My Blog.

The Care and Feeding of the Immune System

kitten exploring plant
Photo: Dimitri Houtteman on Unsplash

Having considered how important the microbiome, all those lovely bugs in our guts, is to our immune system, we can see how easy it might be to have some influence over it.

The digestive system, as we know it, isn’t just for food processing. It does a host of other things.

Our gut bugs, properly called “intestinal flora” take up residence in the delicate folds of our intestinal walls. Once settled, the work they do is incredible.

Obviously they help to digest and absorb nutrients from food. Like the skin, they also stand as a barrier against invaders – bad bacteria, harmful viruses, and injurious parasite. In each category there are good guys, so they also differentiate between friend and foe.

Good Bugs’ Work

The bugs also help with detoxification and act like a second liver. Fewer good bugs in the gut means more work for the liver itself. They help handle stress through their effect on our hormones, and help us with a good night’s sleep. A cool gut is also a cool body, as these bugs also assist us in the control of inflammation.

More important, the gut and all its bacteria have a profound influence on the immune system, and is actually our biggest immune system organ, according to Dr. Perlmutter. It does this by actually regulating the immune response. Why is this important to immunity? It’s because when we are attacked by an invader, most recently the dreaded COVID-19 virus, the body begins its response (so we believe currently) with the innate system’s non-specific response, which includes fire. We start a fever to try to burn out the enemy at the gate.

This is not the “cytokine storm” we are starting to hear about. That’s a wild-fire that adopts a scorched earth policy. A healthy gut with plenty of healthy bugs helps our body to produce the inflammatory response, which has its own shut off valves. It sets fire to the enemy, not the house. And it puts the fire out when the job is done.

If the gut is not healthy, or we lack the full complement of good bugs, we can lose ground to the enemy invaders. This makes it harder to recover from specific bacterial or viral agents.

Photo: Austin Ban on Unsplash

This lets us imagine that we have only good bugs in our system (if we are already healthy). Not so, according to Perlmutter. We contain at every moment through our lives potentially life-threatening organisms that are only held in check by a healthy immune system.

The important thing is that everything is in balance. If our body went after each one of these, it would be like a eugenicist trying to cleanse the world of all its undesirables. And, really, we’ve been there, done that. And it never works out well.

3 Enemies of the Immune System

  1. Anything that kills or harms the composition of bacterial colonies. This includes chemicals and ingredients in our food (like preservatives, sugar and gluten), our water (chlorine) and drugs like antibiotics.
  2. A lack of nutrients that support many families of good bugs, and feeding ourselves with junk that bad bugs love. We starve out the good guys and let the trouble makers proliferate.
  3. Stress. Ah yes. Research on this single beastie continues and the news about it gets worse and worse.

But, you can imagine looking at this list, that it is not like watching the news. It is not hopeless, and there’s a great deal we can do to improve our situation.

Are preservatives, chlorine and antibiotics necessary? Yes, indeedy they are. The trick is to use them properly and not in excess.

Feeding the Immune System

So now we can see that improving our immune system may not be complicated after all. In very simple terms, we begin to reverse the effects of the immune system’s enemies. We can take pro-biotics to repopulate the system when the good bugs have been killed by antibiotics or chemical influences. We need to remember, though, that they also need food.

Photo: Amanda Kirsh from Burst

These are the pre-biotics that include fermented foods – sauerkraut, yogurt and kefir, kombucha or tempeh, kimchi and pickled anything. But there are foods rich in prebiotics, such as onions, garlic, leeks, asparagus and chicory root. If you haven’t got into dandelion greens yet, they are a powerhouse of goodness. (My favourite is to make pesto out of a handful of leaves.)

Coffee, tea, wine and chocolate are back on the menu to loud applause. This is because of their polyphenols, which are powerful antioxidants that help to protect the body and the microbiome. They also have anti-inflammatory properties that keep the right amount of fire going in their proper hearths.


So far, so good. But that last point is the trickiest one; coming away from the chronic, unremitting stress that is part of our lives. The most difficult part of this balance is that stress affects the gut bacteria, but the guts also affect our levels of stress, so that we can create one mighty tangle.

Stress hormones (norepinephrine especially) can alter the behaviour of the gut’s bugs, making aggressive and dangerous zombies out of perfectly nice neighbours. This shift can quickly occur when for example, under super stress, we have an attack of IBS and bam, the whole gut evacuates. Most people have experienced this at least once. It’s the body’s response to a sudden super stress, because when the tiger appears in front of you, the last thing you need is bladder, stomach or bowel contents slowing you down.

When we’re already under stress, and a new stress comes along, or that last straw is gently placed on top of everything else, we can over react, flying into a totally inappropriate reaction than is called for in the situation. This affects our relationships, both personal and professional.

Stress, therefore, is something to be handled carefully. Learning how to breathe deeply and calmly is the first and easiest step. The breath is built right into the body, and is simple and effective medicine for as long as you are on the planet. If you don’t or can’t meditate, learn to now. Your physical and emotional health depend on it.


Dr. Permutter suggests 5 important supplements that work in sync with gut bacteria. They are:

  • DHA (Omega 3): particularly for brain health
  • Turmeric: an anti-inflammatory and antioxidant, it also helps improve sugar metabolism
  • Coconut oil: to reduce inflammation
  • Alpha-lipoic acid (in with your Omegas): powerful antioxidant for the brain
  • Vitamin D: actually a hormone, this “vitamin” has far-reaching benefits beyond bone health. It protects our neurons in the brain by regulating the gut bacteria. In North America, we tend to get enough in the summer (if not slathered in sunscreen), but overall we are thought to be at deficient levels, especially over the long winter (which includes any day our skin is covered in cloth – which tends to be 10 months of the year).

Vitamin D

Important to the current fear of COVID-19, sufficient vitamin D stores allow the body to build cathelecidins . These play a crucial role in both the innate and adaptive systems, in three ways;

  • they help to eliminate harmful invaders (very accurate snipers)
  • they help to modulate our own immune response, (calm and measured response) and
  • they promote wound healing, (a MASH tent right on the battlefield).

If we are deficient in vitamin D, seasonally or generally, we can’t hope to harness this crucial fighting power. This happens to many North Americans over winter, as we go indoors for several months at a time. Just imagine what happened to us all during a lengthy lock down. 10 years ago, taking vitamin D was a scandalous idea, with a modest recommended daily dose of about 2000 IUs. Now, doctors are coming around to it. (Be careful, though. 15 minutes in the sun will earn you 10,000 units, but taking that much orally will push you into toxic levels. See a nutritionist.)

It is even being suggested that those deficient in vitamin D, and therefore not manufacturing cathelecidins, do not do well with the dreaded COVID. So, if you only take one supplement, this is the one to consider, for the moment anyway.

Otherwise, protect your guts and their critters. Eat the way your grandma taught you to (except for the bread, because wheat has been bastardized since then). Sleep well, live calmly, filter the chlorine out of your tap water and get some sunshine.

Keep your fear down, too. Fear is one of our greatest stressors, and has the power, all by lonesome, to blow great holes in our immune defenses .

  • References:
  • Brain Maker, by Dr. David Perlmutter
  • The Mind-Gut Connection, by Dr. Emeran Mayer
  • Science Direct

Share this post with your friends

Leave a Comment

Your email address will not be published. Required fields are marked *


Subscribe to Newsletter

Subscribe to receive my latest updates and blog posts direct to your inbox.
You’ll also have access to my free eBook

Scroll to Top