Summary of Study ST002014

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001278. The data can be accessed directly via it's Project DOI: 10.21228/M8HQ49 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002014
Study TitleImpact of microcin J25 on the porcine microbiome in a continuous culture model
Study SummaryThe increased prevalence of Salmonella spp. resistance in swine spurs the search for alternatives to antibiotics. Microcin J25 (MccJ25), a bacteriocin produced by Escherichia coli, is a potent inhibitor of several pathogenic bacteria including Salmonella enterica. In this study, we aimed to evaluate in vitro the impact of MccJ25 on the metabolic activity of the swine colonic microbiota. The PolyFermS in vitro continuous fermentation model was used with modified Macfarlane medium to simulate the porcine proximal colon. During 35 days of fermentation, a first-stage reactor containing immobilized swine fecal microbiota fed two second-stage control and test reactors operated in parallel and used to test the effectsof MccJ25 on the composition and the metabolic activity of the microbiota. Reuterin, a broad spectrum antimicrobial produced by Limosilactobacillus reuteri and the antibiotic rifampicin were tested for comparison. LC-MS analysis of the cell extracts was used to assess the bacteriocin/antibiotic degradation products and monitor changes in the swine colonic microbiota metabolome.
Institute
National Museum of Natural History
Last NameZirah
First NameSeverine
AddressMuseum national d'Histoire naturelle, Unité MCAM UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, FRANCE
Emailseverine.zirah@mnhn.fr
Phone+33(0)1 40 79 31 40
Submit Date2021-11-13
Num Groups6
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailLC-MS
Release Date2022-09-14
Release Version1
Severine Zirah Severine Zirah
https://dx.doi.org/10.21228/M8HQ49
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001278
Project DOI:doi: 10.21228/M8HQ49
Project Title:PolyFerm
Project Summary:The increased prevalence of Salmonella spp. resistance in swine spurs the search for alternatives to antibiotics. Microcin J25 (MccJ25), a bacteriocin produced by Escherichia coli, is a potent inhibitor of several pathogenic bacteria including Salmonella enterica. In this study, we aimed to evaluate in vitro the impact of MccJ25 on the metabolic activity of the swine colonic microbiota. The PolyFermS in vitro continuous fermentation model was used with modified Macfarlane medium to simulate the porcine proximal colon. During 35 days of fermentation, a first-stage reactor containing immobilized swine fecal microbiota fed two second-stage control and test reactors operated in parallel and used to test the effectsof MccJ25 on the composition and the metabolic activity of the microbiota. Reuterin, a broad spectrum antimicrobial produced by Limosilactobacillus reuteri and the antibiotic rifampicin were tested for comparison. LC-MS analysis of the cell extracts was used to assess the bacteriocin/antibiotic degradation products and monitor changes in the swine colonic microbiota metabolome.
Institute:National Museum of Natural History
Laboratory:Communication Molecules and Adaptation of Microorganisms
Last Name:Zirah
First Name:Severine
Address:Museum national d'Histoire naturelle, Unité MCAM UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, FRANCE
Email:severine.zirah@mnhn.fr
Phone:+33(0)1 40 79 31 40

Subject:

Subject ID:SU002095
Subject Type:Bacteria
Subject Species:swine colonic microbiota
Gender:Not applicable

Factors:

Subject type: Bacteria; Subject species: swine colonic microbiota (Factor headings shown in green)

mb_sample_id local_sample_id group
SA188424J25F1_t0_BC4_01_3123J25 | ferm:F1
SA188425J25F1_t4_BA7_01_2968J25 | ferm:F1
SA188426J25F1_t4_RB8_01_3073J25 | ferm:F1
SA188427J25F1_t10_BC5_01_3124J25 | ferm:F1
SA188428J25F1_t0_RE4_01_3097J25 | ferm:F1
SA188429J25F1_t6_BC8_01_3127J25 | ferm:F1
SA188430J25F1_t8_GB2_01_3157J25 | ferm:F1
SA188431J25F1_t24_BD8_01_3137J25 | ferm:F1
SA188432J25F1_t2_BD4_01_3133J25 | ferm:F1
SA188433J25F1_t8_BC5_01_2986J25 | ferm:F1
SA188434J25F1_t2_BC6_01_3125J25 | ferm:F1
SA188435J25F1_t12_BB2_01_2971J25 | ferm:F1
SA188436J25F1_t10_GB8_01_3029J25 | ferm:F1
SA188437J25F1_t24_RB1_01_3066J25 | ferm:F1
SA188438J25F1_t12_GC7_01_3036J25 | ferm:F1
SA188439J25F1_t6_GD2_01_3039J25 | ferm:F1
SA188440J25F2_t4_GE4_01_3051J25 | ferm:F2
SA188441J25F2_t12_RD3_01_3086J25 | ferm:F2
SA188442J25F2_t0_GA5_01_3152J25 | ferm:F2
SA188443J25F2_t24_BE4_01_3141J25 | ferm:F2
SA188444J25F2_t8_BD5_01_3134J25 | ferm:F2
SA188445J25F2_t0_RA8_01_3065J25 | ferm:F2
SA188446J25F2_t24_BC3_01_3122J25 | ferm:F2
SA188447J25F2_t10_BE5_01_3006J25 | ferm:F2
SA188448J25F2_t8_BB8_01_2979J25 | ferm:F2
SA188449J25F2_t10_BD7_01_2998J25 | ferm:F2
SA188450J25F2_t2_GB1_01_3020J25 | ferm:F2
SA188451J25F2_t4_GC6_01_3169J25 | ferm:F2
SA188452J25F2_t6_BA6_01_3107J25 | ferm:F2
SA188453J25F2_t12_RB7_01_3072J25 | ferm:F2
SA188454J25F2_t2_GB3_01_3024J25 | ferm:F2
SA188455J25F2_t6_GC3_01_3166J25 | ferm:F2
SA188456QC_BA2_01_2960QC | ferm:QC
SA188457QC_GE1_01_3094QC | ferm:QC
SA188458QC_GE1_01_3076QC | ferm:QC
SA188459QC_GE1_01_3058QC | ferm:QC
SA188460QC_GE1_01_3112QC | ferm:QC
SA188461QC_GE1_01_3130QC | ferm:QC
SA188462QC_GE1_01_3148QC | ferm:QC
SA188463QC_BA2_01_3040QC | ferm:QC
SA188464QC_BA2_01_3012QC | ferm:QC
SA188465QC_BA2_01_2972QC | ferm:QC
SA188466QC_BA2_01_2982QC | ferm:QC
SA188467QC_BA2_01_2992QC | ferm:QC
SA188468QC_BA2_01_3002QC | ferm:QC
SA188469QC_BA2_01_2962QC | ferm:QC
SA188470QC_BA2_01_3022QC | ferm:QC
SA188471ReutF1_t4_BE7_01_3144Reut | ferm:F1
SA188472ReutF1_t8_GC4_01_3033Reut | ferm:F1
SA188473ReutF1_t12_BE6_01_3143Reut | ferm:F1
SA188474ReutF1_t2_RE8_01_3101Reut | ferm:F1
SA188475ReutF1_t0_RB3_01_3068Reut | ferm:F1
SA188476ReutF1_t10_RB5_01_3070Reut | ferm:F1
SA188477ReutF1_t10_GB7_01_3028Reut | ferm:F1
SA188478ReutF1_t24_GD3_01_3042Reut | ferm:F1
SA188479ReutF1_t12_BB5_01_2976Reut | ferm:F1
SA188480ReutF1_t4_BA5_01_2966Reut | ferm:F1
SA188481ReutF1_t0_RC4_01_3079Reut | ferm:F1
SA188482ReutF1_t6_GC1_01_3164Reut | ferm:F1
SA188483ReutF1_t6_GB2_01_3021Reut | ferm:F1
SA188484ReutF1_t24_GB3_01_3158Reut | ferm:F1
SA188485ReutF1_t8_RB2_01_3067Reut | ferm:F1
SA188486ReutF1_t2_BC2_01_3121Reut | ferm:F1
SA188487ReutF2_t12_RE5_01_3098Reut | ferm:F2
SA188488ReutF2_t8_GB4_01_3159Reut | ferm:F2
SA188489ReutF2_t10_RB4_01_3069Reut | ferm:F2
SA188490ReutF2_t6_RA5_01_3062Reut | ferm:F2
SA188491ReutF2_t2_GA1_01_3010Reut | ferm:F2
SA188492ReutF2_t6_RB6_01_3071Reut | ferm:F2
SA188493ReutF2_t10_RD2_01_3085Reut | ferm:F2
SA188494ReutF2_t0_BB8_01_3119Reut | ferm:F2
SA188495ReutF2_t0_GB8_01_3163Reut | ferm:F2
SA188496ReutF2_t4_BA3_01_3104Reut | ferm:F2
SA188497ReutF2_t4_BD3_01_3132Reut | ferm:F2
SA188498ReutF2_t8_GE8_01_3055Reut | ferm:F2
SA188499ReutF2_t24_GC4_01_3167Reut | ferm:F2
SA188500ReutF2_t12_GB5_01_3026Reut | ferm:F2
SA188501ReutF2_t2_RC5_01_3080Reut | ferm:F2
SA188502ReutF2_t24_GE2_01_3049Reut | ferm:F2
SA188503RifaF1_t24_GB5_01_3160Rifa | ferm:F1
SA188504RifaF1_t4_GC2_01_3165Rifa | ferm:F1
SA188505RifaF1_t0_RA7_01_3064Rifa | ferm:F1
SA188506RifaF1_t24_BD1_01_2990Rifa | ferm:F1
SA188507RifaF1_t2_RC6_01_3081Rifa | ferm:F1
SA188508RifaF1_t12_RD4_01_3087Rifa | ferm:F1
SA188509RifaF1_t6_GE3_01_3050Rifa | ferm:F1
SA188510RifaF1_t12_BD6_01_2997Rifa | ferm:F1
SA188511RifaF1_t10_RC1_01_3074Rifa | ferm:F1
SA188512RifaF1_t4_BB3_01_3114Rifa | ferm:F1
SA188513RifaF1_t8_BE1_01_3138Rifa | ferm:F1
SA188514RifaF1_t0_BA7_01_3108Rifa | ferm:F1
SA188515RifaF1_t8_BB7_01_2978Rifa | ferm:F1
SA188516RifaF1_t6_BD1_01_3128Rifa | ferm:F1
SA188517RifaF1_t10_GD7_01_3046Rifa | ferm:F1
SA188518RifaF1_t2_BA8_01_3109Rifa | ferm:F1
SA188519RifaF2_t4_BE3_01_3140Rifa | ferm:F2
SA188520RifaF2_t6_BB7_01_3118Rifa | ferm:F2
SA188521RifaF2_t8_BC8_01_2989Rifa | ferm:F2
SA188522RifaF2_t12_BD6_01_3135Rifa | ferm:F2
SA188523RifaF2_t10_GA8_01_3019Rifa | ferm:F2
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Collection:

Collection ID:CO002088
Collection Summary:The PolyFermS in vitro continuous fermentation model was used here with modified Macfarlane medium to simulate the porcine proximal colon. During 35 days of fermentation, a first-stage reactor containing immobilized swine fecal microbiota fed two second-stage control and test reactors operated in parallel and used to test the effects of MccJ25 on the metabolic activity of the microbiota.
Sample Type:Bacterial cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002107
Treatment Summary:Performed simultaneously in TR1 and TR2, the four treatments consisted of adding by adding Salmonella enterica subsp. enterica serovar Newport ATCC 6962 alone at an initial concentration of 107 cfu/mL to each reactor, followed by adding the bacteria at this cell density along with each tested antimicrobial: 0.4 mM MccJ25, 4 mM reuterin or 0.6 mM rifampicin.

Sample Preparation:

Sampleprep ID:SP002101
Sampleprep Summary:The metabolites were extracted from swine colonic microbiota in methanol/chloroform/water. The aqueous phase was collected.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN003282
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS
Column Thermo Acclaim Polar Advantage II
MS Type ESI
MS instrument type QTOF
MS instrument name Bruker Maxis II ETD
Ion Mode POSITIVE
Units m/z

Chromatography:

Chromatography ID:CH002424
Chromatography Summary:Low pH polar
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Thermo Acclaim Polar Advantage II
Chromatography Type:Reversed phase

MS:

MS ID:MS003054
Analysis ID:AN003282
Instrument Name:Bruker Maxis II ETD
Instrument Type:QTOF
MS Type:ESI
MS Comments:Proprietary analytical software for MS acquisition Data processing with xcms (R package)
Ion Mode:POSITIVE
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