Mapping Microbes




About: A brief bio here:

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

Step 2: Perform DNA Sequencing on Collected Specimen

A DNA sequencing facility will extract the microbial DNA from your specimen and sequence specific regions of the genomes present in the sample. The region of the genome that should be sequenced, depends in part on what organisms you're trying to identify. You might sequence one thing for animals (e.g. CO1) and another for microbes (e.g. rRNA).

The ribosomal RNA (rRNA) genes are often examined by biologists for identification of microbes. They are ancient, highly conserved, and common across species. Different microbes have different versions of rRNA genes. The specific version of a rRNA gene possessed by an organism can help scientists (and you!) tell apart one microbe from another.

16S ribosomal RNA gene sequencing is particularly helpful in distinguishing one type of bacterium from another. Is it a cyanobacterium, proteobacterium, or a firmicute? Depending on the number of different bacteria in your original sample, the sequencing results may include hundreds (or thousands!) of unique 16S rRNA sequences. Each DNA sequence will be 200-300 base pairs long and can be used to characterize the bacteria that were present on the surface where you collected a specimen.

Having a bunch of 16S rRNA gene sequence data will help you to identify the microbes that were on the surface where you collected a specimen. But this analysis will require some work involving bioinformatics. For example, you might compare your sequence data to the data available in public databases, to see if others have characterized any microbial DNA with similarities to your data.

Why not share your data online and let others help you characterize it? Beyond crowd-sourcing the computational effort, there are numerous exciting possibilities once people start sharing their data...

Step 3: Visualize: Map Your Microbes and Compare With Others

Lets say on a cold December day you characterized the microbes living on a cross-walk button near your apartment in Harvard Square (Cambridge, Mass) and you published your data online. The next spring, some curious person living across the Charles River in downtown Boston wonders whether the cross-walk button nearest her apartment would yield different results. Do crosswalk buttons only a few miles apart share similar microbiomes or do they differ? Do microbial communities living on a particular surface change like the weather over time?

Much like a weather map, a BioWeatherMap shows how conditions vary in different regions over time. Publishing your microbial data online will enable the possibility of visualizing the temporal and geographic variation of microbial communities living on surfaces around the world.

DIYbio and the PGP are working to bring BioWeatherMaps to home near you soon. Stay tuned! Sign-up here here if you want to be contacted when more information is available.

We are also grateful for the support of the George Church Lab at Harvard Medical School. The first mention of the term "bioweathermap" is from George in 2005 ( see this PDF, p.24).

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    13 Discussions


    10 years ago on Introduction

    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 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!

    4 replies

    Reply 10 years ago on Introduction

    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


    Reply 10 years ago on Introduction

    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


    Reply 8 years ago on Introduction

    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.


    Reply 10 years ago on Introduction

    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...


    Reply 9 years ago on Step 1

    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?


    9 years ago on Step 3

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

    1 reply

    Reply 9 years ago on Step 3

    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:


    Reply 10 years ago on Introduction

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


    10 years ago on Step 3

    wow, someday this will be a website, like the news or the weather. cool