You Are an Ecosystem

gut microbiotaYou are not yourself today. In fact, you are not yourself any day. Neither am I. We are collectives of trillions of selves, and most of these selves are not our selves: of the 130 trillion or so cells that make up our bodies, about 30 trillion are human and the other 100 trillion are bacteria, archaea, fungal, and other single-celled microbes.* Collectively, these are our microbiota.

Each of us is an ecosystem, one that has evolved over millions of years** to maintain some semblance of balance amid the vagaries of the outside world. Now we are screwing this balance up, with numerous unintended consequences for our health. What took millions of years to assemble is being rapidly undone in a matter of decades. The main culprit is antibiotics, which generally kill all bacteria indiscriminately, including the thousands of good species in our gut, mouth, nose, ears, skin, and nether regions. Of course, antibiotics have also saved millions of lives since their use became widespread in the 1940s. No one is suggesting that we stop using antibiotics, only that we use them more wisely.

Over the past couple years I’ve been annoying my friends by ascribing every ailment to problems with our microbiota. “The obesity epidemic is caused in part by changes to our gut microbiota.” “Oh, your friend’s son has autism – have you heard that gut microbiota might play a role?” “Broke your leg? Must be problems with your microbiota.” OK, not so much the last one (but who knows, maybe some of those little suckers help us incorporate calcium more efficiently). In short, I am a grotesque when it comes to the panacean influence of our microbiota. I believe we have just begun to understand our microbiota’s significance to our health and well-being.

Maybe we’re at the beginning of a paradigm shift in medicine. Michael Pollan seems to think so. “The drive for absolute control leads to unanticipated forms of disorder,” he says, referring to medicine’s efforts to control (destroy mostly) our microbiota and sterilize our environment. Microbiota testing will become more important in determining the cause of many ailments, and cures will often involve replacing missing microbiota. As it stands, when it comes to microbiota, most doctors don’t know shit about shit.

One who does is Martin Blaser, who has been working with human microbes for years. His book Missing Microbes is a convincing argument that we need to reduce antibiotic use where it’s unnecessary, create more antibiotics that target specific bacteria, and do more research on how our microbiota affect our health. From the book:

  • Up to 15% of calories in our food are extracted by bacteria in our colon
  • Nearly all chemicals in our blood come from microbial activity
  • 99% of the unique genes in humans are bacterial
  • The function of 30-40% of our microbial genes is unknown
  • Children in the U.S. receive about 17 courses of antibiotics before they’re 20
  • Children in the U.S. receive about three courses of antibiotics before they’re two
  • Babies born through cesarian section do not receive the natural complement of bacteria that babies born vaginally do
  • 258 million courses of antibiotics were prescribed in the U.S. in 2010
  • Antibiotics only work on bacteria, but they are often prescribed without knowing whether a sickness is caused by bacteria
  • Livestock in the U.S. are given 70-80% of all antibiotics to increase feed conversion ratios (making them fatter quicker), not primarily to prevent disease
  • Overuse of antibiotics has increased the resistance of many dangerous pathogens
  • Antibiotic resistance, combined with our compromised microbiota, increase the likelihood of a pandemic
  • The European Union banned antibiotics in animal feed in 1999
  • A remote Venezuelan tribe had more than 100 unique species of bacteria not found in a group of people in the U.S.
  • Aside from a long-forgotten study in the 19th century, it was believed that our stomachs harbored no bacteria until 1979
  • Some microbes are amphibiotic, meaning that they can be beneficial under some circumstances and pathogenic in others
  • There is evidence that Type I diabetes, celiac disease, Crohn’s disease, ulcerative colitis, asthma, allergies, eczema, obesity, autism, and some forms of cancer increase as a result of antibiotic use
  • Fecal microbiota transplantation (FMT) – transferring poop from a healthy person to a sick person – is already being used with much success for treating certain ailments, and may become more common for treating things such as obesity, autism, and bowel infections

We use antibiotics to make our livestock fat – what’s to make us think that antibiotics aren’t also having an effect on our own waistlines? There are about 80 million obese people in the United States, and obesity is the leading cause of death in the U.S. Our diets certainly have something to do with this, but according to Blaser, diet alone doesn’t explain the rapid rise in obesity over the past few decades. One study found that captive animals (lab and zoo animals), generally fed very strict diets, are also getting fatter – might we have changed their gut microbiota as well?

We have many studies linking our microbiota to our health, but we need much more information. With that purpose, the National Institutes of Health began the Human Microbiome Project in 2007. With our relatively recent ability to quickly and easily assay DNA, we are exponentially increasing our knowledge of what our microbiomes (the genes of our microbiota) consist of. Armed with this information, we should see some major changes in the next few years in how we look at many modern diseases.

I’ve been happily playing with my diet and exercise regime over the past few years, and tracking some health and well-being outcomes. In another Study of One, I plan to get my microbiome assayed soon. I’ll post the results here. Following are a few links to some studies and projects looking at our microbiota:

  • The Promise of Poop. This Science article outlines how fecal transplants have been quite successful for treating C. difficile infections and are being tested for other ailments.
  • This article implicates a certain gut bacteria in the onset of rheumatoid arthritis. Because this is an autoimmune disease, it leads to the hypothesis that gut microbiota may play a role in other autoimmune diseases.
  • This study indicates that Crohn’s disease, another autoimmune disease, is “marked by dramatic changes in gut bacteria,” and early courses of antibiotics may make things worse.
  • A brief history of antibiotic use to make farm animals grow faster and how this might have implications for people.
  • This study showed that mice given gut microbiota from fat and thin twin humans became fat or thin themselves, and that, when living together, the fat mice (who happen to eat some of the droppings of their thin brethren) eventually developed similar gut microbiota to the thin mice, and subsequently lost weight (but not vice versa).
  • Our friend Martin Blaser has another study indicating that early use of antibiotics may lead to obesity.
  • Some microbiota in obese people’s guts may even cause cancer, by increasing certain types of acid.
  • How autism may be affected by gut microbiota.
  • Gut microbiota may even affect our mood and behavior. What are the implications for mental illness and depression?
  • Summary of new findings in 2013.
  • Some gut microbiota can be quickly altered.
  • This is tangential, but some bacteria not normally associated with humans may be used to combat cancer tumors.
  • Gut bacteria turn cocoa into an anti-inflammatory.
  • Gut bacteria in the Hadza.
  • This guy’s trying to see if he can change his gut microbiome to be more like the pygmies.
  • And, this just in: Antibiotic use is correlated with the development of allergies. This study suggests that peanut allergies may be alleviated by the introduction of Clostridia bacteria. How about a few carefully tailored probiotics to get rid of your allergies? Might be a couple years out, but it will be a reality soon.


*Not to mention the trillions of viruses that are also part of our microbiota.

**Modern humans are about 250,000 years old, but we are part of an evolutionary tree that goes back over a billion years, and guts evolved in animals several hundred million years ago.

***Mice sure do get the shit kicked out of them in our health research. I’m not quite sure where I stand on this – is it better to kill a chicken for a few meals or kill a mouse for useful knowledge that may save lives? I guess it depends on how useful that knowledge is and how necessary a certain protocol is – it seems like much of the information we gather from animal studies could be amassed in humane human studies and trials.

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