FIG 1.

AMiGA infers microbial growth parameters and characterizes diauxic shifts. (A, B) AMiGA predicted the mean growth and growth rate of a ribotype 053 C. difficile clinical isolate grown on 20 mM fructose as the primary carbon source using three technical replicates. Model estimates of the log-transformed growth and its derivative can be used to describe the following parameters: carrying capacity (K), area under the curve (AUC), maximum growth rate (r), maximum death rate, lag time, adaptation time, and stationary death. The black dashed oblique line indicates the tangent to the growth curve at maximum exponential growth. The gray dashed vertical lines map growth parameters to their respective time points, which are also exported by AMiGA. (C, D) AMiGA characterized the diauxic shift of a C. difficile clinical isolate of an unknown ribotype grown on minimal medium with 20 mM glucose as the primary carbon source using three technical replicates. AMiGA automatically detected two growth phases (separated by dashed vertical line), reaching maximum growth rates at 6.0 and 15.3 h, respectively. The inset text states the estimated carrying capacity, K, and maximum growth rate, r, for each unique phase. Bold green lines plot the predicted mean of the growth function or its derivative, and green bands indicate the predicted 95% confidence interval including measurement noise. The thin gray lines plot actual growth measurements.