Data from: Niche exclusion of a lung pathogen in mice with designed probiotic communities
Data files
Jul 17, 2026 version files 868.86 KB
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2021_12_20_Bt_CarbonUtilization_DF.xlsx
29.65 KB
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2021_12_20_CP13_CarbonUtilization_DF.xlsx
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2021_12_20_CP17_CarbonUtilization_DF.xlsx
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2021_12_20_CP18_CarbonUtilization_DF.xlsx
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2021_12_20_CP19_CarbonUtilization_DF.xlsx
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2021_12_20_CP20_CarbonUtilization_DF.xlsx
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2021_12_20_CP26_CarbonUtilization_DF.xlsx
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2021_12_20_CP4_CarbonUtilization_DF.xlsx
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2021_12_20_CP7_CarbonUtilization_DF.xlsx
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2021_12_20_CP8_CarbonUtilizaton_DF.xlsx
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2021_12_20_CP9_CarbonUtilization_DF.xlsx
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Figure_1_figure_supplement_1.xlsx
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Figure_3_figure_supplement_1.xlsx
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Figure_4_figure_supplement_1.xlsx
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Figure_4_figure_supplement_2.xlsx
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Figure_5_figure_supplement_1.xlsx
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Figure_5_figure_supplement_2.xlsx
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Figure_5_figure_supplement_3.xlsx
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Figure1C_Data.xlsx
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Figure2B.xlsx
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Figure2D.xlsx
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Figure2E_Data.xlsx
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Figure3A_3B.xlsx
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Figure3E.xlsx
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Figure3F.xlsx
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Figure3G.xlsx
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Figure3H.xlsx
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Figure4C-E__G.xlsx
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Figure4F.xlsx
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Figure5B_D_E.xlsx
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Figure5F.xlsx
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NicheIndex_Calculation_Dryad.xlsx
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README.md
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Abstract
For years, the airway microbiota have been theorized to be gatekeepers of respiratory health, as pathogens entering the airway make contact with resident microbes prior to or coincident with their interaction with host cells. Thus, modification of the native airway community may serve as a means of altering the local environment in favor of health. In this work, we hypothesize that synthetic bacterial communities introduced into the airway can serve as prophylactic countermeasures against infection by Burkholderia thailandensis in mice. The data here is composed of competition experiments between various candidate probiotics and the model pathogen, as well as carbon utilization, metabolomics, and in vivo colony count and survival data.
Dataset DOI: 10.5061/dryad.ht76hdrxw
Description of the data and file structure
These files contain the data pertinent to the article "Niche exclusion of a lung pathogen in mice with designed probiotic communities". Data are organized by figure number.
The data herein are composed of carbon utilization data, co-culture inhibition data, supernatant inhibition data, in vivo activity data, as well as metabolomics and niche index calculation data. See below for more details on the contents of each file.
In cases where data from more than one replicate was collected for a particular condition, header cells may be merged to indicate that samples are replicates.
Files and variables
File: 2021_12_20_Bt_CarbonUtilization_DF.xlsx
Description: Carbon utilization data for Bt tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: 2021_12_20_CP4_CarbonUtilization_DF.xlsx
Description: Carbon utilization data for CP4 tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: 2021_12_20_CP7_CarbonUtilization_DF.xlsx
Description: Carbon utilization data for CP7 tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: 2021_12_20_CP8_CarbonUtilizaton_DF.xlsx
Description: Carbon utilization data for CP8 tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: 2021_12_20_CP19_CarbonUtilization_DF.xlsx
Description: Carbon utilization data for CP19 tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: NicheIndex_Calculation_Dryad.xlsx
Description: Niche Index calculation
Variables
- Compound: Compound name
- Electrons contributed total: This describes the total number of theoretical electron equivalents a carbon source can contribute to energy production in a cell based on the amount in Lung Simulating Medium
- C-RANK: Ranking of each compound by the total electron equivalents contributed, where 1 represents the carbon source with the greatest electron equivalents in Lung Simulating Medium and 21 the lowest number of electron equivalents
- Weight: This is a weighting each carbon source is given based on the total electron equivalents present in Lung Simulating Media. This is a number between 0-1 and is generated by dividing the total electron equivalents that the source can contribute divided by the total equivalents from glucose.
- Organism name: This is listed as one of the following: CP4, CP7, CP8, CP9, CP13, CP17, CP18, CP19, CP20, CP26, Bt-GFP
- Numerator: Numerator of the niche index calculation composed of the sum of the weighted electron equivalents for each carbon source used by an organism
- Denominator: The sum of all weighted electron equivalents used by Bt plus those used by each isolate from ornithine
- Niche Index (NI): Calculated niche index calculated by dividing the numerator value by the denominator value
- NI RANK: Ranks each isolate by highest niche index (1) to lowest niche index (10) with the pathogen. NA indicates that the organism is unable to be ranked because it is the pathogen.
File: Figure2E_Data.xlsx
Description: Percent growth of Bt in co-culture competition experiments with either the wildtype CP8 or the CP8 sfp mutant
Variables
- Isolate:Bt: The ratio of isolate cells to Bt cells inoculated at the start of the experiment
- CP8 WT: Percent inhibition of Bt in co-culture with the wildtype CP8, 4-5 replicates were performed
- CP8 sfp KO: Percent inhibition of Bt in co-culture with the CP8 sfp mutant, 5 replicates were performed
File: Figure2B.xlsx
Description: Data from supernatant inhibition studies in Figure 2B
Variables
- Combination: The combination of isolates co-cultured
- Relative Growth: The fraction of total growth of Bt grown in the co-culture supernatant relative to Bt grown in supernatant from itself
- CFU/ml of Bt: The total CFU/ml that was generated by Bt grown in the supernatant. A total of 5 replicates were generated for each sample.
File: 2021_12_20_CP20_CarbonUtilization_DF.xlsx
Description: Carbon utilization data for CP20 tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: Figure_4_figure_supplement_2.xlsx
Description: qPCR data from a co-culture growth curve of Bt, CP8 and CP19. Timepoints were collected every hour from 4-30 hours after inoculation, and one timepoint was collected at 36 hours.
Variables
- Time: the time in hours that elapsed in the growth curve
- Bt: OD600 values calculated for Bt in the co-culture. A total of 6 replicates were collected for each timepoint.
- CP8: OD600 values calculated for CP8 in the co-culture . A total of 6 replicates were collected for each timepoint.
- CP19: OD600 values calculated for CP19 in the co-culture . A total of 6 replicates were collected for each timepoint.
File: Figure2D.xlsx
Description: Growth curve of CP8 and CP8 sfp mutant
Variables
- Time: time at data collection measured in hours
- CP8 KO: OD600 reading at an indicated timepoint for the CP8 sfp mutant. A total of 4 replicates were collected for each timepoint.
- CP8: OD600 reading at an indicated timepoint for the wildtype CP8. A total of 4 replicates were collected for each timepoint.
File: Figure3A_3B.xlsx
Description: Percent growth of Bt in co-culture competition experiments with CP7 in the standard amount of glucose for lung-simulating media (5.5mM Glucose) or with added glucose (43mM glucose).
Variables
- Isolate:Bt: The ratio of CP7 cells to Bt cells inoculated at the start of the experiment
- 5.5mM Glucose: Percent inhibition of Bt grown with CP7 in the presence of 5.5mM glucose. A total of 5 replicates were collected for each isolate:Bt ratio.
- 43mM Glucose: Percent inhibition of Bt grown with CP7 in the presence of 43mM glucose. A total of 5 replicates were collected for each isolate:Bt ratio.
File: Figure_1_figure_supplement_1.xlsx
Description: Growth curves of all organisms used in the study (A) and the effect of co-culture with Bt on the growth of each isolate.
Variables
- Time: time at data collection measured in hours
- CP4: OD600 values of the culture of CP4. A total of 5 replicates were collected at each timepoint.
- CP7: OD600 values of the culture of CP7. A total of 5 replicates were collected at each timepoint.
- CP8: OD600 values of the culture of CP8. A total of 5 replicates were collected at each timepoint.
- CP9: OD600 values of the culture of CP9. A total of 5 replicates were collected at each timepoint.
- CP13: OD600 values of the culture of CP13. A total of 5 replicates were collected at each timepoint.
- CP17: OD600 values of the culture of CP17. A total of 5 replicates were collected at each timepoint.
- CP18: OD600 values of the culture of CP18. A total of 5 replicates were collected at each timepoint.
- CP19: OD600 values of the culture of CP19. A total of 5 replicates were collected at each timepoint.
- CP20: OD600 values of the culture of CP20. A total of 5 replicates were collected at each timepoint.
- CP26: OD600 values of the culture of CP26. A total of 5 replicates were collected at each timepoint.
- Bt: OD600 values of the culture of Bt. A total of 5 replicates were collected at each timepoint.
- Organism: Name of each organism in co-culture with Bt
- -Bt: CFU/ml of each organism listed in in the "organism" cell when grown without the presence of Bt. A total of 3-6 replicates were collected for each organism.
- +Bt: CFU/ml of each organism listed in in the "organism" cell when grown in the presence of Bt. A total of 3-6 replicates were collected for each organism.
File: Figure_4_figure_supplement_1.xlsx
Description: Co-culture experiments of Bt with a combination of CP20 and CP17 (A) or CP19 and CP26 (B)
Variables
- Isolate:Bt: The ratio of total isolate cells to Bt cells inoculated at the start of the experiment
- CP20/CP17: The percent inhibition of Bt when grown in co-culture with a combination of CP20 and CP17. A total of 3-5 replicates were collected for each ratio.
- CP20: The percent inhibition of Bt when grown in co-culture with CP20. A total of 3-5 replicates were collected for each ratio.
- CP17: The percent inhibition of Bt when grown in co-culture with CP17. A total of 5-10 replicates were collected for each ratio.
- CP19/CP26: The percent inhibition of Bt when grown in co-culture with a combination of CP19 and CP26. A total of 4-10 replicates were collected for each ratio.
- CP19: The percent inhibition of Bt when grown in co-culture with CP19. A total of 5 replicates were collected for each ratio.
- CP26: The percent inhibition of Bt when grown in co-culture with CP26. A total of 4-5 replicates were collected for each ratio.
File: Figure3E.xlsx
Description: Data for correlation between percent growth of Bt and Niche Index
Variables
- Organism: Organism name
- Rank [NI]: Rank of the niche index value associated with a given organism
- Rank [Percent growth of Bt (1:1 Ratio)]: Rank of the percent growth of Bt when grown at a 1:1 ratio with a given organism
File: Figure3G.xlsx
Description: Total electron flux of 3 organisms grown in lung simulating media
Variables
- Organism: Organism name
- Electron flux: The number of electrons remaining in the media after 24 hours of culture. A total of 5-6 replicates were collected for each organism.
File: 2021_12_20_CP9_CarbonUtilization_DF.xlsx
Description: Carbon utilization data for CP9 tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: Figure_5_figure_supplement_1.xlsx
Description: Colonization of CP8 with and without co-infection with the pathogen
Variables
- -Pathogen: Colony forming units of CP8 without co-infection with the pathogen
- +Pathogen: Colony forming units of CP8 with co-infection with the pathogen
File: Figure1C_Data.xlsx
Description: Co-culture inhibition data for each candidate probiotic co-cultured with model pathogen (Bt)
Variables
- Isolate:Bt: The ratio of isolate cells to Bt cells inoculated at the start of the experiment
- Percent Bt Growth: Growth of Bt in co-culture relative to a monoculture control. A total of 4-10 replicates were collected for each organism at each ratio.
File: 2021_12_20_CP18_CarbonUtilization_DF.xlsx
Description:
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: Figure4C-E__G.xlsx
Description: Co-culture inhibition experiments of Bt co-cultured with a combination of CP19/CP8, CP19/CP13, CP8/CP13 or CP8 sfp mutant/CP19
Variables
- Isolate:Bt: The ratio of total isolate cells to Bt cells inoculated at the start of the experiment
- CP8/CP19: The percent inhibition of Bt in co-culture with a combination of CP8 and CP19 at a given ratio. A total of 5 replicates were collected for each ratio
- CP8: The percent inhibition of Bt in co-culture with CP8 at a given ratio. A total of 5 replicates were collected for each ratio
- CP19: The percent inhibition of Bt in co-culture with CP19 at a given ratio. A total of 5 replicates were collected for each ratio
- CP19/CP13: The percent inhibition of Bt in co-culture with a combination of CP19 and CP13 at a given ratio. A total of 5 replicates were collected for each ratio
- CP13: The percent inhibition of Bt in co-culture with CP13 at a given ratio. A total of 5-10 replicates were collected for each ratio
- CP8/CP13: The percent inhibition of Bt in co-culture with a combination of CP8 and CP13 at a given ratio. A total of 4-5 replicates were collected for each ratio
- CP19/CP8sfpKO: The percent inhibition of Bt in co-culture with a combination of CP19 and the CP8 sfp mutant at a given ratio. A total of 5 replicates were collected for each ratio
File: Figure4F.xlsx
Description: Lactate consumption in a co-culture with CP8, CP19 and Bt in comparison to a co-culture of CP19 and Bt and CP8 and Bt
Variables
- CP8/Bt: ng/CFU of lactate consumed by a co-culture of CP8 and Bt
- CP19/Bt: ng/CFU of lactate consumed by a co-culture of CP19 and Bt
- CP8/CP19/Bt: ng/CFU of lactate consumed by a co-culture of CP8 and Bt
File: Figure5F.xlsx
Description: Quantification of Bt colony forming units retrieved from the lungs of mice pre-treated with a CP 3 days prior to infection
Variables
- Vehicle: Mice infected without pre-treatment with a CP
- CP8: Mice pre-treated with CP8
- CP13: Mice pre-treated with CP13
- CP17: Mice pre-treated with CP17
- CP19: Mice pre-treated with CP19
- CP20: Mice pre-treated with CP20
- CP26: Mice pre-treated with CP26
File: Figure_5_figure_supplement_2.xlsx
Description: Data from mice pre-treated with live CPs or UV-killed CPs prior to Bt infection
Variables
- Days prior to Bt challenge: Number of days prior to Bt infection that a given treatment was administered
- No CP: Number of days surviving in mice that were not pre-treated with a CP
- CP8: Number of days surviving in mice pre-treated with CP8
- CP13: Number of days surviving in mice pre-treated with CP13
- CP17: Number of days surviving in mice pre-treated with CP17
- CP19: Number of days surviving in mice pre-treated with CP19
- CP20: Number of days surviving in mice pre-treated with CP20
- CP26: Number of days surviving in mice pre-treated with CP26
File: Figure_5_figure_supplement_3.xlsx
Description: Lactate consumption in ex vivo lung tissue by CP19 and resulting growth of Bt
Variables
- -CP19 lactate (uM): concentration of lactate in uM measured from lung tissue without CP19 treatment
- +CP19 lactate (uM): concentration of lactate in uM measured from lung tissue treated with CP19
- Time: Time of measurement in hours
- -CP19 gc: OD600 value of Bt grown in lung tissue without CP19 pre-treatment
- +CP19 gc: OD600 value of Bt grown in lung tissue with CP19 pre-treatment
File: 2021_12_20_CP17_CarbonUtilization_DF.xlsx
Description: Carbon utilization data for CP17 tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: 2021_12_20_CP26_CarbonUtilization_DF.xlsx
Description: Carbon utilization data CP26
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
File: Figure_3_figure_supplement_1.xlsx
Description: Percent growth of Bt in co-culture competition experiments with CP19 in the standard amount of glucose for lung simulating media (5.5mM Glucose) or with added glucose (43mM glucose).
Variables
- Isolate:Bt: The ratio of CP19 cells to Bt cells inoculated at the start of the experiment
- 5.5mM Glucose: Percent inhibition of Bt grown with CP19 in the presence of 5.5mM glucose. A total of 5 replicates were collected for each isolate:Bt ratio.
- 43mM Glucose: Percent inhibition of Bt grown with CP7 in the presence of 43mM glucose. A total of 5-10 replicates were collected for each isolate:Bt ratio.
File: Figure3F.xlsx
Description: Total carbon-derived electrons consumed in LSM by CP7, CP19 or CP8
Variables
- CP7: Total carbon-derived electrons consumed in LSM by CP7
- CP19: Total carbon-derived electrons consumed in LSM by CP19
- CP8: Total carbon-derived electrons consumed in LSM by CP8
File: Figure3H.xlsx
Description: Summed electron flux of lactate, praline and aspartic acid from cultures of CP7, CP19, and CP8
Variables
- Organism: Organism cultured in the sample
- Lactate: Electrons of lactate consumed. A total of 5-6 replicates were collected.
- Proline: Electrons of proline consumed. A total of 5-6 replicates were collected.
- Aspartic acid: Electrons of aspartic acid consumed. A total of 5-6 replicates were collected.
File: Figure5B_D_E.xlsx
Description: Colonization of candidate probiotics and survival of mice treated with CPs prior to infection
Variables
- Candidate probiotic: Organism inoculated to test for colonization potential
- Colony forming units: Colony forming units of the relevant candidate probiotic isolated from mouse lung and tracheal tissue 7 days post-inoculation. A total of 3-12 replicates are collected for each condition.
- Days prior to Bt challenge: Number of days prior to Bt infection that a given treatment was administered
- No CP: Number of days surviving in mice that were not pre-treated with a CP
- CP8: Number of days surviving in mice pre-treated with CP8
- CP13: Number of days surviving in mice pre-treated with CP13
- CP17: Number of days surviving in mice pre-treated with CP17
- CP19: Number of days surviving in mice pre-treated with CP19
- CP20: Number of days surviving in mice pre-treated with CP20
- CP26: Number of days surviving in mice pre-treated with CP26
File: 2021_12_20_CP13_CarbonUtilization_DF.xlsx
Description: Carbon utilization data for CP13 tested against 95 different carbon sources.
Variables
- Well: Location of replicate in the 384-well plate
- Compound: Compound name
- Concentration: Initial concentration of compound in the well prior to addition of media and cells
- Units: concentration units of the carbon source (mM or mg/mL)
- Absorbance: absorbance reading at 600nm after growth
- Blank: absorbance reading at 600nm prior to growth
Code/software
Excel or text editor