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.







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.



Social + citizen science meets my porch

The envelope arrived a few days ago. Happy to see that my data loggers from the North Carolina State project known as Your Wild Life arrived. They are tiny metal cylinders, but powerful in their own way. For those of you who don’t know much about citizen science, I’m a volunteer helping gather data for a lab run by Rob Dunn, a biologist and writer. I was lucky enough to meet Rob and hear a lecture from him during the NASW conference in 2012.

Meeting Rob and hearing him discuss the microbiomes of our homes made me sign up for one of his lab projects called “The Wild Life of our Homes.” Rob’s team is collecting data from about 1,000 houses across the United States. When I write “data” you should picture a giant Q-tip.

To help Rob’s project, I had to swipe this giant Q-tip across a few surfaces in my house. The microbes captured by these swabs will be analyzed in a laboratory in Colorado. (Wild Life has promised me photos of this lab.) Just to return to the data loggers – some of us who sampled our homes are gathering additional information on temperature and humidity. (That’s what the two loggers at my home will be doing.)

But my participation in Rob’s project is honestly just part of an evolving interest of mine in what some people call big data. For someone like myself, who writes mostly about medicine and health, big data might have seemed more the territory of computer scientists. But believe me, big data is a part of all of our health lives. Carl Zimmer has written eloquently about this in this story.

Collecting information on the thousands of microbes (and their genetic footprints) in my house may turn out – years from now – to yield some useful information about health. As you may know, there are already people studying the internal (gut) microbiomes of people for clues to how that data may be mined for useful patterns. One of these research groups is also using citizen volunteers – Ubiome.

You can follow both Wild Life and Ubiome on Twitter at @yourwild_life and @ubiome

In Seattle, I meet scientists who are working at this intersection all the time. The Institute for Systems Biology is just one example. ISB has held conferences about the microbiome for several years, and you can listen to archives from 2012 at that link.  On the campus of the University of Washington, there are dozens of people I know who use algorithms to analyze giant data sets related to human health. There is much more to come on all of this.