Are you there Al Gore? It’s me, Microbiome

In the 50 years since the book “Silent Spring” sounded the alarm on humankind’s poisoning of the biosphere with synthetic pesticides like DDT, the grass roots environmental movement has tackled issues ranging from clean air and water, animal rights and acid rain to the more recent mega issue of global warming. Despite these and many other efforts, a mere 19% of Americans report being active participants in the environmental movement, which might account for why humanity appears to be doubling down on its effort to degrade global ecosystems, putting us on a trajectory with an unfavorable outcome. But this might be about to change. Results of the Human Microbiome Project published this past summer may have unwittingly handed the environmental movement its Great Leap Forward by turning all of us into ecologists overnight.

No less than 200 scientists from more than 80 institutions published the results of the 5-year, $170M Human Microbiome Project in a series of major scientific papers. Though countless studies linking the trillions of microbes on and in our bodies to human health and wellbeing had appeared over the last decade, the results of the Human Microbiome Project has completely captured the public’s imagination with all things microbial.

As it turns out, 90% of the cells in our body are microbial – making us more microbe than mammal – a supraorganism, thus making the human body best viewed as an ecosystem. This biological reality and changing definition of Self is quickly making our current perspectives and views on nutrition antiquated. While we eagerly await the promise of that other genome project – the Human Genome Project – to deliver us from sickness and disease, microbiologists can predict with 90% accuracy whether someone is lean or obese from their gut bugs alone

While researchers are cautious and right not to oversell the microbiome (much work is still needed to confirm causation for many ailments), the direct or indirect implication of microbes in a staggering number of ailments and diseases of the modern world, reinforces that we are on the cusp of a paradigm shift from the orthodox notions of health and disease.

While modern medicine will be quick to put into practice this new knowledge and accepting of its roots in the principles of ecology and evolutionary biology, the field of nutrition science, given its myriad and tangled history of stake holders and its entrenched notions, may be a little slower on the uptake. Nevertheless, the emergence of the microbiome as a key player in human health represents an extraordinary opportunity that cannot be missed.

Currently 50% of the world’s population lives in urban settings, with that number set to increase dramatically as more people move from poverty to middle class. This reality has always been and will always be the greatest challenge to modern human health and to creating a global sustainability agenda for humanity. It is at this interface between the terra firma of our evolutionary past and the enhanced material standard of living that modern development promises, that ecological principles underpinning human-microbiome interactions and our success as species will allow an entire generation to reconnect with nature.

By reframing human health in social-ecological terms against the unprecedented shift from village to urban culture, we can move away from the tired rhetoric of a calorie is a calorie and eat less, move more messaging, to a more thoughtful framework that recognizes health and disease on the basis of the ecological tenets of diversity, stability and resilience.

The shift to urban settings is characterized by improved hygiene and rapid adoption of highly processed westernized food. Though improved hygiene has many benefits, scrubbing soil from our bodies and food has thrown our immune system into an over reactive tailspin and is responsible for the skyrocketing increase in allergies and autoimmune disease. Researchers recently discovered that as the amount of glass and concrete in your neighborhood increases, and the diversity of native plants decreases, the microbial composition of your skin changes and the risk for allergies goes up.

As we unwild our bodies, food and lifestyle, we reduce diversity – changing the time-honored symbiosis of ‘us and them’ on which our immune system came to depend. For our personal health, rewilding our surroundings and being less phobic about dirt in our lives, would go a long way towards increasing diversity and possibly have the knock-on effect of extending the knowledge of a diverse Self into a broader stewardship of estuaries, forests and agriculture.

Once we start down that road of awareness that the host-microbe relationship is an embedded part of the larger biosphere, we begin to start thinking about health as part of a social-ecological system and provide an on-ramp to connect the dots on the very abstract issue of global stewardship. The burning and clear-cutting of vast swaths of the world’s rain forests begin to register as a moral imperative when considered from the very personal experience of the scorched-earth strategy of broad-spectrum antibiotics on your own inner ecosystem. In both cases, stability and resilience are tested – left untended; will either ecosystem return to its original or some altered state, with less resilience to future perturbations?

Just as invasive species move into recently slashed and burned ecosystems once bolstered by diversity, the clear-cutting bursts of antibiotics or slow eroding of resilience through repeated dosing, opens the pathogens door to disease.

Forthcoming book by the folks at Human Food Project. Click Here if you would like to receive a notice when this book becomes available.

Further example of how ecosystems respond to perturbations is provided by the Deepwater Horizon oil spill in the Gulf of Mexico in 2010. The deep-sea oil plume caused a shift in the sea-going microbes, with an enrichment of species and genes capable of hydrocarbon degradation. Our shift to an urbanized diet of highly processed and easily digested carbohydrates is somewhat analogous in that studies in animals and humans show a substantial shift in microbial communities when challenged with these substrates in their novel abundance. Since there is no precedent for such a diet in the evolutionary history of the human-microbe relationship, our westernized diet is best viewed as a perturbation. The impact on the long-term resilience of the microbial community, and thus the health of the host (us), is unknown. However, the precipitous rise in ‘diseases of civilization’ suggests we have shifted the equilibrium of our inner ecosystem to a new state.

Human-driven change to the global environment has many outcomes, of which climate change is the most prominent. Away from the public microphone, climate scientists have begun to think the Earth System is likely headed to an undesirable state unless dramatic and radical changes in governance and public behavior is experienced. It could be said that the health of humanities inner-ecosystem due to urbanization is fast approaching the same tipping point – though our current disease burden suggests we may already be there.

Moral psychologists (yes, there is such a field) suggest that climate change does not register emotionally with most people, in the same way that terrorist attack might, but if you could connect personal moral norms to climate change as a wrong that needs to be righted, then you stand a chance of rallying people to action in greater numbers. In other words, get people to feel it in their gut

So pick the ‘meat issue’ for example. If you think our overconsumption of meat is contributing unnecessary green house gases to the atmosphere and contributing to global warming and squandering limited water resources, then connect it back to the human gut – a little closer to home. Researchers recently discovered that 42 known antibiotic resistant genes originating from antibiotic treated livestock have been recently found in the human gut microbiome and may be contributing to clinical antibiotic resistance in humans (proponents against GMO take note). This just might be the kind of gut feeling an entire generation of squiggly light bulb environmentalist needs to feel.

14 Comments Add yours

  1. Just a quick suggestion. I and some others I know sometimes will not post about things on the web unless there is an author (even a pseudonym) attached to the item. Having this listed as by “The Human Food Project” is a bit awkward in that regard …

    1. good point jonathan. actually, nvr occurred to me as important. i scribble everything posted on the site – Jeff

  2. sunwriter22 says:

    If being human includes being 90% bug…and we kill the bugs with too much cleanliness and antibiotics etc,, then will we still be human ??

  3. RadiantLux says:

    Pastured meat raised the traditional way without anti-biotics and hormones is still a healthy food for humans. It is the most nutrient-dense part of the meal. Raising animals this way is a renewable system, as the waste is used for fertilizer. Land that cannot grow crops can feed herding animals. Corn and soy are not the natural diet of ruminants.

  4. @RadiantLux, currently 10 billion animals (compare that with 300 million human population) are raised for slaughter in the U.S. every year. Most of them come from factory farms. Let’s say we put them all out to pasture, where would we put them?

    You are also confusing caloric density vs nutritional density. Compare for example chicken ( and cabbage (

    Lastly, please research, i.e. go out and survey land where pastured animals eat vs where they don’t. Here is an example of what you might see:

    Contrary to what you might have been told, raising animals in confined areas, be they factory farms or pastures, is not good for the environment.

  5. Lars says: = True, you MIGHT see this. But it is called OVERgrazing. Plus, perennial polycultures grow the soil while annuals deplete it and will require cover crops. Think about the fertility of great plains due to the prairies and millions of bison.

    1. The great plains you are talking about do not have animals confined in a limited area. They are free to roam the lands and migrate as seasons change. I do not know of any farmer who will not put up fences to protect his or her property and thus limit the movement of the animals within that perimeter. That land is devoid of flowering plants that support bee populations and really any other wildlife that contributes to the life cycle of that ecosystem.

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