The gut microbiome.

Hopefully, by now, everyone knows that there are billions (trillions?) of microbes that live in and on our bodies. The most influential of which, are the ones in our gut. This population of microbes which is comprised of bacteria, viruses, phages, fungi, protozoa and helminths are together called the gut microbiome. This population exists in a dynamic equilibrium. And this equilibrium is crucial to health.

Consider the words”dynamic equilibrium”. It implies a balance between the various species that is ever changing, in response to it’s host (you) and the substrate available (food you eat, water you drink, acid/alkaline conditions in the gut, food produced by the host for the microbes)

Everything that you do, think and feel, affects the gut microbiome, and everything that the gut microbiome does, affects you. Of course, there is no way to micromanage this chaotic orchestra made up billions of individual living things (one of which is you). However, by following very basic rules, you can turn into something as natural as the sound of waves on a seashore or it could be something like a jackhammer tearing up concrete outside your window. The choice really is yours

  • Diet
  • Sleep
  • Movement (exercise is only part of it)
  • Sun exposure
  • Microbial exposure
  • Stress management
  • Emotions

Diet for the microbiome

Massive quantities of vegetables. You’re not eating enough now. I’ll guarantee that. Use at least 3 to 4 times the volume of veggies compared to the volume of rice or wheat that you’re consuming. The more variety in vegetables you consume, the more diverse your gut microbiome, the more resilient it will be to other stressors that try to disturb it. Using the same kind of food and fiber sources daily will give an upper hand to certain species in your microbiome and let them obtain undue influence over the state of your health. This is what happens when you use grains thrice a day, every day for decades. The protein you consume is for you. The fat and fiber you consume is for your microbiome. I’m being overly simplistic here, but it is just to get the point across. It’s not enough if you feed yourself. You need to feed your microbiome intelligently if you would like to be optimally healthy.

Sleep for your microbiome

When you sleep at regular times and you synchronize your sleep with the rhythm of the sun, you change the environment inside your body too. This helps in stabilising the microbiome.

Exercise and your microbiome

The kind of exercise you do changes your microbiome. This will amplify or dampen the direct effect of exercise you are investing time in. Spend too much time or energy overdoing something, and your gut microbiome will change to one that will help you survive the stress. And the response to chronic stress, is universally, sacrificing muscle and accumulating fat. The exercise you do, should be periodized. Providing an ebb and flow, rather than a constant torrent. Or even worse floods followed by drought. A continuous drizzle of movement with interspersed periods of predictable rainy seasons and the occasional thunderstorm, would give the most pleasing results on a landscape. Similarly with exercise, you’d need constant low intensity movement (all day) interspersed with regular high intensity work that lasts for short periods (20 minutes or less) and the occasional epic session of hard work that lasts all day. Constant sitting , which we all indulge in, harms us in more ways than one. Sitting on the floor prevents that.

Squatting (special note)

Needs special mention because this aspect of human movement is now missing or deficient, for most modern humans. The Asian squat, or the third world squat, is a position of active relaxation, rather than an exercise. It should be effortless. If isn’t effortless, you need to practice it, till it becomes effortless. Squatting as a movement practice, improves flexibility and keeps the pelvic floor well aligned. This will prevent chronic low level constipation that has serious knock on effects on general health. Constipation on a daily basis causes bacterial overgrowth of certain species and also disrupts the mucosal barrier, which lets toxins enter the circulation instead of being eliminated.

Sun exposure

There are multiple clocks in the organ systems of your body that run at slightly different rates. The sun is what helps you synchronize them daily and avoid discordance. The sun is not just for vitamin D. It is the “Zeitgieber”. About which I’ve written earlier. Adequate vitamin D levels are important for a gut microbiome health too. Some bacteria rely on the host to provide the vitamin D that they themselves need.

Microbial exposure

If born through natural means, humans end up with a healthy guy microbiome that they obtain as they travel through the mother’s birth canal (provided the mother was healthy to begin with). However, in case that doesn’t happen, the body still recovers by getting exposed to all of these microbes, as you go about your daily life. The microbes find ways to enter your gut through the things we touch, the food we eat and the people we interact with. An unhealthy obsession with hygiene and sanitizing everything around us takes these opportunities away. Missing a keystone species of microbe in your gut can result in unpredictable (unfavorable?) effects. Fixing your microbiome is easy, all you need to do is get out of the way.

Stress management.

Note that I said stress management. Not elimination of stress. Stress is essential for life. Stress is what challenges you and makes you stronger. Continuous stress that you can’t recover from adequately is the killer. Intermittent stress is useful (exercise is the best example). A continually stressed animal will change it’s microbiome towards one that helps it hoard energy and reduce it’s activity. Chronic stress that alters the microbiome and makes you gain fat and reduce your physical activity is an adaptation to the stress. The adaptation becomes a problem when the stress is unrelenting.


Body systems tend to like staying where they are. At an equilibrium , while expending the least amount of energy to sustain that state. Microbiome could be considered an organ system, taking into account the effect it has and the way it works on your body. A microbiome that is used to an emotional state and it’s accompanying hormonal and dietary patterns, will tend to reinforce you to stay in that state for longer. And the reverse is true too. An emotional state will tend to foster a microbiome that suits it. The way you think and feel has an effect on your microbiome. People with depression have consistently shown a less diverse and robust gut microbiome. And an improvement in mood usually results in an improvement of the microbiota.

If you’re looking at the microbiome in the simplistic, LKG , linear style you’ll not succeed. It’s not a straight line. It’s a tangled web. It has its own system, that might not be easily decipherable for us humans at this moment. So we need to apply the basic evolutionary medicine principles. Provide the niche. And the microbiome will establish itself. Do the work. Enjoy the process, and the results will turn up on their own. Just don’t set a deadline for it. Are you looking for a manicured lawn that needs constant external input? Or are you going to try and build a vibrant permaculture garden that sustains itself on the available resources, water and climate?

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