Who’s in Control: The Human Host or the Microbiome?

superorganismYes, I know; the idea that we’re not in control of our own body seems like it could be taken right out of a science fiction movie, and the “quack alarm” is probably ringing in many people’s heads when they hear that microorganisms could manipulate our mind. However, for those who’ve been keeping up with the research on the human microbiome, the idea that bacteria are in many ways the masters, while the human host is the puppet, probably doesn’t seem so far-fetched.

As you know if you’ve been reading my posts on this blog or the dozens of articles I’ve published for other sites such as BretContreras.com, PaleoMagOnline.com, and ThePTDC.com, my writing usually revolves around the following themes: Exercise, nutrition, ancestral health, and bacteria. For many, it might seem strange to write a lot about microbiology on a health & fitness site. To explain this focus on these microscopic  organisms that dominate our planet, let me turn the clock back a couple of years.

When I first started getting interested in nutrition, I, like so many others before me, spent years clinging on to nutritional dogma. It seemed like everywhere I went for advice and information about diet and food, I received the same message: Saturated fat clogs your arteries, whole grains are the foundation of a healthy diet, breakfast is the most important meal of the day, avoiding unhealthy foods is “just” about self-discipline, etc. I thought I was doing everything right, but as I now look back, I clearly realise that I was doing pretty much everything wrong. After years of poor results from sticking to conventional health wisdom, I finally started to open my eyes, and I quickly realised that high quality information on health & fitness is definitely out there – I had just been looking in the wrong place.

Conventional nutritional wisdom was – and to a certain degree still is – so ingrained among the general public that it took some time before I realised that there are a whole bunch of intelligent researchers/scientists, bloggers, trainers, etc. out there that have a completely different perspective on things. I began to understand that evolutionary biology and ancestral health principles provide the foundation that is needed to achieve good health, and after digging into the scientific literature on my own, I discovered that many – if not most – or the conventional beliefs people hold about nutrition and health actually aren’t supported by the best science. I had started looking at fitness from an evolutionary perspective, and I realised that up until that time, I had been grasping in the dark.

This evolutionary template gives us the basis we need to make sense of pretty much everything in health & fitness – and many other aspects of life for that matter. However, it’s important to note that although the evolutionary outlook provides a powerful framework – it rarely gives us any definite answers. At the time, I still had many burning questions, and it seemed that no matter how much research I did, I couldn’t find any conclusive findings. Actually, it seemed that nobody really knew the answers to many of the questions I were asking. I had started to understand that mismatch theories are the key to understanding health & disease, and inadequate sun exposure, lower levels of physical activity, poor nutrition, and chronic stress could certainly help explain why diseases of civilization were on the rise. But in my mind, there had to be something else that I was overlooking. Something that could help explain…

  • Why so many people report symptoms of “food sensitivity/intolerance”, even when adopting a paleo-type diet.
  • Why the prevalence rates of gastrointestinal disorders such as IBS, IBD, and celiac disease have skyrocketed over the last several decades.
  • How humans are able to adapt so “rapidly” to new diets/foods.
  • Where the low-grade chronic inflammation that characterizes conditions such as obesity, acne vulgaris, type-2 diabetes, and colorectal cancer stems from.
  • Why some people find it almost impossible to stay away from processed foods such as doughnuts, cake, and pizza, while others have no problem sticking to a nutritious, whole foods diet.
  • Why healthy eating, adequate sun exposure, regular exercise, and good sleep often aren’t enough to achieve good health.
  • Why mental disorders such as ADHD and autism have become increasingly more prevalent.
  • Why some health disorders run in families. There’s clearly a genetic (human genes) explanation for this inheritance, but in my mind this could only be part of the picture.

The microbial self

Finally, about 6 years ago, I slowly started to put the pieces together, and I realised that I had ignored large parts of the puzzle. What I found is that to really understand how to be healthy and fit, simply looking at the human being as a singular organism doesn’t get us very far. To really be able to make sense of health & fitness, we have to also include the organisms that have co-evolved with us for millions of years.

In retrospect I’ll say that it wasn’t really a surprise that it took me that long to discover what is now widely known as the human microbiome. Back in 2008-2009, few people paid any attention to the microorganisms that live in and on the human body, doctors who talked about candida overgrowth and leaky gut were labelled as quacks, and when bacteria were discussed in the context of human disease, it was usually as pathogens that needed to be wiped out.

In the years that have passed, a lot has changed. The human microbiome has made its way out of the research journals and into blogs and newspapers, new books, such as the recently published Missing Microbes, are devoted to the ecosystem that is our body, and the human microbiome market (e.g., probiotics, drugs, prebiotics) has grown substantially and is estimated to be worth $658 Million by 2023. We’ve learned that 99% of the unique genetic material in the human body is microbial and that the state of this microbiome largely determines whether we’re healthy or sick.

When it comes to nutrition, microbes provide the “missing” component that can help answer many of the questions I was pondering over several years back. While the human host is only able to break down some of the food ingredients we eat (e.g., starch, simple sugars), the gut microbiome can adapt to break down a wide range of food ingredients. It therefore doesn’t come as a surprise that lack of microbial diversity (“western gut”) results in food intolerance/sensitivity. Recent studies also show that it’s not just the more “obscure” food sensitivities that are largely driven by microbial disturbances, but also conditions such as peanut allergy and celiac disease. And our digestive function is far from the only thing that is affected by bacteria. More than 70% of our immune system is located in and around the gastrointestinal tract, and perturbations of the gut microbiota will have systemic effects throughout the body.

Although gut bacteria have received the most attention, more and more research is also coming out on the microbiome of the skin, lungs, mouth, and the rest of the human body. So, you can probably see why the human microbiome is such as recurrent theme on this site.

One of the major problems with the western lifestyle isn’t just that we’re losing microbial diversity, but we’re also altering the composition of the microbiome and starving our microbial self. Here’s a quote from a recent paper:

The gut microbiota of a healthy person may not be equivalent to a healthy microbiota. It is possible that the Western microbiota is actually dysbiotic and predisposes individuals to a variety of diseases. The asymmetric plasticity between the relatively stable human genome and the more malleable gut microbiome suggests that incompatibilities between the two could rapidly arise. The Western lifestyle, which includes a diet low in microbiota-accessible carbohydrates (MACs), has selected for a microbiota with altered membership and functionality compared to those of groups living traditional lifestyles. Interactions between resident microbes and host leading to immune dysregulation may explain several diseases that share inflammation as a common basis.

Basically, what the quote says is that the western lifestyle, with an emphasis on the refined, western diet low in microbiota-accessible carbohydrates, selects for a unhealthy microbiota. We’re neglecting our microbial residents.

Okay, I think that was an important introduction to the key point of today’s article, as jumping right in with the microbe-brain connection can seem a bit science-fictiony if you’re not aware of the massive impact these critters have on our general health.

Bacteria manipulate our eating behaviour


Craving chocolate? Your gut microbes are partly to blame.

One of the most interesting developments that has occurred over the last couple of years has to do with the influence bacteria have on our brain. While most people now get that microorganisms have a major impact on our skin health, digestive function, and immune system, the idea that microbes exert influence over our minds still seems far-fetched to many. However, the fact is that there are now hundreds of scientific papers out there that focuses on the ways bacteria affect our mood, behaviour, and thoughts.

I can count on my fingers the number of times I’ve read something that is so perfect and thought-provoking that it leaves a lasting impression on me. Those few selected books, articles, and papers that make up this hall of fame have provided evidence for my existing ideas and hypotheses, opened me up to new and exciting concepts, and shaped my outlook on health & fitness. Recently, a lot of media attention was given to a new review paper that focused on the role gut bacteria play in determining our dietary preferences. I posted a link to one of these articles in the mainstream media on my facebook page a while back, but it wasn’t until yesterday that I really took the time to dig into the actual full text review paper. I quickly realised that this article is one of those few groundbreaking reads you don’t come across very often. Unlike many other papers on the topic, these authors don’t just discuss a couple of ways bacteria could influence our mind; instead they take a look at the broader picture, include the evolutionary perspective, and produce hypotheses that are consistent with “everything” we know about cravings, food preferences, and obesity.

Why are we in the midst of an obesity epidemic? Why do so many people essentially become addicted to processed foods such as pastries, potato chips, and chocolate? Why do people who switch to a “healthy diet” often report that their cravings for foods rich in refined fat, sugar, and refined grains slowly disappear?

I strongly believe the information in this article can help explain all of these things. I’ve previously written about how microbes influence our eating behaviour and food cravings, so instead of repeating myself, let’s just finish with a couple of quotes from the article (Sentences in bold: My emphasis):

The struggle to resist cravings for foods that are high in sugar and fat is part of daily life for many people. Unhealthy eating is a major contributor to health problems including obesity [1] as well as sleep apnea, diabetes, heart disease, and cancer [2-4]. Despite negative effects on health and survival, unhealthy eating patterns are often difficult to change. The resistance to change is frequently framed as a matter of “self-control,” and it has been suggested that multiple “selves” or cognitive modules exist [5] each vying for control over our eating behavior. Here, we suggest another possibility: that evolutionary conflict between host and microbes in the gut leads microbes to divergent interests over host eating behavior. Gut microbes may manipulate host eating behavior in ways that promote their fitness at the expense of host fitness. Others have hypothesized that microbes may be affecting our eating behavior [6-8], though not in the context of competing fitness interests and evolutionary conflict.

Conventional wisdom often blames unhealthy eating on a lack of willpower. However, binge eating is not just a matter of mental control [101]; food cravings are unlike other cravings. Many other addictions, such as drugs and alcohol, require ever-increasing doses to maintain the same mood-altering effect. This habituation does not happen with food. For some individuals, the more they indulge their food cravings, the more enjoyment they get from them [102]. These results, and recent work showing distinct mechanisms of food-reward and morphine sensitization in mice suggest that overeating has a different underlying mechanism from drug abuse, and is not consistent with an addiction [103].

Modern biology suggests that our bodies are composed of a diversity of organisms competing for nutritional resources. Evolutionary conflict between the host and microbiota may lead to cravings and cognitive conflict with regard to food choice. Exerting self-control over eating choices may be partly a matter of suppressing microbial signals that originate in the gut. Acquired tastes may be due to the acquisition of microbes that benefit from those foods. Our review suggests that one way to change eating behavior is by intervening in our microbiota.

Competition between genomes is likely to produce a variety of conflicts, and we propose that one important area, impacting human health, is in host eating behavior and nutrient acquisition. Genetic conflict between host and microbiota – selecting for microbes that manipulate host eating behavior – adds a new dimension to current viewpoints, e.g. host-microbiota mutualism [11], that can explain mechanisms involved in obesity and related diseases.

Food for thought: How much influence do bacteria have over us? Are humans simply elaborate vessels for the propagation of microbes (Quote Justin L. Sonnenburg, PhD. Department of Microbiology and Immunology Stanford University)?

Bottom line

We’ve moved from an ancestral state of mutualistic symbiosis to a modern state of dysbiosis. Also, recent research suggests that we’ve entered into a vicious cycle where a western lifestyle perturbs the microbiome, which in turn promotes more unhealthy behaviour. On a positive note, the microbiome can be manipulated so that we achieve a new state where the types of behaviours that promote the fitness of the microbiota are more aligned with the types of behaviours that promote the fitness of the human host. Let’s finish by answering the question in the title: Who’s in control, the human host or the microbiome? I think the answer to this question is pretty clear; both are. We can manipulate the microbiome, and microbes can exert control over us.


  1. Good piece. The 1st thing I thought of when realizing the importance of the microbiome is “we truly are symbiotic beings.”

    • I would like to thank you very much for your excellent work and advice.. Human hubris has us believe that we are intelligent and considers everything far less intelligent than we are. And when we get down to the level of cells, we essentially don’t consider them as possibly having intelligence. We think of ourselves as a singular entity, but the reality is that we are an interactive community of 100 trillion individual cells. It is their technology and their intelligence that created us. The reflection of their intelligence is in their technology—they can manage their environment and manage their world with technologies that we haven’t even comprehended yet. For millions of years, their social activities have made possible the evolution of all life forms on this planet. In fact, we are struggling on this planet with how to form a cooperative world with only about 7 billion people. Within us there has been a cooperative world of about 100 trillion citizens that have created a philosophy and politics of life that has enabled them to live and thrive over a million years. And what is unique about these cellular civilizations is that they can live in total bliss, which is reflected in the health and vitality that we experience..

  2. I feel smarter and more well informed after reading this. Your stuff is top shelf and opens my mind. Thanks.

  3. Well done as usual. I think too many people confuse cravings with true hunger. I doubt too many experience that any more.

  4. Well, how do you manipulate the microbiome?


  1. […] I explained in my previous post on microbes, my interest in the human microbiome began because I was wrapping my mind around things that […]

  2. […] covered the connection between gut bacteria and food cravings in several posts now (e.g., here and here). It’s definitely an intriguing subject. When a person transitions from a refined […]

  3. […] couple of months back I posted an article where I discussed a scientific paper linking the gut microbiota to food cravings and appetite, and […]

  4. […] The microbiome-gut-brain axis has received a lot of attention both in the scientific community and mainstream press lately – and for good reason. Over the last decade we’ve learned that the gut microbiota impacts our mood, behaviour, and thoughts, and to some people’s surprise, ev…. […]

  5. […] Although the effects of diet on the gut microbiota are best documented in the case of dietary fibers being subjected to fermentation in the colon, there’s little doubt that other foodstuffs can have a major impact on your gut symbionts as well. Let’s take refined sugar for example, a component of our diet that is notorious for promoting an inflammatory oral microbiota (think tooth decay and gingivitis) when eaten in excess; effects that can also extend further down the GI tract (2). There’s even compelling evidence which suggests that a high intake of refined sugar could lead one into a vicious cycle, as gut bugs influence the host’s food cravings and appetite. […]

  6. […] depression. The diet-gut microbiota-depression connection is a vicious circle, because we know that gut bacteria have the ability to impact our dietary preferences and that depression can lead to increased consumption of “unhealthy” […]

  7. […] “Humans simply elaborate vessels for the propagation of microbes.” (7) […]

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