AMiGA: Software for Automated Analysis of Microbial Growth Assays

ABSTRACT The analysis of microbial growth is one of the central methods in the field of microbiology. Microbial growth dynamics can be characterized by meaningful parameters, including carrying capacity, exponential growth rate, and growth lag. However, microbial assays with clinical isolates, fastidious organisms, or microbes under stress often produce atypical growth shapes that do not follow the classical microbial growth pattern. Here, we introduce the analysis of microbial growth assays (AMiGA) software, which streamlines the analysis of growth curves without any assumptions about their shapes. AMiGA can pool replicates of growth curves and infer summary statistics for biologically meaningful growth parameters. In addition, AMiGA can quantify death phases and characterize diauxic shifts. It can also statistically test for differential growth under distinct experimental conditions. Altogether, AMiGA streamlines the organization, analysis, and visualization of microbial growth assays. IMPORTANCE Our current understanding of microbial physiology relies on the simple method of measuring microbial populations’ sizes over time and under different conditions. Many advances have increased the throughput of those assays and enabled the study of nonlab-adapted microbes under diverse conditions that widely affect their growth dynamics. Our software provides an all-in-one tool for estimating the growth parameters of microbial cultures and testing for differential growth in a high-throughput and user-friendly fashion without any underlying assumptions about how microbes respond to their growth conditions.


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Reviewer comment s:
Reviewer #1 (Comments for the Author): In general terms, the authors have responded satisfactorily to my observations. However, there are still some minor comments and details that the authors should consider before accepting the manuscript.
-In Figure 2A the term Non-carbon control still appears -The Materials and Methods section does not indicate where the data for C. sedlakii and Y. Enterocolitica come from. If it is mentioned that Growth data for ancestral strain and transposon mutants of P. aeruginosa were obtained from reference 28. This is indicated in the results section (line 315). In the materials section, it must be clear where all the data come from if they were not obtained experimentally.
Reviewer #2 (Comments for the Author): I previously reviewed this manuscript and the authors have thoroughly addressed all of my initial concerns, which were minor. The methodology, software, and documentation are a very important contribution and will be of broad interest.
Reviewer #3 (Comments for the Author): The authors have appropriately taken into account most of my comments.

Reviewer comments (Author response in red):
Reviewer #1 (Comments for the Author): In general terms, the authors have responded satisfactorily to my observations. However, there are still some minor comments and details that the authors should consider before accepting the manuscript.
-In Figure 2A the term Non-carbon control still appears Thank you for catching this error. We have corrected the figure by changing "No-carbon Control" to "Minimal Media".
-The Materials and Methods section does not indicate where the data for C. sedlakii and Y. Enterocolitica come from. If it is mentioned that Growth data for ancestral strain and transposon mutants of P. aeruginosa were obtained from reference 28. This is indicated in the results section (line 315). In the materials section, it must be clear where all the data come from if they were not obtained experimentally.
We initially combined the Software Availability section and the Data Availability section as a single section titled "Software implementation and data availability". For clarity, we have separated them into their own individual sections. Now, we also include links to the public repositories where the data for C. sedlakii, P. aeruginosa, and Y. Enterocolitica are available, in addition to citing their corresponding references.
Reviewer #2 (Comments for the Author): I previously reviewed this manuscript and the authors have thoroughly addressed all of my initial concerns, which were minor. The methodology, software, and documentation are a very important contribution and will be of broad interest.

Reviewer #3 (Comments for the Author):
The authors have appropriately taken into account most of my comments.
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