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Eating Dirt: The Benefits of Being (Relatively) Filthy

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Two of the most monumental developments in the history of human civilization, likely the innovations that have saved more human lives than any other, are soap and sanitation. When large numbers of people congregate in a single location for prolonged periods of time, excrement and waste quickly rise to unimaginable levels and are capable of spreading disease incredibly quickly. As I mentioned in my first post here at Food Matters, many pathogens utilize the fecal-oral transmission route, in which poop from an infected individual makes its way into the water supply or onto food by serial contact (touching a contaminated surface then touching food). Lack of hygiene dramatically increases the likelihood of this sort of infection, as many infectious microbes can grow unchecked on filth outside the body, and many viruses can linger on unwashed surfaces for long periods of time.

You are what you touch

Part of a Purell ad campaign in Australia (click for source)

Thankfully, In modern developed countries, we don’t have to worry about this much. Most of us live in places with sanitation infrastructure that carries away our waste and delivers fresh water, and we tend to have bottles of life-saving soap in every room with a sink. In the absence of soap and sinks, waterless hand sanitizers, sanitizing wipes and bleach-containing cleaning products promise to keep away the dreaded germs. Yet while there’s no doubt that sanitation and hygiene are critical in reducing the spread of infectious disease, it’s possible that we’ve gone too far in trying to live a sterile life.

In 1989, British physician David Strachan proposed the “Hygiene Hypothesis,” which sought to explain a puzzling series of observations: Children in cities in developed countries and had fewer siblings, those that lived more sanitary lives and presumably had less exposure to infectious diseases, were more likely to develop allergies, asthma and other atopic diseases than those that lived on farms or in developing countries, or that had many siblings. In the nearly 25 years since this was first proposed, a great deal of research has shown that exposure to diverse bacteria or even parasitic worms helps to train and regulate the immune system, preventing it from becoming over-active.

Many of the ideas put forward to explain how microbes might regulate the immune system are, in my opinion, problematic. I’ll spare you the details for now (if you ask in the comments, I may just have the motivation to write it up!), but basically, they boil down to suggestions that turning on certain types of immune responses take energy away from other types of immune responses that might cause disease*. But there’s also evidence that, even in the absence of a full-blown immune response, exposure to different populations of bacteria can have a significant impact on the way that our immune system responds to other threats.

Take, for instance, the relationship between the denizens of our intestines and diabetes. I’m not talking about the science showing that these gut microbes can affect obesity (though that’s pretty amazing), I’m talking about the fact that having different populations of bugs can influence your liklihood of developing diabetes, regardless of weight. In 2008, a group of researchers led by Alexander Chervonsky at the University of Chicago showed that, in a mouse model of diabetes, mice lacking gut microbes had more severe disease, while those with gut microbes were protected. Three years later, a lab here at Harvard reported that the presence of a single type of bacterium called segmented filamentous bacteria (SFB) in the gut was sufficient to provide protection (unfortunately, consuming SFB is not a really a viable prevention strategy, since many other autoimmune disorders are more prevalent in animals with SFB in their guts). Other research has shown that diabetic humans have very different microbial populations in their guts, though this is probably an effect of altered metabolism rather than the cause.

Bok choy fresh from Red Fire Farms in central Mass. Tasty! (click to enlarge)

All of which brings me to my dinner last Friday night. My fiancé and I receive a CSA farm share every week, and this week we got bok choy that had been pulled from the ground in central Massachussetts the same day. When shopping at a supermarket, it’s easy to forget that our vegetables are grown in the dirt – our obsession with cleanliness and sanitation has seeped into our food, and any produce that’s not squeaky clean is discarded or ignored by consumers. Again, it’s important to remember that this concern for cleanliness is not without merit – we know what happens when contaminated food gets into the retail pipeline – but though many microbes live in the earth, soil is not the source of most infectious disease.

Bok choy is particularly prone to gathering dirt in the base. The folds of the leaves form a tight cup that's near the ground. (click to enlarge)

A little rinse with water (clean, sanitized water from a municipal water system) was enough to remove most of the dirt on the bok choy, but what about the microbes that hitched a ride? Many environmental bacteria form biofilms that can prevent easy removal, and a cursory hand-scrub isn’t likely to do the trick. During most of human evolution, humans have been consuming microbes from the environment, and it’s clear that this exposure shapes the populations of microbes in our guts. A experimental link between microbes consumed in the diet and specific health conditions has not been shown, but it’s quite plausible that at least some of the observations linked to the hygiene hypothesis aren’t just due to passive microbial encounters, but because of what we put in our mouths.

As for dinner, it was delicious: spaghetti with bok choy, poached egg and romano cheese. Note: the recipe I linked to does not include the dirt.

The recipe is dead simple - the only hard part is poaching the egg (but it's easy after the first couple of tries)

*The short version of my objection to these ideas is that bacteria elicit one type of immune response that, when over-active, causes some types of diseases (like multiple sclerosis, type-I diabetes etc), while parasitic worms activate a different type of response that, when over-active, causes other problems (like allergies and asthma), yet exposure to both bacteria and worms seems to correlate with decreased prevalence of all of these disorders. Clearly, we still have a lot to learn.

Kevin Bonham About the Author: Kevin Bonham is a Curriculum Fellow in the Microbiology and Immunobiology department at Harvard Medical school. He received his PhD from Harvard, where he studied how the cells of the immune system detect the presence of infectious microbes. Find him on Google+, Reddit. Follow on Twitter @Kevbonham.

The views expressed are those of the author and are not necessarily those of Scientific American.

Comments 16 Comments

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  1. 1. jerryd 4:40 pm 09/18/2013

    I find the dirt theory viable. We were designed for 200k yrs to have dirt on and in us and not having it now, causing problems, shouldn’t be surprising.

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  2. 2. DrKrishnaKumariChalla 1:03 am 09/19/2013

    The best way to develop immunity is to allow low amounts of microbes to enter the system – much below the inoculum potential – that way you don’t develop a disease caused by the microbes at the same time develop immunity. If your nutrition is poor – like people in several developing countries face – again the immune system will be weak and this situation is different from those where people get adequate and proper nutrition to develop a good immunity to diseases. Therefore sanitation is more important in the areas of the poor.
    I am happy to say I never got a fever or a cold for the past 20 years! All that I get when I go to a place of high density microbes is a low intensity sour throat. This is not magic. I am a Microbiologist and I know how to hoodwink these little creatures that cause suffering around the world! And, most importantly, I have the whole picture of microbial world in my mind to do this! Yes, I am well armed with knowledge to fight the cute little devils successfully!!

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  3. 3. louisianaboy 3:54 am 09/19/2013

    This may gross some people out, but my grandmother used to give us a concoction made from cow chips, cow pies, cow patties, cow poop. We drank it at least three times a year. We never got colds, no one ever missed a day of school and other than the usual fractures from falls and sports, everybody grew up healthy.
    We ate sugar cane straight from the stalk, fruits straight from the tree or vine, even crawdads raw from swamp water. To this day I still pick, crack and eat my own pecans.

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  4. 4. darrellperu 8:17 am 09/19/2013

    Here is a question for you. We live in Peru and were instructed to rinse all of our fruit and veggies in a light iodine solution for 20 minutes before anything. How does this process affect he gut microbes and what type of possible long term effects might this have on us and our kids? Would you consider this a smart method for dealing with microbes our bodies are not accustomed to having been raised in the clean US?

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  5. 5. Kevbonham 1:08 pm 09/19/2013

    @ JerryD – true, it makes intuitive sense, but that’s not always the best gauge for truth. In this case, there seems to be a lot of experimental evidence as well though.

    @ Louisianaboy – That concoction *does* sound gross, and seems like a recipe for intestinal infections. Also, I think you may have missed the point here – the idea of exposure to microbes isn’t to guard against infectious disease, but to regulate the immune system in order to protect against inflammatory disorders (where the immune system is *over*-active).

    I’m not convinced those poop shakes had any effect on your lack of colds, but if you don’t have allergies as an adult, they might have helped a bit with that.

    @ Darrellperu – Iodine will kill most of the microbes on the fruits and veggies, but in your case, I’m guessing this is a good thing. If you’ve been advised to do so, it’s probably because there are infectious diseases that are being transmitted on food stuff, and the public health consequences of infectious diarrhea are much higher than the consequences of allergies.

    There are always risks and trade-offs for public health interventions. In developed countries with good sanitation, we can afford to be a bit more cavalier about cleanliness. In a developing country, where the water you use to rinse your veggies might itself be contaminated, using something like iodine is probably a good solution.

    To answer your questions directly – a cursory search of the medical literature did not show any research on the effects of iodine on intestinal microbes. Iodine has been used for a long time as a microbicide, and its (low) toxicity is pretty well understood. My guess is that the long-term effects of using it in a rinse at low concentrations will be far less troubling than the risks to your kids of ingesting infectious diarrhea-causing microbes.

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  6. 6. smartpatrol 1:45 pm 09/19/2013

    On this same subject a thought occurred to me while reading an number of different articles covering the pervasiveness of parasitic round worm infections in ancient and medieval times(round worm eggs in coprolites) that perhaps partially obesity is a result of an adaptation to accommodate/prepare for the extra energy it takes to sustain a parasitic infection. The idea being that in the absence of such an infection obesity and perhaps overeating as the result.

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  7. 7. Kevbonham 2:31 pm 09/19/2013

    @ Smartpatrol – That’s an intriguing hypothesis, but I don’t think it’s necessary to explain obesity. A normal attraction to calories (which would have a selective advantage regardless of roundworm infections), coupled with a plentiful supply of cheap calories in the modern world is sufficient.

    I’m trying to imagine how you could test this idea experimentally… Would be hard.

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  8. 8. smartpatrol 4:39 pm 09/19/2013

    @Kevbonham sure, I am not suggesting it is “the” answer to obesity for the very reasons you listed. Just a thought in the same vein as micro gut bugs vs macro gut bugs.

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  9. 9. Kevbonham 11:48 am 09/20/2013

    @ smartpatrol – fair point. Helminths do figure in quite prominently to the hygiene hypothesis as well, and there are people working on potential therapeutics based on them.

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  10. 10. Bora Zivkovic 1:37 pm 09/20/2013

    We actually published something about this and worms:

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  11. 11. DougAlder 3:42 pm 09/20/2013

    Couldn’t help but think of the old saw – you need to eat a pound of dirt before you die.

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  12. 12. BixBW 7:23 pm 09/22/2013

    What about pesticides? Will a brief rinse leave behind any agricultural chemicals?

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  13. 13. Kevbonham 9:43 am 09/23/2013

    @ BixBW – To be honest, I don’t know. I doubt rinsing supermarket veggies will get much improvement over the washing they already do before it hits the shelves.

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  14. 14. zdomike 9:09 am 09/27/2013

    As you know, FDA recently doubled allowable glyphosate residues in food.
    My concern is that human and animal digestion is changing with a constant diet of foods under the spray regimen of RoundUp. RoundUp, or glyphosate and/or AMPA, has antimicrobial, antibiotic or antihelmintic action and a long half-life in most conditions. Are RoundUp-resistant bacteria evolving – and are these beneficial bacteria or the most damaging types?
    The mystery of digestion is the WildWestFrontier right beneath our noses.

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  15. 15. Kevbonham 12:22 pm 09/27/2013

    @ zdomkie – It’s possible, though there have also been studies showing certain microorganisms can consume glyphosate as a nutrient and grow better in its presence. Of course, which microbes are inhibited and which are helped is an important question, though I’m not familiar enough with this specific literature to draw any conclusions. Maybe I’ll do some more reading and do a post on this topic. Stay tuned!

    There are two things I’d like you to keep in mind though:
    1) In vitro studies where a particular chemical is added to culture medium with some bacteria is a far cry from the behavior of that same chemical and the same microbes outside of the lab. And the effects of the food once it reaches your table are even further removed. These studies can certainly be informative, but they are by no means definitive (whether they show harm or lack of harm).

    2) This is more important: you *cannot* evaluate glyphosate on its own. Let’s say someone determines that glyphosate inhibits the growth of some beneficial bacteria. This is not evidence that glyphosate is bad. Farmers are going to use herbicides – even organic farmers use herbicides – and you have to evaluate one option against other potential options.

    There’s a conversation to be had about how to reduce herbicide usage – there are farming techniques that are a bit more costly but would be much better than herbicides, but remember that the use of roundup doesn’t replace no herbicide, it replaces herbicides that are in many cases far more dangerous and used at far higher concentrations (

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  16. 16. lisagene 8:13 pm 10/3/2013

    This was a very interesting article. I have noticed that street people in my city, Austin, Texas, never appear sick, yet are obviously dirty in their person and wherever they live. I noticed a similar article on

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