Intro: 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.
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).