Understanding the role of horizontal gene transfer (HGT) in adaptation is a key challenge in evolutionary biology. In microbes, an important mechanism of HGT is prophage acquisition (phage genomes integrated into bacterial chromosomes). Prophages can influence bacterial fitness via transfer of beneficial genes (including antibiotic-resistance genes, ARGs), protection from superinfecting phages, or switching to a lytic lifecycle which releases free phages infectious to competitors. We expect these effects to depend on environmental conditions because of, for example, environment-dependent induction of the lytic lifecycle. However, it remains unclear how costs/benefits of prophages vary across environments. Here, studying prophages with/without ARGs in Escherichia coli, we disentangled effects of prophages alone and adaptive genes they carry. In competition with prophage-free strains, benefits from prophages and ARGs peaked in different environments. Prophages were most beneficial when induction of the lytic lifecycle was common, whereas ARGs were more beneficial upon antibiotic exposure and with reduced prophage induction. Acquisition of prophage-encoded ARGs by competing strains was most common when prophage induction, and therefore free phages, were common. Thus, selection on prophages and adaptive genes they carry varies independently across environments, which is important for predicting the spread of mobile/integrating genetic elements and their role in evolution

Sata have been collected from experimental work including competition assays, growth rate measurements, MIC assays, reduction in bacterial growth assays and spot assays

The folder contains files needed perform the analysis described in “FITNESS BENEFITS TO BACTERIA OF CARRYING PROPHAGES AND PROPHAGE-ENCODED ANTIBIOTIC-RESISTANCE GENES PEAK IN DIFFERENT ENVIRONMENT” by Carolin C Wendling, Dominik Refardt, Alex R Hall

A brief description of each file is given below.
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Competition_Data.txt

This file contains the raw data which was used to calculate the selection rate constant of lysogens relative to the YFP-labelled wild-types as well as to infer the absolute cel densities for each population per pair-wise competition. The column headings are:
    
    Strain-Which lysogen was used during pair-wise competition against the YFP-labelled WT. For a detailed description of each lysogen see Table 1 in the main manuscript.

    Timepoint-Indicates if cell densities were measured at the beginning (T0) or after 24 hours of pair-wise competition (T24).

    Environment-In which of the 8 environmental conditions strains were competing (A1: IC20, A2: IC30, A3: IC50, M: MitomycinC, A1_M: IC20+MitomycinC, A2_M: IC30+MitomycinC, A3_M: IC50+MitomycinC, LB: LB-medium).

    Replicate-Which replicate.

    Antibiotic-Which antibiotic was used for the experiment (Amp: ampicillin, Kan: kanamycin, Cm: chloramphenicol).

    Phage_Type-Which phage-type the lysogen contained (lambda, HK022, Phi80, mEp234, or no for competition between WT and YFP-lablled WT, which was later used to correct for the fitness effect of the YFP marker).

    ARG-Indicates presence or absence of a resistance gene.
    
    WT_YFP-Measurment of absolute cell densities of the YFP-labelled WT.

    Lysogen-Measurement of absolute cell densities of the lysogen.

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Free_phages.txt

This file gives the absolute number of free phages in plaque forming units (PFU) per ml. The column headings are:

    Strain-Which lysogen was used during pair-wise competition against the YFP-labelled WT. For a detailed description of each lysogen see Table 1 in the main manuscript.

    Antibiotic-Which antibiotic was used for the experiment (Amp: Ampicillin, Kan:kanamycin, Cm:Chloramphenicol).

    Replicate-Which replicate.

    ARG-Indicates presence or absence of a resistance gene.

    Phage_Type-Which phage-type the lysogen contained (lambda, HK022, Phi80, mEp234, or no for  YFP-labelled WT).

    Environment-In which of the 8 environmental conditions strains were competing (A1: IC20, A2: IC30, A3: IC50, M: MitomycinC, A1_M: IC20+MitomycinC, A2_M: IC30+MitomycinC, A3_M: IC50+MitomycinC, LB: LB-medium).

    PFU-Measurement of of free phages in (PFU/ml).

    

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RBG.txt

This file gives the OD readings used to calculate reduction in bacterial growth (RBG). The column headings are:

    Strain-Which lysogen was used during pair-wise competition against the YFP-labelled WT. For a detailed description of each lysogen see Table 1 in the main manuscript.

    Replicate-Which replicate.

    Phage_Type-Which phage-type the lysogen contained (lambda, HK022, Phi80, mEp234, or no for YFP-labelled WT).

    Resistance-Which resistance gene is encoded in the respective prophage.

    ARG-Indicates presence or absence of a resistance gene.

    Antibiotic-Which antibiotic was used for the experiment (Amp: Ampicillin, Kan:kanamycin, Cm:Chloramphenicol).

    Concentration-Which antibiotic concentration was used (no, low=IC20, middle=IC30, high=IC50).

    OD_T0-OD reading at 660nm for time-point zero.

    OD_T24-OD reading at 600nm for after 24 hours.

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GR_Monoculture.txt

This file gives the OD readings from overnight growth assay used to calculate bacterial growth rates. The column headings are:

    Strain-Which lysogen was used during pair-wise competition against the YFP-labelled WT. For a detailed description of each lysogen see Table 1 in the main manuscript.

    Replicate-Which replicate.

    Antibiotic-Which antibiotic was used for the experiment (Amp: Ampicillin, Kan:kanamycin, Cm:Chloramphenicol).

    ARG-Which resistance gene was encoded on the prophage (A: ampicillin, K: kanamycin, C: chloramphenicol, No: no resistance gene).

    Phage_Type-Which phage-type the lysogen contained (lambda, HK022, Phi80, mEp234, or no for WT_YFP).

    Concentration-Which antibiotic concentration (µg/ml) was used in that assay

    OD_0-reading of optical density (OD) at 660 nm at timepoint 0.

    OD_24-reading of optical density (OD) at 660 nm after 24 hours.

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MitomycinC_Induction.txt

This file gives the OD readings from the mitomycin C induction growth assay. The column headings are:

    Strain-Which lysogen was used during pair-wise competition against the YFP-labelled WT. For a detailed description of each lysogen see Table 1 in the main manuscript.

    Replicate-Which replicate.

    ARG-Which resistance gene was encoded on the prophage (Amp: ampicillin, Kan: kanamycin, Cm: chloramphenicol, No: no resistance gene).

    Phage_Type-Which phage-type the lysogen contained (lambda, HK022, Phi80, mEp234, or no for WT_YFP).

    Timepoint-at which timepoint the measurement was taken.

    OD-reading of optical density (OD) at 660nm.

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MIC_Assay.txt

This file gives the OD readings from the MIC assay. The column headings are:

    Strain-Which lysogen was used during pair-wise competition against the YFP-labelled WT. For a detailed description of each lysogen see Table 1 in the main manuscript.

    Replicate-Which replicate.

    ARG-Which resistance gene was encoded on the prophage (Amp: ampicillin, Kan: kanamycin, Cm: chloramphenicol, No: no resistance gene).

    Phage_Type-Which phage-type the lysogen contained (lambda, HK022, Phi80, mEp234, or no for WT_YFP).

    Timepoint-at which timepoint the measurement was taken.

    OD-reading of optical density (OD) at 660nm.

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WT_Lysogen_Fitness.txt

This file contains the raw data which was used to calculate the selection rate constant of WT-lysogens relative to the one of three ancestral strains.The column headings are:
    

    Strain-Which WT-lysogen was used during pair-wise competition against one of the three ancestors.

    Antibiotic-Which antibiotic was used for the experiment (Amp: ampicillin, Kan: kanamycin, Cm: chloramphenicol). 

    Phage_Type-Which phage-type the lysogen contained (lambda, HK022, Phi80, mEp234, or no for competition between WT and YFP-lablled WT, which was later used to correct for the fitness effect of the YFP marker).

    ARG-Which resistance gene was present in the WT-lysogen (Amp: ampicillin, Kan: Kanamycin, Cm: Chloramphenicol).

    Competitor-Which competitor the WT-lysogen was competing with (WT: phage-free, antibiotic-susceptible WT, P: Lysogen, witouht ARG, P_ARG: lysogen with ARG)

    Replicate-Which replicate.

    Environment-In which of the 2 environmental conditions strains were competing (A3: IC20, LB: LB-medium).

    Timepoint-Indicates if cell densities were measured at the beginning (T0) or after 24 hours of pair-wise competition (T24).
    
    WT_lysogen-Measurment of absolute cell densities of the WT-lysogen.

    Competitor-Measurement of absolute cell densities of one of the three different competitors.

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