Data for: Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model

Chemotactic bacteria not only navigate chemical gradients but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real-time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering new insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.

Methods
See Methods in the paper for details. These are density measurements of E. coli cells migrating as a band along a straight microfluidics channel as they consume and chase aspartate. Both the cell density and the concentration of aspartate are measured using fluorescent microscopy. The data was analyzed using MATLAB. Raw data, processed data and codes used to process the data are provided. See the Methods section of the paper and README file located with the data.