Bugs ‘R Us
Rebecca Johnson
Word Count 1412
When I mentioned to a friend that I was researching the microbiome for a magazine story a few years ago, she asked if that was the project in Arizona where people lived under a dome and went crazy? That’s the biosphere. The microbiome is the term used for the trillions of bacteria that live on and in our bodies, outnumbering our own cells by an astonishing 10 to 1. Technically, bacteria, which often consist of a single cell, are not insects. They don’t have legs, they don’t bite, they don’t hatch eggs. But when we get sick, “we have a bug” and if you look at some bacteria under a microscope, they look “bug-like.” Perhaps we should call them our inner critters.
We’ve been trained to believe that bacteria are bad—thus antimicrobial soaps and the antibiotics we take for a sore throat– but we now know that the majority of the bacteria in our gut are actually performing all sorts of essential functions such as digesting our food, creating vitamins and a lot of other things we’re only just beginning to understand.
Among the more astonishing revelations: the intestinal microbes of obese mice transplanted into thin mice will make the fat mice thin, as well as vice versa. A microbiologist can tell with 90% accuracy whether a person is obese just by looking at her microbiome. Life threatening cases of diarrhea can be cured by “fecal transplants”, taking the poop of a healthy person and putting it into the bowels of a sick person. Even personality seems to be affected by our microbes. As a species, mice seem innately fearful, staying close to walls and avoiding open spaces but mice raised in sterile, bacteria-free environments, don’t skulk. They’re happy to strut across the middle expanse of an empty cage.
Health food store shelves are filled with “prebiotics” and “probiotics”, to promote your “good bacteria”, but those claims are largely unsubstantiated. Remember those ads for Activia yogurt where Jamie Lee Curtis lounged on a couch and promised the yogurt could cure irregularity? Turns out, not so much. The Federal Trade Commission forced the company to drop the ads and fined them twenty one million dollars for deceptive advertising.
Despite all the fascinating things I learned in my research, the magazine that assigned the piece killed it. The problem was that scientists were too hesitant to make any claims about humans given that most of the research had been done on mice. Take Ilseung Cho, Phd, then a researcher at N.Y.U., who made headlines when he published an article explaining how antibiotics cause mice to gain weight (short answer—polysaccharides), something cattle ranchers have always known. The faster you can get a cow fat, the less money you need to spend on feed, which is why so much of the meat we eat contains traces of antibiotics. After Cho’s research went public, he spent a few sleepless nights worrying how people might react. “I don’t want anyone to stop taking antibiotics they need because they’re afraid of gaining weight,” he says. “This is probably one of the most rapidly developing fields of medicine right now, but we have to be very careful about what we say to the public. We have a lot of information right now, but I like to compare it to the census of a city. We know who lives there, but how do they get along? How are they related? We’re still figuring all that out. There is so much variation among individuals. We don’t even know what a healthy microbiome is.”
The Human Gut Project, a crowd sourced science project initially based out of the University of Colorado and now housed at UC San Diego, is hoping to answer those questions by asking ordinary individuals to keep track of the food they eat for a week and send in a sample of their poop, all of which I did. A few months later, I received my results in a gaily colored set of charts, the contents of which can be boiled down to….the best selling writer Michael Pollan has better poop than I do. (He volunteered his results after doing an article on the subject for The New York Times.) My personal profile showed a dominance of firmicutes and bacterioides, the two most common microbes in all the samples--while his registered five different types. Even though we are not exactly certain what constitutes a healthy biome, it is generally accepted that diversity is better than uniformity. By that measure, a five beats a two. Then again, no real surprise there. Pollan is a famously good eater, the kind of person who keeps his own worms for composting and ferments kimchi. I’ll eat a salad if someone else makes it. But all that chopping and washing? The spirit flags.
“Wow,” I joked to the three scientists from the Gut Project dispatched to discuss my results over a conference call. “I’m surprised I’m alive.”
“It’s very hard to draw any conclusions,” they reassured me.
“Come on,” I pressed. “Who can live up to Michael Pollan? Why is he even on the chart?”
“I guess we put him there as something to aim for,” they admitted.
Given the sadly uniform state of my personal microbiome, it’s tempting to say, who cares about a bunch of bacteria? But, in fact, many of the microbiologists in this field believe that the modern diseases now plaguing the first world—asthma, obesity, diabetes, celiac disease, ulcerative colitis, Crohn’s disease, eczema, some cancers, even autism—may actually be linked to the poor state of our microbiome. Whether through repeated exposure to antibiotics, which tend to wipe out both the good and the bad, or our fiber-poor, heavily processed diet, the “old friends” theory holds that our degraded gut bacteria can no longer accurately determine friends vs. foes, thus causing the body’s immune system to turn on itself. When your microbiome sucks, everything is a foe.
On the one hand, it’s kind of creepy to think that our health is being determined by a trillion tiny organisms busily reproducing, waiting to be fed. On the other hand, this so-called “second genome,” as some have dubbed it, does provide us with a way of viewing our health in which we could potentially be more active participants, if we knew what we were doing.
Impatient with the slow roll out of data, Justin and Erica Sonnenburg, two Phd scientists in the microbiology department of Stanford University took matters into their own hands by writing, The Good Gut: Taking Control of your Weight, Your Mood and Your Long-Term Health . I interviewed them the year before it came out. It turned out to be a best seller. As Justin explained, “We both realized it would take decades for this stuff to be useful at the therapeutic or diagnostic level. Alternatively, we could just teach people how to eat.” Thinking about your microbiome every day will require a complete paradigm shift for most people, one probably best started when young. When Sonnenburg’s children (then ages 5 and 8) complained about not wanting to eat broccoli, he reminded them that they’re not just eating for themselves. “I tell them they have a pet inside them that needs to be fed.” Both of Sonnenburg’s children were breastfed for over a year and each has only been on antibiotics once in their lifetime, compared with a national average of eighteen.
“We are early in the research,” Sonnenburg says, “but I am willing to go out on a limb because it is empowering for people to know. We should be getting 30 grams of fiber a day, most people only get 10. If you don’t get it, the microbes eat the mucus in the intestines and that’s where we get the leaky gut and the inflammation.” Rural societies in Malawi and Venezuela get an astonishing 60-70 grams a day and have a radically different microbiome from people like me. Not surprisingly, they rarely develop all those first world diseases; then again, people like me tend to live longer because if I do get pneumonia, I have access to antibiotics, not to mention indoor plumbing. What Sonnenburg is advocating is a marriage of the best of both worlds. “We have cleaned up our water supply,” he says. “But our diet has gone downhill. The microbiome is telling us to go back and recapture the way we used to eat.”
Rebecca is a writer and editor whose work has appeared in various publications including (alphabetically) Elle, Mademoiselle, The New Yorker, The New York Times, The NYT Magazine, Salon, Vogue (contributing editor 1999-2020). Johnson is the author of the novel And Sometimes Why. She lives in Brooklyn, New York with her husband and two children.
