But Allison and his colleagues have taken a closer look at E. coli and their research is yielding novel insights, and raising new questions, about of this prevalent unicellular organism. For one thing, it appears that E. coli may not always be unicellular. The research team explained it all in their study, “Evidence of a possible multicellular life cycle in Escherichia coli,” published this month in the journal iScience.

“We’ve identified some things that have never been seen before in bacteria,” said Allison, whose Emory-based lab closely studies individual bacteria to better understand antibiotic resistance and multicellular biofilms. Collaborating with Allison were two members of his lab, graduate researcher Devina Puri, who was the lead author, and postdoctoral researcher Xin Fang.

Microbe Communities

In nature, bacteria live in communities called biofilms, which are clusters of microbes encased in a self-made, self-sustaining slime matrix, and attached to many kinds of wet surfaces. They’re everywhere around us and inside of us. Common, everyday examples of biofilms include dental plaque and pond scum. 

They can grow on plant and animal tissue, like the inside of our digestive tract, and cause serious infections. On top of that, the bacteria living inside a biofilm’s protective matrix are less likely to be affected by antibiotics.

“We know that biofilms are clinically important, particularly in relation to infection,” said Allison, who noted that approximately 80% of all bacterial infections have a biofilm component. “And almost any bacteria that’s ever been studied can make them.” 

For this study, Allison’s team developed devices that combined microfluidics and agarose pads (which are used for live cell imaging) and used automated microscopy to track and record morphogenesis in E. coli. 

They discovered something new – a multicellular self-assembly process in E. coli. Researchers observed unattached, single-celled organisms combining into four-cell rosettes, a natural multicellular formation thought to be uncommon in bacteria.

“Rosettes are rather significant in higher organisms, like mammals, because they initiate developmental processes like embryogenesis,” Allison said.

Multicellular Chains

They observed E. coli rosettes grow into constant-width chains, which continue growing for 10 generations before attaching to a surface and creating a biofilm. They saw and recorded the bacterial processes that had never been seen or recorded before.

“What we’re seeing here is bacteria maybe are not what we’ve considered them to be in the past,” Allison said. “My suspicion is that what we found is far more common that we knew.”

What they learned about the diversity of E. coli and biofilms has implications for synthetic biology, the treatment and prevention of bacterial diseases, and our understanding of multicellular development. For example, Allison can see his lab’s study being useful as a blueprint for other areas of research – biofilm engineering, for example, which harnesses the beneficial uses of microbial communities, resulting in programmable biofilms.

“Based on what we’ve learned, probably the most effective approach to biofilm engineering is to let the organisms do what they want to do,” Allison said. “Then, for the last stage, the idea would be to program it to do what you need it to do – create a molecule for drug development, express an enzyme to help degrade a bioplastic, or something harmful in the environment. Our work gives some clear evidence on how to proceed.”

CITATION: Devina Puri, Xin Fang, Kyle R. Allison. “Evidence of a possible multicellular life cycle in Escherichia coli.” iScience (Jan. 2023).  https://doi.org/10.1016/j.isci.2022.105795

FUNDING: This work was supported by funding from the NIH Director's Early Independence Award to Kyle R. Allison (NIH DP5OD019792)