Instructables

Mapping Microbes

Picture of 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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ndpm5 years ago
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)  ndpm5 years ago
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)  jasonbobe5 years ago
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
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 jasonbobe5 years ago
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...
Rlangg4 years ago
How much does the sequencing cost? 
jasonbobe (author)  Rlangg4 years ago
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?
Rlangg4 years ago
I would need to tell them which part of the DNA to sequence?  Where are these intructions?  This is so interesting.
jasonbobe (author)  Rlangg4 years ago
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/
regisd5 years ago
about how much does the sequencing cost per q-tip?
jasonbobe (author)  regisd5 years ago
It costs somewhere around ~$30 per swab today, dropping to $3 or less per swab in about 1 year.
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
foobear5 years ago
wow, someday this will be a website, like the news or the weather. cool