To Get To The Bottom Of Your Microbiome, Start With A Swab Of Poo

Understanding the human microbiome takes much more work than just identifying the organisms that live in a person's gut. A genetic census of these microbes is really only the start of figuring out what they have to do with health and disease.

To find helpful patterns in the microbe populations, researchers also need to gather a host (no pun intended) of information from the people providing the samples. As participants in the American Gut Project, that means we — myself, my mom, my husband and our dog — answered questions about our life history. (Well, we helped the dog with his.)

Some of the basic questions were like the things I've answered to get a passport:

In what country were you born? U.S.

Some that I find on so many user surveys:

What is your race? Caucasian.

Then there were the questions about health that reminded me of a trip to the doctor's office:

Do you have asthma? No.

Were you born via cesarean section? Yes.

Have you had your appendix removed? Nope.

But the lifestyle questions were all over the map:

Do you take a multivitamin? No.

Do you bite your fingernails? No way.

Do you use fabric softeners? Why, yes, I do, the "natural" type.

For all of us, including the dog, we provided detailed dietary information. We tracked our food intake for a week, which, as anyone who has ever tried this for diet or health purposes knows, is no small task.

So my husband and I diligently logged the contents of our breakfasts (toast, almond butter and fruit), salad (kale, avocado and tahini-and-vinegar dressing), smoothies (oranges, protein powder and bananas), and splurge dinners (chicken tacos, margaritas and ice cream). We also logged our exercise as we trained for our second New York City Marathon together.

My mother back on the East Coast kept a diary of her diet. On a typical day she had kefir and granola for breakfast, homemade chicken soup for lunch, lasagna and red wine for dinner. The dog diligently chomped his usual kibble, making him the easiest of the bunch to report on.

But as a science journalist, I couldn't help but focus on the missing details.

There was no way to specify whether our toast was made from regular, whole or sprouted grains. Did our salad greens come from the farmer's market or pre-rinsed in a bag from the supermarket.

These factors, I thought, must have some effect on gut flora. Maybe there were extra nutrients from the sprouted grains and perhaps odd organisms lived on recently picked, hand-washed greens.

I asked Rob Knight, at the University of Colorado, Boulder and one of the leaders on the American Gut Project, if there were a million other questions he would like to ask study participants. Had he wondered if skipping details would mean he was going to miss some potentially big lessons about diet and gut health later.

But he had a pragmatic outlook. For now, he said, It's about opening the project to as large a population as possible, not gathering every possible piece of data. A 30-page questionnaire might turn up a few more correlations, but it would undoubtedly deter people, too.

The current eight-page version was, in truth, plenty long. And since these are still the early days of microbiome research, painting the broad strokes — more veggies versus fewer — and trends — chronic gut disease versus good health—is the initial goal. Perhaps future studies will be able to drill down on specific populations to find these more minute differences, he said.

The other trouble, of course, is relying on self-reported data. You can believe me. Honest. But can you rely on what other people say about what they ate and how much they exercised or flossed their teeth?

But, since Knight and the other researchers can't send out monitors to follow each participant around, information provided by the volunteers is the only feasible option. And other validation studies have found that questions like the ones they used result in answers that are close enough at this point in the research.

Our diets tracked, our surveys answered, it was time for the event some of us had been waiting for (me, my mother) — and others had been dreading (my husband) or oblivious to (our dog). It was sample time.

So I ripped into the plain white envelope that had arrived in the mail. Inside there were four clear tubes with two cotton swabs each. I ventured out into the backyard to find a fresh sample from our dog. The other two awaited private time at home.

The trick for collecting fecal samples, according to Knight, is to avoid overloading the swabs with, er, material. That'll just clog the lab's processing machines, he says. The slightest swipe from a used piece of toilet paper captures enough microbial genetic material to paint a detailed picture of your gut's full microbiota.

Samples discreetly taken, we wrote the dates and times on the tubes, wrapped them in clean tissue as instructed, and placed them back in the mail to the American Gut Project's lab at the University of Colorado, Boulder, where I caught up with them and the ones my mom sent from Connecticut the next week.

This is the second 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.