Microbial Exposure

handful-of-dirtWe live in a microbial world, which the human body is constantly connected to through its microbial inhabitants. The human superorganism consists of the human host, with its human genome, living symbiotically with trillions of microorganisms, with their collective genomes called the human microbiome (Other organisms that are not strictly speaking microorganisms (e.g., some worms) are also sometimes a part of the superorganism). These organisms colonize the skin, gastrointestinal tract, lungs, and many other parts of the human body, where they perform various important functions – often ones that the human host can’t perform itself. The human microbiota – all the microorganisms living “in” and on the human body – is shaped by diet, lifestyle, and microbial exposure from the environment.

In the field of evolutionary medicine a lot of the focus is on how evolutionary mismatches related to diet, physical activity, sun exposure, sleep, and stress contribute to disease. Less attention is often given to the parts of our environment that we can’t see with our naked eyes, namely all of the bacteria, fungi, archaea, viruses, and other organisms that live around us and on our bodies. As for microbial exposure and human health, a lot of the focus is often on the dangers of pathogenic bacteria, but the fact is that most of the microorganisms we encounter aren’t harmful. Actually, adequate microbial exposure is absolutely essential for good health.


Early hominins weren’t aware of it, but their bodies were teeming with trillions of critters that helped them break down the rough plant foods they were eating, aided them in the protection against pathogenic bacteria, and played an essential role in the regulation of their immune systems. As we evolved into more human-like creatures and eventually into anatomically modern humans, microbes evolved with us, living symbiotically side by side with human hosts.

For millions of years, hominins lived in close contact with mother nature, constantly exposed to microorganisms from mud, soil, dirty root vegetables and other foods, fresh water, animals, humans, and the rest of the natural environment. Some were just transient by-passers, while others took up more permanent citizenship in one of the many ecosystems associated with the human body. For many of those that ventured down the esophagus of a human, the trip came to an abrupt halt when they stood face to face with the acidic juices in the stomach, but a minority got through and continued down the system, perhaps taking up permanent residence in the gut or giving off some DNA to bacteria living in the colon through horizontal gene transfer (1).

Our Paleolithic ancestors undoubtedly encountered germs that we today look at as pathogens, but from what we know about isolated hunter-gatherer societies, there’s little to suggest that diarrhea and infections are as big of a problem as a germophobic westerners would perhaps think. As long as they survive past the first years of life, hunter-gatherers tend to be very healthy up until “old” age (2, 3). This is in part due to the fact that hunter-gatherers live at very low population densities, making it difficult for infectious diseases to spread. Also, perhaps more importantly, many of the helminths, viruses, saprophytes, and other organisms we were exposed to in the Paleolithic accompanied mammalian evolution for millions of years and therefore had to be tolerated. Last, but not least, the microbiome plays an essential role in pathogen protection. If it was just up to the human host to set up a good defense against pathogens, all hope would have been lost. By having microbiotas of high biodiversity, our hunter-gatherer-ancestors had a defense against harmful invaders, a defense that is a lot more malleable than the human genome. When all of the ecological niches are already occupied, it’s that much harder for other germs to get a foothold.

Those organisms that have co-evolved with us for millions of years are often referred to as “old friends” (4, 5). Some of these old friends were living deep in the guts of our ancient ancestors, some colonized their skin, lungs, or other bodily organs, and some were just transitory bugs that our immune system evolved to expect and tolerate (4, 5, 6).

When we started to settle down into larger communities and take up farming about 12.000 years ago, new living conditions led to shifts in the types of microorganisms we were exposed to. With the second epidemiological transition, these changes to our microbial environment accelerated; as you can see from the illustration below.

Profound changes to our microbial world affect human health

Hunter-gatherer environments of the Paleolithic are the Environments of Evolutionary Adaptedness for humans. Only minor genetic adaptations have occurred in the ~10.000 years that have passed since the agricultural revolution, meaning that we are very much Stone Agers from a genetic perspective (2, 7). This is important to keep in mind in the discussion of microbial exposure, as it suggests that we are – to a large extent – adapted to a microbial environment that no longer exists. Just like the low dietary fiber intake in western diets compared to Paleolithic diets have a profound impact on human health, the removal of microorganisms that were a natural part of the hunter-gatherer environment will clearly affect us.

Many types of micro- and microorganisms that used to colonize the human body are now gone due to changes in environment and lifestyle, a statement that is supported by several lines of evidence, such as studies of contemporary hunter-gatherers and rural populations which show that these people harbor microbiotas characterized by higher microbial richness and biodiversity than the microbiotas of westerners (8).

Graham Rook, an expert on the human microbiome, speculates that the close co-evolution between man and old friends resulted in a relationship where both parties became dependent on each other (4). This dependence can be classified into three categories, two of which seem to be especially important in our co-evolution with other organisms (4). The first one is initial dependence, where some old friends were present as the human immune system evolved, and became essential components of that system. The second is evolved dependence, a process where an organism adapts to the presence of a partner through loss of genetic material, and can no longer function without that partner.

So, some of the “old friends” present in the microbiota of a hunter-gatherer might have co-evolved with us for millions of years, forging dependent relationships where their genomes have been “written into” the human genome – meaning that the human host depends on their genes to function correctly. In other words, since an “old friend” has been there for millions of years, human hosts never had to evolve the capabilities that the old friend provides. When some of these organisms disappear from the human body, immunoregulatory problems occur, which can set the stage for autoimmunity and infections (4, 9).

… the illnesses that are increasing in high-income countries are associated with failing immunoregulation and poorly regulated inflammatory responses, manifested as chronically raised C-reactive protein and proinflammatory cytokines. This failure of immunoregulation is partly attributable to a lack of exposure to organisms (“Old Friends”) from mankind’s evolutionary past that needed to be tolerated and therefore evolved roles in driving immunoregulatory mechanisms. Some Old Friends (such as helminths and infections picked up at birth that established carrier states) are almost eliminated from the urban environment (6).

The gut is the most important immune organ in the human body and also where most of the microorganisms live. In the gut there’s a constant exchange of genetic material between microbes, meaning that one bacteria can get DNA from another, thereby attaining some of the abilities of its generous contributor (1). This dynamic nature of the gut microbiome, in combination with the fact that different “species” can fill the same niches, explains how people can have so different microbiomes. So, as for the human microbiota we carry with us through life, the genetic material is the important factor, as it is the genes that code for proteins (e.g., enzymes) that the human host can’t produce by itself.

For the human host, the microbiome is an extension of the human genome in the sense that microorganisms provide genes that the host depends on to be able to extract energy from food, maintain the intestinal barrier, etc. The concern isn’t just that we’ve lost many old friends, but also that we have reduced our exposure to beneficial microorganisms in general, thereby “starving” our microbiome of genetic diversity. The human superorganism has lost parts of itself. An ecosystem rid of diversity is unstable and open to invasion. Loss of biodiversity and microbial imbalances – especially gut dysbiosis – have been linked to a myriad of chronic health disorders (10, 11, 12).

It all boils down to the following:
Too little exposure to “old friends” and other beneficial microorganisms.
– Microbial exposure that falls in the category of being too new and/or too much.

Just like the world around us that can be seen with the naked eye has changed dramatically since the Paleolithic era, the invisible microbial world has also undergone profound shifts. These effects extend to the human superorganism, which has lost biodiversity and entered into a new, altered state.

Practical applications

A natural solution to the aforementioned problems is to reconnect with our ancestral environment. However, that’s easier said than done in a world where we’ve disconnected ourselves so profoundly from nature. Also, due to the epidemiological shifts discussed in the section above, many people, pets, and perhaps even the plants now harbor what could be considered dysbiotic microbiotas. That doesn’t mean all hope is lost though.

Strategies you can use to rewild your body:

  • Eat fresh, minimally washed plant foods from a trusted source (e.g., backyard garden).
  • Occasionally eat small quantities of a diversity of fermented vegetables, preferably organic and homemade. Sauerkraut, kimchi, and other lacto-fermented foods are a rich source of bacteria, some of which could help you boost the diversity of your gut microbiome.
  • Do some gardening.
  • Avoid antibacterial products and harsh cleaning products.
  • If you’re a female, perform vaginal births (if possible) and breastfeed your child(ren).
  • Pick up bacteria from healthy humans and animals.
  • Spend more time in natural environments.
  • Take good care of your home’s microbiome.
  • If your microbiota is severely damaged, consider performing one or more microbiota transplantations or taking a drug designed to restore microbial diversity of the gut.

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