The greenish glow under the microscope might not have rivaled Times Square in its intensity, but to the microbiologist Katharine Coyte, her first glimpse of this bustling city was just as exciting. As a doctoral student at the University of Oxford, she had engineered a small plastic slab studded with holes, like the world’s tiniest slice of Swiss cheese, called a microfluidic chip. It was meant to resemble the porous environments, such as soil, in which many bacteria live, and she had seeded it with different strains of E. coli. She tagged each of the strains with a fluorescent protein to give it a distinctive color, which would allow Coyte to measure how many of each cell type were present. As a steady stream of water brought nutrients to the setup, she stood back and watched the bacteria build a microbial megalopolis known as a biofilm.
Biofilms are everywhere. Far from being rare alternatives to the lone microbe swimming in a flask or sprawled in a petri dish, 99.9 percent of the simple cells called prokaryotes default to living in close quarters among millions of their compatriots. These biofilms of clustering bacteria can create impossible-to-eradicate infections on central lines and catheters; they foul everything from sewer lines to our teeth. The billions of bacteria that can live in a single biofilm cover themselves with a sticky combination of sugar and protein called the extracellular matrix, which effectively glues them to their surface of choice. Both the matrix and the physical shape of the biofilm protect those cells living at the center of the structure from attack by predators and antibiotics. The size of the biofilm and the interaction of cells within it give the different cells the opportunity to specialize in a particular task, such as acquiring food, subverting predators or acting as a reservoir of genetic material from which to regrow the entire structure.