There are millions of microorganisms in a drop of pond water—but who are they? There are bacteria, protozoa, hydras, arthropods—all manner of critters are in that drop of water. Dividing them up by genera and species, though, is tricky because many bacteria look similar. That makes identifying the members of a microbial community difficult.
A new way of identifying microbes is with the tools of the genomicist. Just as we can sequence the genome of a single organism, so too can we now sequence a drop of pond water, kefir, milk, or fecal material to see who lives there.
Researchers look at a particular gene, called 16S, which is common to most bacteria. The 16S gene has nine hypervariable regions that vary by species. A sequencer can pick up on those variations, thus enabling scientists to identify bacteria by taxa, genus, or even species.
It’s not a perfect method by any means. One complicating factor is that even in a single-celled bacterium there might be multiple 16S genes with individual variations. And closely related species can be 99 percent identical, making differentiation tricky.
But two trends working hand in hand are rapidly making bacterial identification cheaper, faster, and more reliable. One trend is data science. Biologists are generating and analyzing huge data sets that help them see patterns of variability. Databases like GreenGenes collect and collate data specific to 16S. Another trend is sequencing itself: Higher resolution and cheaper processing are enabling more labs to parse the genetic codes of more organisms.