Tiny invisible bosses

“We are bulky ornaments on life’s skin,

riding the surface, only dimly aware

of the microscopic multitudes

that make up the rest of the body,”

From the book, The Forest Unseen, by David Haskell.

Sometimes the scale of things makes all the difference. My microbes are invisible to my eyes, but increasingly important to how I “see” my own health and our collective public health.

My gradual change in thinking began a few years ago when I donated information from my home and my own body to two different research projects. One was the Ubiome project, which is mapping the microbes in thousands of human guts. The other was the Wild Life of our Homes project, which is mapping the microbes of homes in all 50 states in the United States.

For the Wild Life project, I used a swab that looked like an overgrown Q-tip to take samples from doorways and my kitchen counters and my pillow. I mailed that swab in a vial to the researchers. For the Ubiome project, I took a sample of feces from my toilet paper and sent that. In each case, the samples eventually were sequenced. A lab checked a portion of the RNA sequences in the samples to identify the microbes.

Do the microbes in my own gut make me healthy? Is the ecosystem of my gut different than my husband’s? Each project is asking a question about the vast largely uncharted multitudes of microbes that live in and on our bodies, and in our homes. I wrote in  earlier blog post about these projects.

Donating these microbes made me curious. Learning more about my own skin – literally what lives on my skin – made me wonder more and more. Living in Seattle, I am surrounded by science that probes what is known as “big data.” Our town is especially full of scientists who specialize in mind-bogglingly  large sets of data, including terabytes of information from the genetic sequences of thousands of bacteria living in the human gut, to name one example. These data scientists have to invent their own education, because typical classes don’t serve them. I met some of them when writing a story for Seattle Business magazine.

Many microbiologists will tell you – the microbes don’t just outnumber us on Earth, they add up to more biomass than all the terrestrial mammals of earth added together.  While the comparison may seem unfair, the point is that we should not overlook the microscopic world of our planet.  Our indifference to these creatures because of their scale is exactly what author David Haskell in the quote above eloquently points out is blindness.

During a recent conference of citizen scientists, I had reason to think about this blindness. Our session explained how people donate microbes  for a variety of research projects. The participation itself, I would argue, changes the way you look at the microbes. But it also changes the way you think about scale. You appreciate that the collective action of millions of small creatures may influence bulky organisms like ourselves. In a similar way, going to a conference can make one appreciate the collective ecosystem of thousands of citizens. Might we make big changes happen?

During the conference, many of us talked about whether people who volunteer to collect data for science emerge from the experience with new outlooks. There are more and more people involved in citizen science, so it is worth wondering whether they will vote or spend money differently because of it.

What may seem like an abstract discussion could save the life of someone you love, if they spend time in a hospital and come home with an infection from an organism known as clostridium difficile. These organisms can make people terribly sick and transplants of gut bacteria (in fecal matter) from healthy people have cured some of those patients. Recently, the Centers for Disease Control released new statistics suggesting that nearly half-a-million Americans are  infected per year.

Thinking differently about scale is one reason that pioneers thought of the fecal transplants to treat patients with C. diff infections. While we don’t understand enough to define a “healthy” microbiome, the change in thinking is mammoth. Most people share some similarities within their families of their gut microbiome and there’s some evidence we acquire our microbiome from our Mom.  Many questions spin out from this change in thinking.

One day when washing some carrots from a local farm, I wondered if the microbes in the dirt I was washing away might actually hold more benefit for me than the carrots themselves. At my local gym, I wondered if the reason people who exercise in groups seem to live longer could be related to to the microbe sharing that happens when we share mats and weights. I’m not suggesting either of these ideas is true but just pointing out that once you view the microbes as potential actors in your health, it makes you see differently.

Scientists around the world are now asking questions about microbial life in relation to human health, as well as the ecological health of our built environment and our wild places. They are demonstrating a new way to “see” questions about health. There is research on the relation of gut health to autism, obesity, diabetes and depression, just to give some examples.

As our knowledge about microbes increases, we may see our world very differently. We may be minor players in a game driven partly by these microscopic actors. Stay tuned for more posts on this topic. I welcome your questions.

Let me leave you with a wonderful 25-minute video by  microbiome reseacher,  Jonathan Eisen, who presented in March at a meeting called the Future of Genomic Medicine.  Sorry that the video begins with a short advertisement.

Image above used with permission of the Pacific Northwest National Labs. Taken by Janine Hutchison. Green is lactobacillus reuteri, purple is collagen microsphere, and brown is intestinal cell.

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.

Sharing my microbial fingerprints

Any day  now, I’m going to get lab results I’ve been waiting months to know. They will tell me something about my deep insides.  These will be maps of  thousands and thousands of microbes that live inside my gut and in my house.

But just like some ancient relics pulled from tombs of lost civilizations, nobody knows exactly how to read these maps yet. I’ll get the names of my microbes and the sequences of their DNA, but I won’t know exactly what the maps mean.

At a public meeting in Seattle on Feb. 25, I’m joining scientist Scott Meschke to talk about the human microbiome.

For more than a year, I’ve been part of two different citizen science programs. Both are aimed at understanding more about our health and the myriad ways we are tethered to the health of the microscopic creatures that share our homes and our bodies. One project sampled my body and the other my home.

While much of these projects happens via computers and online interactions, it began in a face-to-face encounter that I had with scientist and author Rob Dunn. I was on a field trip as part of a meeting of the National Association of Science Writers at the University of North Carolina.  During one stop, Dunn pinned me as tightly as an insect sample to styrofoam display while he talked about microbes. Science knows more about exotic environments from mountains to the sea floor, but little about the  “wild life” inside our homes. He launched a project to collect samples from every state and try to find patterns of meaning there. I sent in my samples to The Wild Life of Our Homes. More than one thousand other people joined me.

Wild Life sent detailed instructions for me. They wanted samples of dust from different parts of my house.  They wanted dust that had not been disturbed for a while, so one sample location was the upper sill above a doorway. The other project, Ubiome, asked me to mail in a sample of feces.  The two projects are separate, but both are measuring microbiomes associated with me. Both have promised results soon.

Researchers have found intriguing differences between microbiomes.  To give one example, people with diabetes have different microbial percentages than people who don’t have diabetes.  Obese mice (and perhaps people) have different organisms in their gut than non-obese mice.  A subset of children with autism seem to have differences from children without the diagnosis, and more mouse research suggests that changing the gut may change the behavior of the mice. Lots of speculation, but very little research that would prove causation.

If you will be in Seattle in February, join me and Scott Meschke to talk about microbiomes. What might I learn from mine? What might we all learn collectively from thousands of samples?

If you are new to these ideas, enjoy an  animator’s vision of what it all might mean, courtesy of National Public Radio.

 Image above used with permission of the Pacific Northwest National Labs. Taken by Janine Hutchison. Green is lactobacillus reuteri, purple is collagen microsphere, and brown is intestinal cell.