Mapping Microbes

Although you can't see them with the naked eye, microbes are everywhere. Your body and nearly every surface around you is covered in these tiny microscopic organisms. I'm going to explain how you will soon be able to characterize the microbial communities that live among us -- on surfaces like door knobs, crosswalk buttons, or the palms of your hands -- and compare your findings with those of others.

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Step 1: Collect a Specimen

(1) Moisten a Q-tip with solution (like water or a mild detergent)
(2) Swab your surface with the moistened Q-tip
(3) Place the swab in a sealed container, like a plastic bag
(4) Record information about your specimen collection, such as date, time, geolocation, and weather.
(5) Mail your specimen to a lab that specializes in sequencing, such as this one

ndpm says: Jan 3, 2009. 9:28 PM

Neat idea. Instructions and protocol are inadequate to make this a real science project, even for DIYers. I suggest interested parties draft a better procedure for everyone to use so everyone does it the same way (for example, for starters the swabs have to be sterile before use). I would be willing to help. I did a little snooping around and the 16s rRNA sequencing is fine, however, I haven't seen anyone who does it for less that $80-100 per sample. Do you have a vendor who does it for $30? if we could get middle and high schools involved, it might even be possible to to talk some outfits into to donating their services (that's a big maybe - but hey, dream big). There are about 450 members of DYIbio.com. If we each pitched in about $100 we could team up and buy a Polonator ( I read they are about $50,000) sequencing machine and run our samples or maybe a nominal charge for members. Some could probably afford more, some less. Like I said, dream big!

jasonbobe (author) in reply to ndpmJan 4, 2009. 8:59 AM

This instructable is a preview of the concept, not a detailed how-to. I'm planning a pilot project for late march / early april, and I'm working out the details now. RE: sequencing instrument, 454 is ideal because it provides long read lengths. I'll be posting more details about the pilot project very soon. Thanks, Jason

jasonbobe (author) in reply to jasonbobeJan 4, 2009. 9:06 AM

Oh, and yes I'm in discussions with several commercial lab partners at the moment. On the high end, it looks like the pilot project price will be $60 per sample. On the optimistic end of the spectrum, $20 per swab. For the pilot project, we'll need to get sponsors for somewhere between 300 and 1000 swabs (depending on whether we opt for the 454 FLX or 454 Titanium, and depending on # reads per sample). I'm waiting to announce until after a few logistical / technical details are worked out. I'll post later this week on the DIY group. Thanks, jason

DIY-Guy in reply to jasonbobeDec 8, 2010. 12:36 AM

Nifty geeky idea!
I'd not want to insult the skills and labor of any lab by low-balling the bid, but $1 per sample would fit my idea of doing it for curiosity and the greater good.

ndpm in reply to jasonbobeJan 5, 2009. 1:01 PM

I appreciate the info. Keep me informed. I'd like to be a part of it (M.A. Biological Science). The leader of the science club at my school has shown some interest also. There is a cross walk button 100 meters away, waiting to be swabbed. I might suggest that concurrently, a plate be swabbed also, and anything that grows can be isolated and photographed. Thanks, Phil...

Rlangg says: Feb 4, 2010. 9:22 PM

How much does the sequencing cost?

jasonbobe (author) in reply to RlanggFeb 4, 2010. 10:18 PM

No commercial vendors available yet where you can just send a sample and get data back. Using "next-generation" sequencing like 454 might cost around $200 per sample, including labor, reagents, etc. Cost continues to fall dramatically. Should be radically cheap in the near future. What would you pay?

Rlangg says: Feb 4, 2010. 9:24 PM

I would need to tell them which part of the DNA to sequence? Where are these intructions? This is so interesting.

jasonbobe (author) in reply to RlanggFeb 4, 2010. 10:13 PM

The region of the DNA to sequence depends on the type of organism. For bacteria, scientists typically look at the 16S gene. Check out this site:

http://www.dnabarcodes.org/

regisd says: Jan 1, 2009. 12:10 PM

about how much does the sequencing cost per q-tip?

jasonbobe (author) in reply to regisdJan 1, 2009. 2:41 PM

It costs somewhere around ~$30 per swab today, dropping to $3 or less per swab in about 1 year.

jasonmorrison says: Dec 20, 2008. 6:38 PM

Hi J L Larson,

That is certainly a goal! If you are interested in finding out more, keep an eye on http://bioweathermap.org over the next few months.

Cheers,
-Jason Morrison