Each person car­ries 10 times as many bac­te­rial cells as human cells, the former of which have con­tinued to evolve in response to medicine’s most potent antibi­otics. But micro­scopic bugs don’t just dic­tate human health—they’re also inte­gral to the health of every body of water on the planet. According to Ferdi Hell­weger, an asso­ciate pro­fessor of civil and envi­ron­mental engi­neering at North­eastern, micro­bial pol­lu­tion rep­re­sents one of the most sig­nif­i­cant prob­lems for our lakes, rivers, and estuaries.

Nev­er­the­less, he said, our tools for studying microbes have been, until recently, rather archaic. “The tra­di­tional approach has been to take all the cells, grind them up, and then send them through a machine in the chem­istry lab,” he explained. “It seems absurd now.”

Tra­di­tion­ally, micro­bial ecol­o­gists thought all bac­te­rial cells were the same. “Once you know how one behaves, you know how they all behave,” said Hell­weger, who hosted a work­shop on the changing face of micro­bial mod­eling in 2011.

This per­spec­tive begot a mod­eling approach for bac­te­rial behavior that relied on strate­gies from the phys­ical sci­ences: “We mod­eled them as if they’re mol­e­cules, using chem­ical equa­tions,” Hell­weger explained.

But recent advances in obser­va­tional tech­nolo­gies have shown that pop­u­la­tions of indi­vidual bac­teria are as diverse as the human pop­u­la­tion or any other species. “We’re starting to see all this exciting indi­vid­u­ality from one cell to its neighbor,” said Hell­weger. “We’re inun­dated with a flood of novel obser­va­tions but our tra­di­tional analysis tools can’t handle them.”

In an opinion paper recently pub­lished in the journal Pro­ceed­ings of the National Academy of Sci­ences, Hell­weger and his col­leagues from the work­shop put forth an emerging strategy for dealing with this new micro­bial data: mod­eling indi­vidual bacteria.

The approach also allows for a better exam­i­na­tion of the prop­er­ties that emerge when those indi­vidual agents act as a col­lec­tive pop­u­la­tion, Hell­weger explained. Biofilms, for example, are colonies of bac­te­rial cells that work together almost as a single organism. But the cells that are buried deep within the biofilm are genet­i­cally dis­tinct and behave quite dif­fer­ently from the cells on the sur­face, which have a much greater supply of avail­able oxygen and nutri­ents. To under­stand the biofilm, Hell­weger explained, we need to first under­stand its indi­vidual cells.

Despite the fact that our bodies are teeming with bac­te­rial cells, our under­standing of the microbiome—that col­lec­tion of cells that live in and on us—is quite lim­ited. We know it’s impor­tant, Hell­weger said, but we don’t know how it works. Like­wise, we realize that our water supply is exceed­ingly reliant on a per­fect bal­ance of microor­gan­isms, but we aren’t yet sure what that bal­ance looks like in great detail.

To answer ques­tions such as these, Hell­weger said, researchers need to develop a keen under­standing of the bac­te­rial com­mu­nity. Until sci­ence can accom­mo­date the indi­vid­u­ality of the cells that make up that com­mu­nity, the effort is unlikely to get very far.