Evolutionary expression patterns in developing biofilms of uropathogenic Escherichia coli reveal embryo-like features

Developing biofilms of the gram-positive, soil-dwelling bacterium Bacillus subtilis exhibit expression patterns and evolutionary imprints similar to those observed in eukaryotic embryos. However, the universality of these evolutionary and developmental regularities has not yet been explored in other biofilm-forming bacteria, including pathogens. To broaden the perspective on ontogeny–phylogeny correlations in bacteria, we reconstructed phylotranscriptomic and phyloproteomic trajectories throughout the entire biofilm development of uropathogenic Escherichia coli UTI89. Here, we show that biofilm growth in E. coli UTI89 is associated with progressive expression of evolutionarily younger and more divergent genes over developmental time. These findings suggest that biofilm formation in gram-negative bacteria is not macroevolutionarily naïve and that evolutionary imprints are a pervasive feature of bacterial biofilm development. While these regularities apply to the developmental expression patterns of bulk biofilms, it remains unclear whether evolutionary stratification also occurs within the spatial regions of individual biofilms. To address this question, we analyzed expression profiles across concentric regions of E. coli UTI89 biofilms at 3 developmental stages. This analysis revealed that gene expression, functional patterns, and evolutionary imprints are shaped by both developmental timing and distance from the biofilm center. Together, these findings demonstrate that the growth of uropathogenic E. coli biofilms is governed by both temporal and spatial macroevolutionary logic, drawing intriguing parallels to organismal development in multicellular eukaryotic lineages.