Man makes his microbes into research study

Richard Sprague keeps samples of his own feces, in the family freezer, so he can send them to a Stanford University laboratory. Some days he tries to improve his sleep by swallowing potato starch to feed a certain population of microbes in his gut. Lately, he’s been studying his brain acuity every morning to see if changes in his diet can influence it.

A 52-year-old father of three and an ex-Microsoft manager who lives on Mercer Island, Sprague is a volunteer, among thousands of others, in a movement called “citizen science.” Read more at Seattle Magazine.

The hairball of citizen science

The hairball is jargon for data scientists. It means a special graphic that illustrates intersections.

When I visited the Citizen Science Association’s first conference in San Jose, Calif., in February, it felt like a living hairball. Every one of the 600 people was already a networker, an accelerator, or somehow a person forced by curiosity to ask other people to help assemble science answers.

There were birders (Loon counters from Maine), microbiologists, physicists and policy wonks.  If some of you don’t know the delicious explosion of citizen science, please detour now to read about games of proteins, games of neuron-mapping, games of whale song matching and thousands of other projects here.

But like catching lightning bugs and magic in a bottle, there were people who thought the very labeling and defining of citizen science might break its tender wings. This first-ever conference tried to find the most common ground between projects and hoped that sharing best practices (and sharing conference rooms) would save some people time and trouble finding the right methods.

I don’t have answers for any of the wonderfully provocative questions I heard in San Jose. But I came home from #citsci2015 (as tagged on Twitter) newly impressed with the collective power of citizens. My own panel about microbiology included two projects where I donated samples: The Wild Life of Our Homes and Ubiome.

Our panel included California high-school science teacher, Bethany Dixon, DIY biology volunteer Patrik d’Haeseleer, David Coil and  Jenna Lang, both of the Eisen Lab at the University of California at Davis, Adam Robbins-Pianka of American Gut and Holly Menninger of Your Wild Life at  North Carolina State University.  Collectively, we bonded most over what  is not known about microbial ecosystems rather than what is known.

Studying the ecosystems that microbes create has been compared to discovering a new Amazon rain forest. It is tantalizing to find out that obese people and diabetic people have different microbes in their guts, but we are far from understanding why.  The microbiomes of individual houses differ, as my panel member Menninger is studying, but we may be years from understanding how and why. We were a panel of people at peace with puzzling complexity.

Imagine every one of the thousands of different microscopic creatures living in your gut playing an unknown and changing role in your life and your health. That’s quite a hairball, and untangling it will take years. I’m very glad to have met the people at #citsci2015 as passengers with me on this journey.

If you are pursuing citizen science in some way, please let me know. I will continue writing about it here.

My bacteria and yours – telling stories

Small pictures of the microbes growing in my own gut, and in my own house, are filling my mind with questions.

Why do I have a higher percentage of a bacteria family called Firmicutes than other people? Why did my house have a higher percentage of plant-based material on our door sill than the other houses?

If you are hoping for a satisfying dramatic conclusion to this detective story, you will have to wait. Two different teams of scientists are both asking a fundamental biologic question using some samples from me and my house.  I’m a contributor to both Ubiome and The Wild Life of our Homes. Both teams returned some results to me, but not in their final form.

Join me in Seattle Tuesday, Feb. 25, for a discussion of this with scientist Scott Meschke.

As you can see from the illustration at the top, I’ve been given the chance to test a beta version of the dashboard that will eventually be available to all the participants in the Ubiome experiment. I can compare my own percentages to others in a graph or in other formats. As you can read in an earlier post, I sent a sample of feces to them in 2013. They sequenced the DNA of all the microbes they could find in that sample.

If you are new to the idea of the microbiome, you can see a very clever video about this that explains some of the complex symbiotic relationship with the microbes of our bodies. We need many of them to digest our food, to protect us from other microbes and perhaps, in some cases, to regulate some of our own body processes.

But before you get too excited about all the ways that scientists are studying our microbiomes, remember that the science of understanding exactly what is “normal” for any one person at any one time of their life is pretty primitive.

Scientists in recent years have investigated brain-gut interactions suggesting that mood swings and autistic behavior could be related to the microbiome. Just last week, a study was published about whether geographic variation in obesity is related to the percentage of bacteria known as Firmicutes.

What’s going on now is almost like Darwin sailing off to the Galapagos Islands and trying to catalog everything he found there.  Rob Dunn is the principal investigator on the Wild Life project, which has sampled 1,600 homes in the United States. We are creatures who spend most of our life indoors, but we don’t know much about what lives with us in those indoor spaces. In a similar way, those who are sampling the gut want to establish what species are there, in what relative numbers, and how this differs from person to person.

“It is fundamentally amazing,” Dunn told me during a phone interview. But it may take 10 years, he said, before the reasons and systems behind the microbiomes are better understood. “There are so many threads to pull,” he said.