Fig. 2: Ribosome intensity line profiles reveal ribosome-nucleoid anti-correlation and characteristic phenotypes of antibiotic response.

a Along the long axis of the cell, the mean normalised ribosome (Cy3, grey) and nucleoid (DAPI, magenta) intensities are calculated for each of 100 bins. The shading shows ± 1 standard deviation of the mean. The untreated E. coli line profiles show two nucleoid-rich regions, correlated with decreased ribosome intensity. This figure is composed of profiles from untreated E. coli MG1655 (N = 5286). The ciprofloxacin panel shows the same, for E. coli MG1655 treated with 1 × EUCAST ciprofloxacin for 30 min (N = 3215). The line profile shows a central, compact nucleoid region with greater segregation from the ribosomes. The gentamicin panel shows the same, for E. coli MG1655 treated with 20 × EUCAST gentamicin for 30 min (N = 5935). This line profile shows a diffuse nucleoid region along the long axis of the cell with less ribosome-nucleoid segregation. The chloramphenicol panel shows the same, for E. coli MG1655 treated with 1 × EUCAST chloramphenicol (N = 6438). This line profile shows nucleoid compaction compared to the untreated phenotype, with a centralised DNA region or two dense DNA regions. The carbenicillin panel shows the same, for E. coli MG1655 treated with 3 × EUCAST carbenicillin (N = 1256). This line profile shows ~4 regions of DNA density, indicating that DNA replication and cell growth has continued without cell division. b The cell lengths (μm) are shown for untreated E. coli MG1655 and for each of the antibiotic treatments. The box shows the 25–75% percentile range, the bars show the 1–99% percentile range, and the line denotes the median. Each antibiotic results in a length distribution statistically different from the untreated population with p < 0.05 by the Mann-Whitney non-parametric test. c The cell widths (μm) are shown for untreated E. coli MG1655 and for each of the antibiotic treatments. The box shows the 25–75% percentile range, the bars show the 1–99% percentile range, and the line denotes the median. Each antibiotic results in a width distribution statistically different from the untreated population with p < 0.05 by the Mann-Whitney non-parametric test.