Have You Eaten Enough Bacteria Today?

parisienne carrotsDid you get a lot of beneficial bacteria through your diet today? If you’re like most people living in industrialized societies, the answer is no. So much of the food we eat today have been cleaned, pasteurized, or processed in such a way that little bacteria remain. A lot of people will tell you that this removal of food-borne microorganisms and “sterilization” of our food supply are good things. However, what has become increasingly clear over the last decade is that there are also many negative effects associated with scrubbing our diet for microbes.

How our food has changed

As anyone with some interest in nutrition will tell you, just focusing on which food groups you include in your diet isn’t enough to achieve optimal health. To really be able to design a healthy diet, we also have to take into account how our food is produced, prepared, and processed.

It could be argued that these factors may in some ways even more important than which food groups you choose to include in your diet – as long as you stick with a whole foods dietary template of course. This might sound a bit exaggerated to some, but if we look at how healthy human populations have eaten around the world, it quickly becomes clear that we are an extremely adaptable species. Non-modernized cultures have thrived on everything from diets very high in carbohydrate to almost exclusively meat-based diets (1, 2).

The primary difference between the foods that were consumed among non-westernized, traditional cultures and those we eat in today’s western world, is that isolated, healthy populations ate higher quality foods with a healthier nutrient composition. Also, they put far more emphasis on processing and preparing their food correctly – often using techniques such as lacto-fermentation to make grains, legumes, fruit, and vegetables more shelf-stable and easier to digest.

If you take a trip through your local grocery store you can clearly see that the foods we have available to us now are very different from those consumed by traditional people. Kefir made from raw, grass-fed, and full-fat milk fermented with real kefir grains has been replaced with kefir made from pasteurized, homogenized, grain-fed, and fat-reduced milk fermented by the use of a starter culture, sourdough oatmeal bread has been replaced with refined wheat products, and animal products from wild and pasture-fed animals have been replaced with meat from livestock that have been raised on unnatural food and injected with hormones and antibiotics.

Clearly, I’m exaggerating to make a point, as most of us do have access to food that more closely resembles the types of foods we’ve been eating throughout most of our evolutionary history. However, when we look at the modern food environment as a whole, it’s clear that we’ve completely lost touch with “natural”, real food.

So, to find a healthy eating pattern, we can’t simply discuss which food groups we should include in our diet, we also have to look at what hints evolution gives us about other aspects of human nutrition. This brings us back to the topic of today’s article. When most people think about eating healthy, soil and bacteria are usually not the first things that come to mind. However, I’d argue that they should be…

We’ve already briefly discussed how food quality, preparation and preservation methods, and processing techniques have changed since the pre-industrial days. However, there’s another transition that could be even more important in some regards, but that unfortunately receives little attention. Namely, the transition from eating “dirty” food to eating “clean” food.

The plants and animals we eat all have their own unique microbiome

Just like humans, all plants and animals have their own unique microbial cloud. When we eat raw lettuce from the garden or minimally washed carrots from the farmers market, we’re not just getting a dose of micronutrients, fiber, simple carbohydrates, and phytochemicals, but we’re also ingesting soil bacteria that cling to these foods. For plants, the root is “the gut” – a place where nutrients are absorbed and waste is excreted.

It’s interesting to note that recent studies show that there are many commonalities between human gut and plant root microbiotas (11, 12). It could be argued that the soil bacteria that cling to tubers and other vegetables are an essential component of the food, as these bugs may aid us in the digestion of polysaccharides that are found in the plant.

We’re now starting to understand that our connection to the soil beneath our feet is far more important than what we’ve previously realised.

Our dirty ancestors

Let’s for a moment diverge far away from the industrialized world, into the african habitat of one of the last hunter-gatherer communities on earth, the Hadza. Although most of the Hadza have now transitioned over to a more modern lifestyle, there are still some left who stick to the old ways of doing things: They gather honey when possible, hunt for large and small game, and eat fruits, tubers, and berries that are available in their local environment. Although not a perfect reflection of the African Paleolithic man, these people give us a window into the way of life of our pre-agricultural ancestors.

When the Hadza men are out hunting, women spend their time digging for underground storage organs. Although not as highly valued as meat and honey, tubers rich in prebiotic fibers are relatively easy to gather and constitute a large part of the Hadza diet. These women definitely get their hands dirty – a “dirtiness” that seems to be one of the key characteristics of the Hadza lifestyle. As Jeff Leach of the Human Food Project has reported, the Hadza even eat the intestines of some of the animals they kill and “wash” their hands with the stomach content, a behaviour that really highlights the difference between microbial exposure in an ancestral environment and in the modern world.

It’s simply impossible to avoid getting a daily dose of soil microbes through your diet when you rarely wash your hands, dig up and eat tubers with clinging soil, and in general, live in close proximity to nature.

One could suspect that these types of behaviours would lead to frequent gastrointestinal infections and increased mortality rates. However, while it is true that non-westernized traditional populations tend to have high rates of infant mortality, which can partly be attributed to pathogenic infections, adult hunter-gatherers have had time to develop a diverse, resilient microbiota and a strong immune system, which provides them with a better defense against pathogens.

Also, it’s important to remember that this is the type of environment we evolved to live in. For millions of years, our ancestors ate raw fruits and vegetables with clinging soil, they drank water that had not undergone any form of processing or treatment, and they probably also ate some raw intestines every now and then.

Our primal ancestors didn’t have probiotics containing lactobacilli and bifidobacteria. Rather, they got their daily dose of microbes from foods with clinging soil, untreated water, and the animals and humans living around them. This close relationship between man and microbes during our evolution shaped the microbial ecosystems that live in and on the human body.

The hidden costs of cleanliness

Exposure to microbes/dirt is definitely an important factor to consider in the context of a modern-day Paleo lifestyle. When compared to many of the other evolutionary mismatches we talk about in the ancestral health community, the difference between microbial exposure in a hunter-gatherer environment and in the modern world is especially pronounced. Even the most non-health conscious people in today’s society eat some foods that mimic that of our ancestors’, get in the sun once in a while, and exercise now and then, but most folks don’t even consider the idea that getting some “dirty” vegetables and soil microbes into their diet could be a good idea. On the contrary, most people look at dirt as a bad thing.

While there are certainly many upsides to having access to modern hygiene, it has become increasingly clear that there are also many negative effects associated with the use of hand sanitizers, cleaning detergents, and all of the other tools and products we use to remove bacteria from our homes, clothes, and food (3, 4, 5).

As the readers of this blog know well, the rapidly increasing prevalence of autoimmune conditions and inflammatory disorders in the modern world can largely be traced back to the widespread use of broad-spectrum antibiotics, excessive “cleanliness”, consumption of refined diets, a lack of exposure to biodiversity from the natural environment, and other factors that have a destructive impact on the human microbiome (4, 7, 8).

By significantly decreasing our contact with nature, we’ve basically lost part of our body, in the sense that helminths, bacteria, and fungi that once used to be a part of the human superorganism are now gone (4). The westernized microbiome is only a faint imprint of the microbiome of our ancient ancestors. This loss of diversity has made us prone to invasion from pathogens and left us with an immune system that’s working at half capacity.

Some studies even suggest that a lack of exposure to soil bacteria may be one of the reasons mental disorders are on the rise, as soil bacterium such as Mycobacterium vaccae can help boost our mood and mental health (9, 10).

Adding some bacteria to our plate

Perhaps needless to say, we shouldn’t be as careless about our exposure to microorganisms as our primal ancestors were. We no longer live in a milieu that is untouched by the mark of modern civilization: pollution, widespread use of biocides, conventional farming methods, etc. have changed the soil microbiome and microbial ecosystems around us. Also, we no longer eat as healthy as our primal ancestors and few of us harbour a truly healthy microbiota. For people living in less developed countries, the combination of malnutrition, dysbiosis, and exposure to pathogens can sometimes be deadly.

When we think about it, it’s crazy that we’ve gotten to a point where something as simple as healthy soil with abundant organic matter can be hard to come by for many people. For someone living downtown in a major city, going into the backyard garden to collect and eat some raw carrots and herbs is obviously not an option. However, that doesn’t mean all hope is lost…

One way city dwellers can reconnect with some old microbial friends is to visit the local farmers market, where organic, high quality produce is abundant. Simply eating more fresh and raw plants (preferably organic) can help provide you with a more diverse microbiome. And it’s not just about food. Ditching the hand sanitizers, letting kids play in the dirt, doing some gardening, spending more time in nature, and getting rid of germophobic tendencies are all ways of getting more microbes into your life and returning to a lifestyle that is more in line with our evolutionary heritage.

For those who are immunocompromised in some way, even these “mild” exposures can be enough to cause problems. However, for the vast majority of people, ingesting some soil clinging to quality food from a trusted source, perhaps eating some fermented foods, and in general, reconnecting with some old microbial friends, are good things.

Picture: Creative commons picture by Chlot’s Run. 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! 


  1. I wonder if I can just eat a spoonful of dirt from my backyard once in a while. I don’t spray any chemicals in my yard.

    • Hi Niles,

      Don’t do that. Many of the bacteria found in soil can indeed enhance your health; however, soil is also home to organisms that could do you harm. People who harbor a degraded, imbalanced microbiota are particularly susceptible to getting sick from exposure to pathogens.

      Check out my articles on microbiome restoration (e.g., this one, this one) for tips on how you can diversify your microbiota in a safe manner.


  1. […] If you can, eat some fresh, raw, and minimally washed vegetables from a trusted source (e.g., farmers market, backyard garden). The bacteria that cling to these foods may help you develop a more diverse and resilient gut microbiota. […]

  2. […] ecosystem diversity, such as through traditionally fermented vegetables, high-quality probiotics, “dirty” vegetables, and/or microbiota transplants are also important, especially for those with a gut microbiota that […]

  3. […] of the main ways we acquire new gut bacteria is through eating food. For example, raw plant foods and fermented vegetables harbour a wide range of microorganisms. […]

  4. […] your intake of fiber-rich foods, exchanging bacteria with healthy friends and family members, eating more raw, minimally cleaned fruits and vegetables, spending more time in natural environments, and reducing your use of cosmetic products, lotions, […]

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