Tuesday, August 12, 2014

the quantified microbiome visualization looks strangely like an appflow visualization...,

nationalgeographic |  Some of my friends are sporting wristbands these days that keep track of their bodies. Little computers nestled in these device inside record the steps they take each day, the beats of their heart, the length of their slumbers. At the end of each day, they can sit down at a computer and look at their data arrayed across a screen like a seismogram of flesh.

I got one of these devices as a gift recently. But as much as I enjoy wasting time with technology, I just didn’t care enough to put it on my wrist. I already know that I should run more, walk more, stand more, and avoid sitting in front of monitors more. I don’t need granular data to remind me of that.
But as I read the journal Genome Biology today, I decided that someday I might surrender to the Quantified Self movement. I’ll just have to wait till I can track my trillions of microbes from one day to the next.

Thanks to the falling cost of sequencing DNA, it’s now possible for us to survey the thousands of species that live in our bodies. A couple years ago, for example, I found out that I have 58 species in my bellybutton. But all I knew was that there were 58 species in my bellybutton at one point in time–that moment I swiped a Q-tip around my navel. But everything we know about bacteria tells us that our inner ecosystems can change swiftly. My bellybutton may be remarkably different today than it was when I put a Q-tip in it.

Eric Alm, a biologist at MIT, and a graduate student of his named Lawrence David decided to plumb this change by tracking a year in the life of their microbiomes. Each day, they saved some of their stool, and later, they extracted DNA from it to figure out which species of bacteria were living in their guts. David also spat some of his saliva into a tube each day so that he could compare how his microbiome changed in his gut compared to his mouth.

Even though their study only involved two people, it was still very much a Big Data project. And one of the major challenges of any Big Data project is to visualize the results in a useful way. A number on a wrist watch won’t cut it. Between Alm and David, they and their colleagues identified thousands of species of microbes. Most were rare, while a few hundred made up the majority of bugs in their bodies. Some species showed up briefly and vanished; others lingered all year.

Here’s one way to look at their microbiomes. It shows David’s saliva. Each band represents one of the dominant species (or operational taxonomic units). Species belonging to the same lineage (a phylum) have different shades of the same color.  Fist tap Dale.


Dale Asberry said...

Of course, visualizations have wide applicability to general data sets. Certain visualizations can then be chosen to better emphasize a certain point. For instance, why didn't they choose the same visualization for the gut microbiome?

Still, viewing the mouth as a metaphorical cable and bacteria as packets, what are the endpoints?

CNu said...

Yeah, yeah..., i'm interested in knowing the initiator(s) and responder(s) - beyond that, I'd like to know more about the number of connections, volume of traffic, and time of day, and how all of the above varies in concert by time of day.

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