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

Select appropriate tab below to view additional metadata details:

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