The Large Intestine: Your Body’s Command Center

large-intestineThe human body is a marvelous structure. All of its different organs work around the clock to keep it alive and moving. In order to achieve this feat, they work together and allocate labor so that each organ gets to do what it’s good at: the liver is trusted on to filter out toxins from the bloodstream and produce glucose when it’s needed; the heart is given the task of “controlling” the circulatory system and pumping blood out to the various organs of the body; and the lungs are put in charge of absorbing oxygen from inhaled air and expelling carbon dioxide that has accumulated from cellular production of energy.

Who or what is in charge of directing and controlling this complex biological system? The standard answer to this question would be the brain. When growing up, most of us learn that the brain is the command center of the human body: the organ that is in charge of controlling what goes on in the various parts of the complex biological system of Homo sapiens.

There is no doubt that the brain plays a vital role in shaping how the human body functions and behaves. You wouldn’t be wrong if you said that it acts as a command center. With that said, another organ may actually be even more important than the brain in some respects, particularly in the context of health and disease. The organ I’m talking about is the large intestine, AKA the colon.

Much of what goes on in the human brain is determined by what goes on in the microbial ecosystem of the large intestine; hence, it could be argued that the primary command center of the human body is not the brain, but rather the intestine, in particular the colon. This idea may seem a little scary to some people, seeing as it would imply that they are not in complete control of their actions and behavior. However, other probably find this concept fascinating and liberating, perhaps because they realise that their ability to manipulate what goes on in their brain is much greater than they previously thought.

The large intestine is finally starting to get the attention it deserves

I think most people will find it surprising to hear that the large intestine plays such a vital role in controlling what goes on inside their body. Some have probably never paid much attention to the workings of their lower gut and know very little about what the colon actually does.

This isn’t surprising, as the large intestine historically has received little attention within science and medicine. When compared to the brain, liver, and heart, the large intestine has been largely neglected.

This is now changing. Over the two most recent decades, the large intestine has gone through a renaissance and has made its way onto the center of the stage of science, brightly illuminated by spotlights.

With that said, there’s still a way to go before the large intestine is given the attention it deserves. While most scientists now acknowledge that this organ is vitally important, the average Joe is still very much in the dark when it comes to the significance of the colon. He goes by his daily business, rarely thinking about what goes on deep in the long tube that runs through his body.

This can be both a good and a bad thing. The good thing is that he’s got one less thing to stress and think about. The bad thing is that he overlooks a very important aspect of his health.

A centrally located organ

As I see it, the large intestine is at the center of the network of organs that make up the biological system that is the human body. It controls and directs much of what goes on in the system.

How can that be? How can one part of the system have such a profound impact on all the rest? In order to answer this question, we must examine the properties of the various parts of the system in order to find out what makes the colon special.

The colon is a unique organ in that it harbors more than 90% of the genes that make up the superorganism that is the human body, as well as most of the cells (1, 2). Unlike many other bodily organs, it’s not packed with human cells; rather, it’s a reservoir of bacterial ones.

This is what makes it special. Other organs, such as the small intestine and lungs, are also home to microbes; however, the density of their microbial communities fade in comparison to that of the microbial community found in the colon. The microbial communities of the lungs and small intestine are like small villages when compared to the gigantic city that is the colonic microbiota.

So, to answer the question posed at the beginning of this section: the reason the large intestine has such a profound impact on the rest of the system that is the human body is that it is home to trillions of microorganisms that break down food, fight against each other, stimulate the immune system of the host (which is largely found in and around the intestine), and produce a long list of hormones, nutrients, and neurotransmitters that enter into the circulation of the host and reach various organs around the body. Via these actions, the microbes profoundly impact the behavior, mood, thoughts, energy levels, and sexual activity of the host (3, 4, 5, 6).

Is your command center organized and well-staffed?

Just like any other command center, the large intestine needs to be organized and well-staffed to do its job properly. If some positions are vacant or there is much disorder at the workplace, all of the things that are under the control of the command center will be negatively affected: the immune system won’t function properly, the processes in the brain that regulate appetite could spin out of control, the beta-cells of the pancreas will gradually degrade, and the wall of the intestine will become leaky.

Unfortunately, this is what’s happening inside the body of many modern humans. As a result of excessive use of antibiotics, consumption of processed foods, indoor living, and many other factors associated with our modern way of life, the command center of the body of the modern man has turned into a toxic place: it’s under-staffed, some of the workers occupy positions that they are not qualified for, and there is much disarray. Hence, it shouldn’t come as a surprise that the rates of mood disorders, immune-related diseases, and metabolic conditions have skyrocketed lately.

If your large intestine is healthy, then chances are the rest of your body is healthy as well

I would go as far as to say that the health of your large intestine is likely to be the number one determinant of your overall health. If your large intestine, including the microbiota it holds, is unhealthy, the rest of your body will also be unhealthy, whereas if your colon and colonic microbiota are healthy, then chances are pretty high that the rest of your body is healthy as well.

Perhaps needless to say, if you’ve recently suffered a physical injury or have a genetic disease of some sort, having a healthy colon isn’t going to be sufficient to make you virile and physically robust. However, when these unlikely situations are kept out of the equation, then the earlier statements tend to hold true.

One of the really great things about ancestral-style diets is that they are gut friendly: they are low in antinutrients, grain fiber, and other substances that can irritate the intestine; they are high in soluble fiber, which reaches the large intestine intact and ensures that the workers down there get the energy they need to keep doing their job; and they are low in refined sugar, trans-fats, emulsifiers, and other compounds that are known to negatively affect the composition of the microbial ecosystem of the gut.

There is a limit to how much an ancestral diet can do though. If the command center deep in your gut is under-staffed or has been taken over by workers with bad intentions; simply eating a healthy diet may not be sufficient to make the workplace well-organized. You may also have to bring some new, well-qualified workers into the place, such as by eating small quantities of a diversity of fermented vegetables, performing one or more microbiota transplants, and/or exposing yourself to bacteria associated with healthy plants, humans, and pets.

Not all of these microbes are going to survive past the army of acids that are found in your stomach, but some will. Some of these again may travel all the way down to the large intestine and find an available spot somewhere at the controls of the command center, thereby becoming a part of the superorganism that is you.


  1. We only become aware of our most important organ when things go wrong with it, as you say, so many people now with auto immune issues and IBS type illnesses. I’m one of those people that has found that a strict Paleo diet (even an auto immune Paleo diet) is not enough to fix my food intolerances/IBS. And despite much research, following a strict diet for well over a year (Paleo for 3 years before that) and cleaning out my house and lifestyle, its not enough! I started with a wheat reaction that I’ve perhaps had all my life, that in my 40s spread to all grains, all starches, thickeners and gums, then chocolate, and now recently also wine… I feel like I’m cascading despise doing everything I can to heal my gut. When i look at what I’m reacting to It’s the things that are not in the diet, or in the grey area of Paleo! So maybe my body is telling me that these things are not ok… but it’s terribly frustrating and even scary when I eat once accidentally (thickeners in almond milk, a bean salad, potatoes) but I fight on, reading and researching as much as i can. Hopefully one day i can return to eating starches (I don’t care if I can’t eat grains again) but starches like potatoes I’d really like to not react to.

    • Lucy, have you read my articles on microbiome restoration? It sounds to me like your gut microbiota is in a sorry state.

      A healthy diet will only get you so far. You can eat the healthiest foods on the planet, it’s not going to make you healthy if your microbiota is imbalanced and degraded.

      You might find the following articles helpful:
      The Foundation for Good Health: Species-Appropriate Diet + Species-Appropriate Microbiome
      Microbiome restoration: Repair and Diversify Your Microbiome

      • I’ll read/re-read them now. Thank you! The difficulty is being intolerant/allergic to starches does not make it easy to eat probiotic and resistant starch foods. I’ve spent the last few years, but especially the last year (strictly!) eating fermented foods, growing a few vegetables, playing in my garden with my dog and composting. I’ve had supplements like colostrum and l-glutamine and taken probiotics. I regularly eat yoghurt… I’ve fasted for five days…. I get sun, sleep and low stress. Nothing seems to help. I keep on. Determined. But honestly its hard. In all other regards and as long as I stay away from the starches I feel good! But as soon as I eat one I’m back to square one for about a week with multiple symptoms involving my sinuses digestion and skin. I’m going to try fasting again as soon as I have the perfect opportunity as this is where I’m putting my main hope… thanks for the links!

  2. Eric, my Instagram account is @eating_to_heal and I document all of my attempts at healing and everything I eat… just to document my attempts and my flares. its my healing dairy. Are you on Insta?

  3. Alessio says:

    Also small intestine still hasn’t had the attention that deserves.
    I completely agree with Spreadbury’s research that points out how things that happen in the small intestin are crucial.
    Refined stuff seem to have even more impact there, favouring SIBO and other pathogenic overgrowth that generates a nasty cascade of bad events, systemic inflammation that spread through the vagus nerve.

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