome is one of the most powerful “levers” we have to pull for improving emotional wellbeing + stability. [8][9]

Every year, we learn a bit more the workings of the “gut-brain axis", the name given to the pathways through which the gut and brain communicate. What’s most notable is that the communication goes both ways—that is, the gut is equally capable of sending neuroendocrine signals to the brain. Studies in the past ten years have demonstrated that gut flora participate directly in the modulation of the peripheral and central nervous systems, and thus that gut dysbiosis can hamper cognitive function and contribute to neurodegenerative diseases.[10]


Take Care of Your Gut Flora: Implementation

The Fundamentals: Strategies for Implementation

Supplement With The Right PRObiotic

Eat A Diversity Of PREbiotic Fibers And Starches

Don’t Take Antibiotics (unless absolutely necessary)

Avoid Non-Organic Foods

1. Supplement With The Right PRObiotic

It’s interesting to consider why it’s necessary for us to consume bacteria to maintain a healthy gut microbiome. The full answer to this question is complex (and still largely beyond scientific understanding), but the simplified answer is that our digestive system evolved getting regular exposure to bacteria, via the largely-unwashed foods our hominid forebears ate until very recently, historically speaking. Now, as we wash the dirt and bacteria from our fruits and vegetables (to our great benefit in many other ways), we need to consume beneficial bacteria (i.e. probiotics) intentionally to replicate the bacterial exposure of our ancestral past.

Also interesting is that probiotics don’t necessarily work the way you might think they would. Counterintuitively, the bacterial species in the supplements we take generally don’t themselves colonize the gut. Rather, they stimulate the beneficial bacteria that are already in your gut, which become more resilient and reproduce at a faster rate (thus outcompeting harmful species like yeasts) in response to this stimulus.

Choosing a probiotic supplement capable of exerting this effect is an unfortunately complicated undertaking. Most probiotic supplements on the market today (and essentially every product available at the grocery store) are comprised of genetically-weak bacterial species grown on a sugar medium. These probiotics reliably die in the acidity of the stomach and never reach the small intestine (where they would exert their beneficial stimulatory effect).

A new generation of probiotics attempts to address this failing by developing growing conditions in the laboratory that closely mimic the soil environments where our hominid ancestors would have plucked their food (and their “probiotic” bacteria) from. These new “spore-form” probiotics are a world more resilient and have been shown to survive the acidity of the stomach and reach the small intestine intact.

In 2017 we partnered with Microbiome Labs - one of the few labs with the equipment and technical know-how to produce spore-form probiotics - to develop a new spore-form formula with an explicit focus on improving digestion and immune function. That formula is Micro•Bios | Medical Grade Spore-Form Probiotic.

2. Eat A Diversity Of PREbiotic Fibers And Starches

As important as probiotics are, most microbiologists (and this humble author) would argue that the research points to PREbiotics being even more essential for the health of your gut flora.

Prebiotics are the indigestible fibers and starches in our foods that we’re not able to make use of directly, but our beneficial gut bacteria consume as their preferred nutrient source. When our diet contains an abundance and diversity of prebiotics, beneficial bacteria tend to thrive. Conversely, when our diet is deficient in these indigestible fibers and starches, beneficial bacteria starve and can be outcompeted by harmful species (like sugar-loving yeasts).

There are three primary categories of prebiotics; resistant starches, soluble fibers, and insoluble fibers - and consuming each of these daily will yield the best results for your flora.

Resistant Starch Foods - green plantains, jerusalem artichokes, and sushi rice (realistically, resistant starch is most easily consumed via a prebiotic supplement)

Soluble Fiber Foods - squash, potatoes, carrots, beets, sweet potatoes, turnips, parsnips, plantains, taro, and yucca

Insoluble Fibers Foods - leafy greens, bell peppers, celery, eggplant, cabbage, bok choi, Brussels sprouts, broccoli, and cauliflower

If getting each of these types of prebiotic fibers and starches in your diet each day seems like a big task, you’re not alone. I always try to include foods from the lists above in my meals, but realistically, it’s not going to happen every day, and certainly not in ideal levels. To ensure I have my prebiotic bases covered, I take Pre•Bios | Prebiotic Digestive Support + Cleanse before dinner each day, via which I get a complete set of prebiotic fibers and starches.

3. Don’t Take Antibiotics (unless absolutely necessary)

If you take our society as a whole, the use of antibiotics is unquestionably the most direct and egregious contributing factor to unhealthy gut flora. Antibiotics do not distinguish between good and bad bacterial species—taking a course of antibiotics is equivalent to dropping an atomic bomb on your microbiome. Killing off beneficial bacteria kicks off a vicious cycle, in which your digestion is compromised, your immune system suffers and your body becomes increasingly vulnerable to harmful bacteria and viruses.

Obviously, there are cases where antibiotics are absolutely necessary, but taking them is a decision that shouldn’t be made lightly. Ask your doctor (or dentist) lots of questions before accepting a prescription. Are antibiotics really necessary in this particular situation? Are they (uselessly) being prescribed to fight a viral or fungal infection? Are they being used as a preventative measure against infection, when the actual risk of this is very low? Do the benefits outweigh the adverse effects on gut flora? If you do need to take antibiotics, it’s even more crucial that you implement the rest of these practices in the following weeks and months. After a course of antibiotics, research suggests it can be helpful to take Saccharomyces boulardii, a beneficial probiotic yeast that will outcompete Candida and other fungal parasites.[11]

4. Avoid Non-Organic Foods

Non-organic produce is frequently sprayed with pesticides and herbicides (like glyphosate, aka RoundUp), which have been shown to disrupt gut flora. [12] Generally only trace amounts of these contaminants are present in produce, but they tend to accumulate in the body and their impact on gut flora is compounded over time.

Large-scale-produced meats (including organic meats) and farmed fish present even more issues. The grains these animals are fed are generally of low-quality and contain significantly more pesticide and herbicide residues. Just as these pesticides and herbicides accumulate in our own bodies, so too do they accumulate in the tissues of these animals, meaning that meats often contain contaminants in significant levels. [13]

Large-scale-produced meats and farmed fish present an additional concern as they’re almost always given antibiotics throughout their life, and residues of these remain when they make it to your dinner table.

If meats are part of your diet, try to seek out local, grass-fed, organic meats - ideally from a source where you have a chance to learn more about their animal husbandry practices. There may be some farmed fish out there that use exclusively organic feed and don’t use antibiotics, but I haven’t found one that meets these standards. Until this exists, wild-caught fish are the safest option.


[1] http://www.nature.com/nature/journal/v474/n7351/abs/nature10213.html

[2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733864/

[3] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601187/

[4] https://www.nature.com/articles/4441009a

[5] https://www.frontiersin.org/articles/10.3389/fcimb.2019.00455/full

[6] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082693/

[7] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5867888/

[8] https://pubmed.ncbi.nlm.nih.gov/24888394/

[9] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302292/

[10] https://www.frontiersin.org/articles/10.3389/fnagi.2019.00170/full

[11] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296087/

[12] https://www.sciencedirect.com/science/article/abs/pii/S0892036218300254

[13] https://link.springer.com/article/10.1007/s00003-014-0927-3 






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