Combining evolutionary steering and Coevolutionary Phage training to generate predictable phage-antibiotic synergy
Data files
Jul 08, 2026 version files 30.76 KB
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Fig1.csv
12.92 KB
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Fig2B_Ery.csv
1.21 KB
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Fig2B_Rif.csv
1.21 KB
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Fig3.csv
4 KB
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Fig4.csv
3.82 KB
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Fig5A.csv
2.05 KB
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Fig5B.csv
730 B
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Fig6.csv
277 B
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README.md
4.54 KB
Abstract
This dataset contains raw experimental data supporting a study of phage-antibiotic synergy arising from coevolutionary phage training in Escherichia coli and bacteriophage λ. The dataset comprises seven .csv files corresponding to the main figures of the associated manuscript. Four files (Fig1.csv, Fig2B.csv, Fig3.csv, Fig4.csv) contain raw optical density measurements (OD₆₀₀) collected from 96-well plate assays using a Tecan Sunrise plate reader, used to quantify bacterial growth inhibition and calculate half-maximal inhibitory concentrations (IC50) across multiple antibiotics and bacterial strains, including wild-type E. coli K-12, its lpcA knockout from the Keio collection, and REL606-derived phage-resistant isolates. Fig5A.csv contains binary plaquing data (0/1) tracking the daily emergence of OmpF receptor usage across replicate phage populations over 21- and 23-day coevolutionary training experiments. Fig5B.csv contains time-to-event data used for Kaplan-Meier survival analysis of OmpF acquisition. Fig6.csv contains colony count data from tetrazolium-mannose indicator plates used to quantify manXYZ mutation frequencies in bacterial populations coevolved with and without erythromycin. All experiments were conducted under standard laboratory conditions and involve non-pathogenic E. coli strains; no human subjects, protected species, or sensitive information are involved.
Dataset DOI: 10.5061/dryad.7m0cfxqbt
Description of the data and file structure
File: Fig1.csv
Description: contains the raw optical density (OD600) data collected to calculate the half maximal inhibitory concentration of the bacterial strains of interest in the presence of seven different antibiotics. Each row represents one of three replicates of seven strains of interest. Row 2 lists the antibiotic concentrations used.
Variables:
- Column 1: the antibiotics tested
- Column 2: the bacterial strains (with 3 replicates for each)
- Columns 3-12: the various antibiotic concentrations investigated, ranging from 0 to 100 (μg/mL).
File: Fig2B_Ery.csv
Description: the raw optical density (OD600) data used to compare the antibiotic senistivity of the WT K-12 strain to an lpcA knockout in the presence of erythromycin (Ery).
Variables:
- Each row represents a specified antibiotic concentration (0-100 μg/mL), and each column represents one of 6 replicates of the WT+Antibiotic condition (e.g. “WT+Ery 1-6”) or lpcA KO+Antibiotic condition (e.g. “lpca KO+Ery 1-6”).
File: Fig2B_Rif.csv
Description: the raw optical density (OD600) data used to compare the antibiotic senistivity of the WT K-12 strain to an lpcA knockout in the presence of rifampicin (Rif).
Variables:
- Each row represents a specified antibiotic concentration (0-100 μg/mL), and each column represents one of 6 replicates of the WT+Antibiotic condition (e.g. “WT+Rif 1-6”) or lpcA KO+Antibiotic condition (e.g. “lpcA KO+Rif 1-6”).
File: Fig3.csv
Description: the raw optical density (OD600) data collected to calculate the half maximal inhibitory concentration of the bacterial strains of interest in the presence of rifapentine and novobiocin. Each row represents one of three replicates of seven strains of interest. Row 2 lists the antibiotic concentrations used.
Variables:
- Column 1: the antibiotics tested
- Column 2: the bacterial strains (with 3 replicates for each)
- Columns 3-12: the various antibiotic concentrations investigated, ranging from 0 to 100 (μg/mL).
File: Fig4.csv
Description: the raw optical density data collected from our bacterial suppression assays over 7 days. Phage populations P10, P19, P22, and P23 were found to be capable of using OmpF as a secondary receptor for infection. Each row represents one of three replicates. ‘Ery’ indicates erythromycin.
Variables:
- Column 1: the phage populations and whether Ery was present
- Columns 2-8: the days at which the measurements were taken.
File: Fig5A.csv
Description: the data collected to track OmpF use over time during the course of the coevolution experiment. 0 indicates no plaquing on an REL606-derived LamB knockout, whereas 1 indicates ability to successfully form plaques. Rows represent phages that were coevolved with or without the presence of erythromycin.
Variables:
- Days are indicated in columns 2-24.
File: Fig5B.csv
Description: the data used to run the Kaplan-Meier-style analysis of OmpF use frequency. It contains the populations from the original coevolution experiment as well as the extended repeat (Block 1 and Block 2, respectively).
Variables:
- Block: 1 indicates the data that pertains to the original coevolution experiment performed for 21 days with 6 replicates for each population, whereas Block 2 refers to the 23-day repeat with 12 additional population per group. OmpF use status of 0 indicates no OmpF use, whereas 1 indicates ability to plaque on the REL606-derived LamB knockout.
- Group: designates whether erythromycin (“Ery”) was present or absent (“No antibiotic”) during the coevolution.
- Population: the replicate number in each block.
- Days: the amount of time elapsed before OmpF-use detection if applicable.
- OmpF Use Status: 0=no, 1=yes
File: Fig6.csv
Description: the raw data used to calculate the frequency of manXYZ mutations between bacterial strains coevolved with and without erythromycin. Red colonies suggest the presence of manXYZ mutations, whereas white colonies indicate no mutations. Each row represents one petri dish on which the colonies were grown.
Variables:
Column 1: with or without erythromycin (antibiotic)
Column 2: red colony count
Column 3: white colony count.