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There are entire cities of bacteria inside your body, and Gary Borisy is determined to map them.

But there’s a problem.


“You don’t have the addresses. You don’t have a GPS. You don’t know where they are,” said Borisy, a senior research investigator at the department of microbiology at the Forsyth Institute in Cambridge, Mass. “We’re trying to provide a piece of the puzzle to figure out how the city of microbes works by seeing where they live and who lives next to what.”

Thanks to advances in DNA sequencing, scientists know the names of a lot of the bacteria that live in your body, but they don’t necessarily know how those bacterial communities are organized.

To start their exploration into the microbial unknown, Borisy and his team needed to pick a spot and do a little detective work.


They focused on plaque — the thin film of bacterial gunk coating our mouths — specifically the plaque living on our teeth.

Mapping the bacteria required creating a set of tags to identify each of them. Since there may be hundreds of bacterial species living on our teeth, the researchers needed to figure out which species were most abundant.

They mined the Human Oral Microbiome Database and the Human Microbiome Project for clues and came away with a list of 13 types of bacteria that were usually found on teeth.

The scientists then designed a set of fluorescent probes for each microbe. Each probe sticks to a unique stretch of RNA within the organism and gives off a certain color when excited by a pulse of light.

With the list and probes on hand, the scientists scraped plaque off healthy volunteers near the gumline using floss or a toothpick. The specks were mixed with a solution containing the tags and then put under a microscope.

They used a technique called combinatorial labeling and spectral imaging fluorescence in situ hybridization (CLASI-FISH), which allowed them to take photos of up to 15 types of bacteria at the same time.

“When I first saw the results, it was like, ‘Wow!’” Borisy said. “What we saw exceeded our greatest expectations.”

They found highly organized bacterial communities that had layers where only certain types of bacteria mixed and mingled. Some bacterial communities were so organized that the researchers developed some names to capture the visual patterns they saw, including “the hedgehog” and “the cauliflower.”

Oxygen-loving bacteria lived at the periphery. Filaments of Corynebacterium matruchotii jutted at the bottom, like roots, and were dotted by bacteria like Streptococcus and Porphyromonas at their tips.

In between them was a mix of bacteria that usually thrive in areas without oxygen, like Lautropia, Capnocytophaga, and Fusobacteria.

Their stunning images were published in the Proceedings of the National Academy of Sciences in January.

The team hopes that knowing how bacteria are organized will help guide future studies of microbiomes, the bacterial communities writhing and thriving on every crevice.

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