The Human Microbiome


The Human Skin Microbiome. The human body is best viewed as a superorganism composed of a human host living symbiotically with trillions of microorganisms.

Ever since humans first discovered microorganisms many centuries ago, we’ve known that the human body is host to various types of bacteria and other critters that can’t be seen with the naked eye. During the time that has passed since these first discoveries, the primary focus has been on eradicating germs that make us sick, often by using antibiotics to treat even the smallest sniffle, applying antimicrobial lotions to attack skin problems, and “sterilizing” our homes.

Of course, we’ve nown for some time that not all bacteria are bad and that some microorganisms have a positive effect on our health, for example by producing short-chain fatty acids through the breakdown of complex polysaccharides deep in our colon. However, it’s only recently that we’ve started to understand how complex the microbial ecosystems that travel with us throughout life really are and how essential bacteria are to our health.

The microbial self

Thanks to an ever-growing pool of research on the topic, including data from massive research projects such as The Human Microbiome project and MetaHit, we’ve learned that the number of microbial cells “in” and on our body vastly outnumber the number of human cells (1, 2). This human microbiota – the collection of microorganisms associated with the human host – consists of microbes that colonize the skin, gut, lungs, and several other habitats “in” and on the human body. Most of the microorganisms are found in the gastrointestinal tract, where they maintain our gut barrier, help break down the food we eat, and regulate our immune system.

For the longest time, the human genome received virtually all of the attention in health and medicine, but what we’re now learning is that the human microbiome – the collective DNA of all the microorganisms that colonize the human body – is in some areas even more important than the 23 pairs of chromosomes we get from mum and dad. The genetic repertoire of the microbiome is more than 100-times greater than that of the human genome, meaning that we could look at the human body as 99% microbial (1, 2).

Microorganisms have co-evolved with us throughout our evolution, forging symbiotic relationships. The host provides an environment where bacteria, fungi, archaea, and other critters can thrive, and the host in turn benefits from having outsourced parts of its immune function, metabolism, and digestion to these microbial travelers.

The first influx of microorganisms comes from mum, but contrary to the human genome, which is inherently stable, the human microbiome continues to be shaped all the way throughout life by microbial exposure from animals, other humans, and the rest of the environment, and also by diet and lifestyle (3). Microbes evolve rapidly and can swap DNA between each other, which further contributes to the plasticity of the human microbiome. The complexity and dynamicity of the microbial ecosystems explain why each one of us carry a unique microbial rainforest.

The human microbiota is considered an essential organ of the human body, because without these symbionts we wouldn’t be able to function correctly. However, on the other hand, these microorganisms aren’t us. They are as much a part of our environment as the plants and animals around us. In other words, the microbiome can be thought of both as an organ and an environmental factor. The human microbiome is a bridge between us and our environment, a connection that helps us adapt more rapidly to environmental changes (e.g., diet) than what would have been possible if we only relied on our human genome.

A western lifestyle perturbs the human microbiome


For millions of years, hominins evolved in diverse and various ancestral environments that differ markedly from modern environments in several respects. During this time we not only evolved bodies that were adapted to certain types of physical activity patterns, diets, circadian rhythms, etc., but also to harboring certain types of microbiomes. With the Agricultural Revolution – and even more so the Industrial Revolution and modern age – profound changes to our environment triggered equally profound changes to our microbiomes (4, 5, 6).

Widespread use of antibiotics, new dietary patterns, excessive hygiene, c-sections, and a myriad of other factors have shaped modern microbiotas that are very different from those that our ancient ancestors harbored (4, 5, 6). We’ve not only lost many microbial old friends, but also altered the overall community structure (4, 7). In the blink of an eye – from an evolutionary perspective – we’ve dramatically shifted the balance between man and microbes.

While our human genome has remained relatively unchanged since our days as foragers, the human microbiome has changed dramatically – a statement that is supported by studies showing that hunter-gatherers and other non-westernized populations harbor microbiomes that are very different from “westernized” microbiomes (4).

Many aspects of the modern lifestyle can alter the microbiota and induce a new state where the microbiome isn’t compatible with the human genome. So, it’s not just the environment we can see with our naked eyes that has changed too much over the last several millenia for human biology to keep up, but also the microbial ecosystems that call our body home.

As these microorganisms are such an essential part of us, it doesn’t come as a surprise that perturbations of the human microbiome have major consequences to our health. Dysbiosis (microbial imbalances) has been linked to many – if not most – of the chronic health disorders that now run rampant in the modern world, ranging from gastrointestinal disorders such as gallstones to skin problems like acne (7, 8). Bacteria in the gut also play an important role in body fat regulation, and several studies show that obese individuals harbor different types of microbes than lean individuals (4). The human microbiome even affects our mood, behaviour, and thoughts (9, 10).

Microbiome restoration

Just like an unhealthy lifestyle can alter the microbiome in ways that promote a mismatch between our human genome and the microbiome, a healthy lifestyle can shape a microbiome that flows well with our human self. As previously mentioned, for millions of years, our ancient ancestors evolved in diverse and various environments that differ markedly from modern environments in several respects.

The microbiomes of Paleolithic foragers were shaped by diet, lifestyle, and microbial exposure from animals, other humans, soil, water, and the rest of the natural environments in which they lived. Just like we evolved bodies that were adapted to certain types of physical activity patterns and diets, we also evolved to harboring certain communities of critters.

To shape a healthy microbiome we have to look back at diet and lifestyle through the lens of evolution. There’s still a way to go in terms of understanding human-microbe interactions, making good and cheap treatments available, and establishing whether certain genetic predispositions hinder some people from repairing their gut microbiota. However, we do have many of the tools we need to take charge at once.

For those people with severe gut dysbiosis, microbiota transplantations – or perhaps in a couple of years, advanced probiotic drugs – might be necessary to fix a broken ecosystem. However, for the majority, changes to diet and lifestyle are the main things to consider. If there’s one thing the literature consistently show, it is that a well designed “paleo lifestyle” has many – if not all – of the characteristics that seem to promote a microbiome that is well “matched” with both our lifestyle (especially diet) and our human genome. In other words, exactly the outcome one would expect from looking back at our long history of co-evolution with microorganisms.


These elements are on top of the list of lifestyle factors that help promote a healthy microbiome:

Animated videos explaining the human microbiome

These videos from and are excellent for those people who want a simple description of what the human microbiome really is.


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