All of the microorganisms that colonize the human body – the human microbiota – have gotten a lot of attention lately; not just in the ancestral health community and among scientists, but also in the mainstream press. Overall, more and more people seem to realise that we can no longer dismiss the trillions of microbial travelers that colonize our body as relatively passive bystanders on our journey through life.
Over the last decade we’ve learned that the human body is more microbial than human; both in terms of genetic repertoire and number of cells, and that these microorganisms have a profound impact on our health and well-being.
The gastrointestinal tract is where most of the microorganisms associated with the human body are found, with the main microbial reactor being in the colon. These gut bugs help break down our food, regulate our immune system, and have far-reaching effects on our health and well-being.
Which microbes do we want to dominate?
Compared to the human genome, the gut microbiome – the collective genomes of all the microorganisms that live in the gut – is very dynamic. If you suddenly switch from a diet high in dietary fiber to a meat-centered, low-fiber diet, the composition of your gut microbiota will shift. Suddenly, those microorganisms that were responsible for breaking down complex polysaccharides in plants to simple sugars – and their cross-feeders which turn the sugars into short-chain fatty acids – dwindle in numbers, the pH in the colon goes up, and other microbes – which are better adapted to these new living conditions – get a foothold. Given a major dietary change like this, the gut microbiota can be profoundly altered in less than a day (1).
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.
In other words, the next time you feel a sudden desire to eat a sweet doughnut or drink a sugar-laden beverage, it’s likely that the critters in your gut are partly to blame.
If this sounds scary, just think about what happens if you attack your microbial inhabitants with multiple rounds of broad-spectrum antibiotics; drugs that set in motion a selection event where those microorganisms with antibiotic resistant genes get the upper hand. Suddenly, parts of the community structure are wiped out, and species that were once a small part of the ecosystem could get a chance to take over. In the human gut, one of the most dramatic examples of the latter is the overgrowth of C. difficile: bacteria that are commonly kept in check by commensal microbes, but can grow out of control following antibiotic use.
Nobody’s questioning that antibiotics have helped save millions of lives, but what has become increasingly clear is that these drugs also come with a significant cost, as they spur the evolution of antibiotic resistance and wipe out commensal microorganisms, thereby leaving niches open for exploitation by pathogens.
These types of changes are best documented in the gut, but parallels can be drawn to other locations on the human body. Smoking, regular use of hand sanitizers, and topical application of cosmetic products containing a wide range of potentially harmful chemicals are evolutionarily novel behaviours that have the potential to adversely affect the microbiome.
Antibiotic use, dietary changes, and the use of harsh cleaning products are in some ways analogous to specific environmental pressures (e.g., changes in climate) in a rainforest or garden, where those forms of life having traits that better enable them to adapt will tend to survive and reproduce in greater numbers than others of their kind.
The thing about microbial life is that everything occurs at a very fast pace, as microbes can evolve rapidly and share DNA through horizontal gene transfer. This is why pathogens such as C. difficile can take over in the gut so quickly following antibiotic use, and it’s also the reason the gut microbiome can adapt so quickly to changes in diet.
A dwindling self
The Paleo/ancestral health movement is based on the premise that there’s a mismatch between our ancient genome and the modern environment, and a lot of attention is given to how we can realign our diet, sleeping pattern, and exercise routine with our evolutionary legacy.
What has become increasingly clear over the last several years is that it’s just not the modern environment we can see with our naked eyes that is poorly matched with our Stone Age genes, but also the invisible, microbial world that exists around us and in and on our bodies.
For millions of years, hominins co-evolved with microbiomes that were “matched” to nutrient-rich, whole foods diets and “ancestral lifestyles”. In the modern world we’ve disrupted this balance between man and microbes and selected for a new, westernized microbiome; a microbiome that is incompatible with our more stable human genome (3). The human self isn’t adapted to live symbiotically with the type of microbiota you get from taking antibiotics, eating large amounts of sugar, being bottle-fed as a child, consuming diets very low in fiber, etc.
Studies suggest that microbial diversity has dwindled since our hunter-gatherer days. The human superorganism is less diverse than it has ever been.
The next time you’re out on the street, take a look around you at the people walking by. Many – if not most – struggle with health problems that are a result of modern diets and lifestyles that are at odds with our ancient genome (4, 5). Part of the problem is that the rapid changes to our living conditions over the last several millennia have perturbed the human microbiome, which sets the stage for inflammation and disease.
Taking care of the microbial self
Since the human microbiota is shaped by diet and lifestyle, it doesn’t come as a surprise that populations inhabiting dissimilar habitats around the world can harbour very different microbiomes. As we live in an environment that is very different from that of hunter-gatherers and other traditional, isolated populations, we’re not necessarily best off harboring the same microbes as the Hadza or the Kitavans.
However, I think there’s little doubt that we can learn a lot about how to achieve a healthy microbiota by looking at diet and lifestyle through the lens of evolution. Most importantly because it can give us many clues as to how we can shape a microbiota that the human body is well-adapted to harbor.
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, fecal microbiota transplantations – or perhaps in a couple of years, advanced probiotic drugs – may be necessary to fix a broken ecosystem.
However, for the majority, diet and lifestyle are the main concerns. If there’s one thing the literature consistently shows, it is that a well-designed “paleo lifestyle” promotes a microbiome that matches well with our human self. In other words, exactly the outcome one would expect from looking back at our long history of co-evolution with microorganisms.
True hunter-gatherer diets typically (some exceptions exist) contain more fermentable fiber than contemporary Paleo-style diets, partly because uncultivated fruits and vegetables are much higher in fiber than the domesticated versions found at the grocery store. Making a conscious decision to seek out and eat plenty of plant foods rich in prebiotics (e.g., tubers, leeks, green bananas) is therefore necessary to get closer to “ancestral standards”.
Other factors – such as avoiding harsh cleaning products, eating traditionally fermented vegetables, breast-feeding your child, taking high-quality probiotics, reducing chronic stress, being in contact with healthy people and pets, and eating some semi-clean vegetables from a trusted source – can also help promote a healthy microbial self.
Picture: Creative Commons picture by Environmental Illness Network. Some rights reserved.
Note: A previous version of this article of mine appeared in Paleo Magazine, the first, and only print magazine dedicated to the Paleo lifestyle and ancestral health. You can subscribe to Paleo Magazine here!