Gut Flora and Your Healthy Immune System

Last week, I discussed the importance of gut flora in the digestion of food while briefly touching on its role in early immunity, including the development of asthma and eczema – both of which are immune issues that appear to be exacerbated or caused by disrupted gut flora in children. But it goes much further than “just” asthma and eczema. Our gut flora plays a massive role in mediating our entire immune response. Think about this little factoid: the human gastro-intestinal tract houses the bulk of the human immune system, about 70% of it. And foreign gut flora actually aids and abets our innate immune response system by improving the function of our mucosal immune system and providing a physical barrier to invading microbiota. Before I get into that, though, let’s go over what we mean by immune system.

Some time back, I wrote a post discussing the three tiers of the human immune system:

  1. Anatomical barriers – Skin is the basic line of defense, along with mucus membranes and other physical responses like sweat, tears, and salivation, against the intrusion of foreign bodies and antigens.
  2. Innate/non-specific immune system – The innate immune system is the broad, generic response to bacteria and viruses that have made it past the anatomical barriers. Imagine bacteria entering through an open wound and the resultant inflammation, which is pretty much the body’s attempt at a catch-all response. Technically, the physical barriers are included in the innate system.
  3. Adaptive/specific immune system – The immune system can learn and improve its response to specific microbes over time and with repeated exposure; this is the adaptive immune system, and it’s only present in jawed vertebrates.

It’s generally accepted that gut flora affects and informs our immune systems, and how it does so, though a complicated, multi-faceted process, is beginning to be teased out by researchers.

Intestinal flora helps determine the quality of our mucosal immune system in several ways. First, it provides a physical barrier to colonization by foreign, deleterious microbes. As I mentioned earlier, infants receive the lion’s share of their gut flora from the mother (and surrounding environment) during birth and for the first year or so. This is a crucial time, because the first bacteria to gain a foothold are able to establish a long-lasting, mutually beneficial relationship with the host (that’s us). Good bacteria settles in and keeps bad bacteria out – for life (ideally, barring disruption of the population by poor diet and excessive antibiotic usage), which is why early intestinal colonization is so incredibly important for healthy function later in life. Though we’re talking tiny, invisible organisms, living quarters in the gut are still finite, and there are limits to how many microbes can be established. Compromised gut flora populations, for example, can allow harmful yeasts and bacteria to flourish. Healthy gut flora populations protect against invading microbes by simply taking up space and generally being more proficient at obtaining nutrients than the intruders. They’re playing defense, and informed, experienced defenders who know their way around always have the advantage.

Next, intestinal flora communicates with certain features of the immune system to help them focus on invading microbes. Ever wonder how our immune systems determine which bacteria to attack and which to ignore? After all, foreign microbes are foreign microbes, and immune cells aren’t “intelligent.” There’s got to be a mechanism behind it, some sort of “safe word” that causes immune cells to pass over the trillions of foreign bacteria residing in the gut. Good bacteria talks to the lymph nodes and provides a safe word, and the lymph nodes’ stromal cells produce “normal cell” antigens that tell the immune system not to attack the good bacteria. This conserves resources and improves the immune response by making it more efficient.

Intestinal flora can even influence the growth and formation of organs crucial to proper immune function. Take the thymus, for example, the primary function of which is to produce T-lymphocytes, also known as T-cells. T-cells are a type of white blood cell that has two functions. Killer T-cells destroy the body’s own cells that have been infected by viruses or bacteria; this prevents the offending microbe from replicating and causing more damage. Helper T-cells stimulate the production of antibodies. Both are vital, and both are made possible by the thymus. The thymus, in turn, is dependent on intestinal flora: formula-fed infants have smaller, less productive thymuses than breastfed infants. Okay, but how do we know that it’s the bacteria in breast milk making a difference? What’s one big thing that sets breast milk apart from formula? Beneficial bacteria, specifically Bifidobacteria, which is only present in breast milk. One recent study confirmed the effect of bacteria on thymus size when it compared thymus sizes in breastfed infants, standard formula-fed infants, and infants fed a fermented formula populated with Bifidobacteria. Infants given standard formula had smaller thymuses than infants in the other two groups; thymuses in infants given the fermented, bacteria-rich formula were similar in size and function to breastfed infants.

The study (PDF) of germ-free mice offers clear evidence that the presence of intestinal microbiota impacts the development of immune systems. Mice raised in isolation chambers, completely free of gut flora, exhibit a host of immunodeficiences: systemic lymphopenia, or low levels of lymphocytes, a kind of white blood cell extremely important to immune function; hypoplastic, or underdeveloped, lymphoid structures with compromised immune function; and poorly formed high endothelial venules, which are crucial pathways for the normal immune cell response. Colonization of germ-free mice with normal levels and species of gut flora, for the most part, normalizes immune function and structure.

90% of cells in the human body are microbial; a mere 10% are “human.” Perhaps it’s time we start redefining exactly what it means to be human. We couldn’t function without foreign gut flora. We’d be quivering and helpless, chronic hypochondriacs by necessity. Any variance in diet would probably immobilize us, and the mildest, gentlest pathogen would have its way with our tender bodies. It would be a bad scene all around.

Every organism – at least the larger, multi-cellular ones – has similar relationships with foreign microbes. The difference with humans is that we are consciously aware of their existence, and we devise methods to eliminate them from our bodies and our environment. Wild animals do not fret about such things; they live in ignorance of the teeming bacterial hordes handling the internal machinations. Oh, they may have protectionist instincts, like shying away from harmful or spoiled food, but they aren’t making the conscious decision to avoid bacteria. We have antibiotics, and soap, and surgical gloves, and gas masks. Our entire modern existence can perhaps be described as the avoidance of nature. Nature’s a scary place, with dark, dismal caves, dangerous predators, poisonous plants, and uncertainty, so we built walls, planted crops, tamed animals, and discovered fire. Humans are of “mother nature,” but we number in the billions only because we rejected and excluded her. And that’s the tricky part of being human, isn’t it?

Clearly, the best path for proper immunity is the early establishment of a healthy population of gut flora, ideally initiated immediately after birth. If you’re reading this, you’ve most likely been born, probably for quite some time now, but that doesn’t mean you should throw in the towel. On the contrary, we adults, more than anyone else, need to know the importance of gut flora. If we have children, it’s up to us to ensure they receive the proper exposure to beneficial bacteria. As for adults, the avoidance of sugar, vegetable oils, and lectin-rich grains and legumes to the inclusion of animal fat, protein, Primal starches, and leafy vegetables is a safe way to promote a healthy gut. Eating fermented foods and trying probiotic supplements may also help.

For anyone who’s still interested in this subject, I’d strongly advise you check out Dr. Art Ayer’s fantastic blog, Cooling Inflammation. Art suggests chronic, systemic inflammation stemming from disrupted gut flora as the root of most, if not all, diseases. He may be onto something here.

Let me know your thoughts in the comment board. Thanks for reading!

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

If you'd like to add an avatar to all of your comments click here!