Poo And You: A Journey Into The Guts Of A Microbiome

The trillions of microbes that live in our guts and on our skin have the power to affect our health in big ways — from stomach disorders and autoimmune diseases to acne and mood. The secret life of what scientists call our microbiota has remained largely obscured, however, because many of the organisms in the gut can't be grown in a lab.

Quick and relatively cheap genetic sequencing is at last offering a glimpse of these inhabitants of our bodies. Over the next few posts, I'll investigate what one's microbiome — the genetic profile of these organisms — can tell us about our health as well as what that new view says about us and how we're connected to others.

Unlike the genome, which is relatively fixed, a person's microbiome is changeable over a lifetime — and perhaps even daily.

Early individual microbiome sequences — which show far greater variety among people than the human genome — are now trickling out, painting the picture of gut communities of minor celebrities, including writer Michael Pollan and ultrarunner Dean Karnazes.

Results from small group studies are also bringing new insights. We now know, for example, that changes in the microbiome are linked to some intestinal ailments such as inflammatory bowel disease, and other recent findings suggest that particular gut microbe populations might even affect how our bodies break down medications.

As a health journalist, I wanted to know how it all worked — the guts of the process, so to speak — and what a microbiome sequence can really tell us. So I signed up for the American Gut Project, a crowdfunded effort that is collecting microbiota samples — from guts, hands, mouths, dogs and dirt.

The project was founded by Rob Knight, a professor at the University of Colorado, Boulder's chemistry and biochemistry department, and Jeff Leach, of the Human Food Project and the London School of Hygiene and Tropical Medicine. Dozens of other researchers around the country help coordinate the project, which aims to be the biggest of its kind. It's self-sustaining because participants, including me, pay their own way.

And it doesn't cost much. I ponied up $99 to be in one of the early waves of the sequenced. All I needed to do was send in a sample I would collect at home with one of their kits.

Katherine Harmon Courage, her husband, David, and dog, Raz, at home in Colorado. The three had their microbiomes sequenced by the American Gut Project to see the microbes they shared, and those they didn't.

Courtesy of Daylene Wilson

As with the human genome, the big payoff of microbiome analysis — both scientifically and personally — will be in comparing results among different people.

The project has already received thousands of samples. Knight and his colleagues hope not just to make major headway in demystifying the microbiome, but also to help us understand what changes in the gut are linked to sickness and to health, and what links us to each other.

I decided to conduct my own experiment by buying kits for my husband (who was a bit reluctant to involve his microbes, especially after they had made their natural exit), our mutt (who couldn't care less about what happened with his contributions to our backyard), and my mother (who, as a science teacher, couldn't wait to participate).

The big question is, given so much common human DNA — among family and strangers alike — what makes our personal microbiota populations so incredibly different?

We know that doses of antibiotics can change the balance of bacterial populations in our guts (and often not for the better). And studies have shown that we share microbes with people we are around — but also with people we spent a lot of time around as children. This seems to be especially true of our mothers, from whom we pick up our first dose of microbes via the birth canal — and through breast-feeding soon thereafter.

But you don't have to share genetics to share microbes. One study showed that mice could actually "catch" beneficial microbial populations from their cagemates. And according to a study published last year, dog owners not only share microbes with their pooches, but they also share more microbes with other humans in the household than do those in canineless households.

Would I have more microbes in common with Mom or my husband? She breast-fed me and we lived together for the first 16 years of my life, after all. While he and I have lived together for just a couple of years, we share a home, a diet, a lifestyle and a dog. And what might our personal microbial profiles reveal about our individual health and life histories?

To have even a fighting chance at answering some of these questions, I ordered up our microbiome testing kits to probe the deep, juicy secrets of our guts and some of their inhabitants.

This is the first story in a four-part series.

Katherine Harmon Courage is a freelance health and science writer in Colorado. She is the author of Octopus! The Most Mysterious Creature In the Sea, now available in paperback.