Summary of Study ST001987

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 PR001263. The data can be accessed directly via it's Project DOI: 10.21228/M8FX3C This work is supported by NIH grant, U2C- DK119886.

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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 IDST001987
Study TitleTranscriptomic and lipidomic analysis unravels the response of Faecalibacterium prausnitzii to calcium palmitate
Study SummaryInfant formula is a suggested alternative to human milk if breastfeeding is not an option; vegetable oil blends are commonly used in infant formula (IF) to replace dairy fat, which can induce the formation of the poorly soluble soap calcium palmitate (CP) in the infant’s gut. Previously, we observed that CP at a low concentration of 0.01 mg/ml inhibits the growth of dominant infant bacteria such as Faecalibacterium prausnitzii both during the exponential phase as well as in the stationary phase. Here, we investigate the underlying mechanism of the CP inhibition on infant-gut bacteria using F. prausnitzii as a model by analysing its growth at a transcriptomic and lipidomic level.
Institute
University of Groningen
Last NameHorvatovich
First NamePéter
AddressAntonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
Emailp.l.horvatovich@rug.nl
Phone+31 (0)50 363 3341
Submit Date2021-11-12
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2021-12-15
Release Version1
Péter Horvatovich Péter Horvatovich
https://dx.doi.org/10.21228/M8FX3C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001263
Project DOI:doi: 10.21228/M8FX3C
Project Title:Transcriptomic and lipidomic analysis unravels the response of Faecalibacterium prausnitzii to calcium palmitate
Project Summary:Infant formula is a suggested alternative to human milk if breastfeeding is not an option; vegetable oil blends are commonly used in infant formula (IF) to replace dairy fat, which can induce the formation of the poorly soluble soap calcium palmitate (CP) in the infant’s gut. Previously, we observed that CP at a low concentration of 0.01 mg/ml inhibits the growth of dominant infant bacteria such as Faecalibacterium prausnitzii both during the exponential phase as well as in the stationary phase. Here, we investigate the underlying mechanism of the CP inhibition on infant-gut bacteria using F. prausnitzii as a model by analysing its growth at a transcriptomic and lipidomic level.
Institute:University of Groningen
Last Name:Horvatovich
First Name:Péter
Address:Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
Email:p.l.horvatovich@rug.nl
Phone:+31 (0)50 363 3341

Subject:

Subject ID:SU002068
Subject Type:Bacteria
Subject Species:Faecalibacterium prausnitzii
Species Group:Bacteria

Factors:

Subject type: Bacteria; Subject species: Faecalibacterium prausnitzii (Factor headings shown in green)

mb_sample_id local_sample_id Factor
SA185849Neg38CP0Hour16 Negative
SA185850Neg41CP0Hour16 Negative
SA185851Neg8CP0Hour16 Negative
SA185852Neg35CP0Hour16 Negative
SA185853Neg42CP0Hour16 Negative
SA185854Neg26CP0Hour16 Negative
SA185855Neg18CP0Hour16 Negative
SA185856Neg19CP0Hour16 Negative
SA185857Neg20CP0Hour16 Negative
SA185858Neg7CP0Hour16 Negative
SA185859Neg30CP0Hour16 Negative
SA185860Neg13CP0Hour16 Negative
SA185861Pos26CP0Hour16 Positive
SA185862Pos20CP0Hour16 Positive
SA185863Pos19CP0Hour16 Positive
SA185864Pos18CP0Hour16 Positive
SA185865Pos35CP0Hour16 Positive
SA185866Pos38CP0Hour16 Positive
SA185867Pos7CP0Hour16 Positive
SA185868Pos8CP0Hour16 Positive
SA185869Pos42CP0Hour16 Positive
SA185870Pos41CP0Hour16 Positive
SA185871Pos13CP0Hour16 Positive
SA185872Pos30CP0Hour16 Positive
SA185873Neg23CP0Hour5 Negative
SA185874Neg29CP0Hour5 Negative
SA185875Neg22CP0Hour5 Negative
SA185876Neg21CP0Hour5 Negative
SA185877Neg6CP0Hour5 Negative
SA185878Neg33CP0Hour5 Negative
SA185879Neg17CP0Hour5 Negative
SA185880Neg16CP0Hour5 Negative
SA185881Neg43CP0Hour5 Negative
SA185882Neg5CP0Hour5 Negative
SA185883Neg36CP0Hour5 Negative
SA185884Neg37CP0Hour5 Negative
SA185885Pos36CP0Hour5 Positive
SA185886Pos37CP0Hour5 Positive
SA185887Pos43CP0Hour5 Positive
SA185888Pos33CP0Hour5 Positive
SA185889Pos6CP0Hour5 Positive
SA185890Pos21CP0Hour5 Positive
SA185891Pos16CP0Hour5 Positive
SA185892Pos17CP0Hour5 Positive
SA185893Pos22CP0Hour5 Positive
SA185894Pos23CP0Hour5 Positive
SA185895Pos29CP0Hour5 Positive
SA185896Pos5CP0Hour5 Positive
SA185897Neg4CP2Hour16 Negative
SA185898Neg39CP2Hour16 Negative
SA185899Neg45CP2Hour16 Negative
SA185900Neg47CP2Hour16 Negative
SA185901Neg10CP2Hour16 Negative
SA185902Neg32CP2Hour16 Negative
SA185903Neg48CP2Hour16 Negative
SA185904Neg31CP2Hour16 Negative
SA185905Neg15CP2Hour16 Negative
SA185906Neg12CP2Hour16 Negative
SA185907Neg25CP2Hour16 Negative
SA185908Neg27CP2Hour16 Negative
SA185909Pos27CP2Hour16 Positive
SA185910Pos25CP2Hour16 Positive
SA185911Pos15CP2Hour16 Positive
SA185912Pos31CP2Hour16 Positive
SA185913Pos12CP2Hour16 Positive
SA185914Pos39CP2Hour16 Positive
SA185915Pos48CP2Hour16 Positive
SA185916Pos10CP2Hour16 Positive
SA185917Pos45CP2Hour16 Positive
SA185918Pos4CP2Hour16 Positive
SA185919Pos32CP2Hour16 Positive
SA185920Pos47CP2Hour16 Positive
SA185921Neg28CP2Hour5 Negative
SA185922Neg2CP2Hour5 Negative
SA185923Neg14CP2Hour5 Negative
SA185924Neg11CP2Hour5 Negative
SA185925Neg1CP2Hour5 Negative
SA185926Neg24CP2Hour5 Negative
SA185927Neg3CP2Hour5 Negative
SA185928Neg46CP2Hour5 Negative
SA185929Neg44CP2Hour5 Negative
SA185930Neg40CP2Hour5 Negative
SA185931Neg34CP2Hour5 Negative
SA185932Neg9CP2Hour5 Negative
SA185933Pos9CP2Hour5 Positive
SA185934Pos34CP2Hour5 Positive
SA185935Pos40CP2Hour5 Positive
SA185936Pos44CP2Hour5 Positive
SA185937Pos46CP2Hour5 Positive
SA185938Pos3CP2Hour5 Positive
SA185939Pos28CP2Hour5 Positive
SA185940Pos11CP2Hour5 Positive
SA185941Pos14CP2Hour5 Positive
SA185942Pos2CP2Hour5 Positive
SA185943Pos24CP2Hour5 Positive
SA185944Pos1CP2Hour5 Positive
Showing results 1 to 96 of 96

Collection:

Collection ID:CO002061
Collection Summary:Lipids were extracted using the MTBE method (Gil et al., 2018). The bacterial cell pellet was resuspended into 75 μL water, then it was incubated with 200 μL methanol and 625 μL MTBE (methyl tert-butyl ether) for 1 h on a shaker. The bacteria/methanol/MTBE mixture was further incubated with 100 μL water to induce phase separation. After 10 min centrifugation at 1000 × g, the upper organic phase was collected. The lower phase was re-extracted with 250 μL MTBE/methanol/water 10:3:2.5 v/v/v and incubated on a shaker for 30 min. After 3 min centrifugation at 1000 × g, the upper organic phase was collected. The combined organic phases containing the lipids were dried in a vacuum centrifuge at 30 ºC and then dissolved in 25 μL CHCl3/methanol/water 60:30:4.5 v/v/v. 75 μL isopropanol/acetonitrile/water 2:1:1 v/v/v was added to dilute the lipid solution.
Sample Type:Bacteria
Collection Location:University Medical Center Groningen (UMCG)

Treatment:

Treatment ID:TR002080
Treatment Summary:The diluted lipid solution was separated using a Zorbax Eclipse Plus C18 column (1.8 μm, 50 × 2.1 mm) on an Acquity UPLC system (Waters, Manchester, UK). Mobile phases consisted of 10 mM ammonium formate in water/acetonitrile/formic acid 2:3:0.005 v/v/v (eluent A) and 10 mM ammonium formate in isopropanol/acetonitrile/formic acid 9:1:0.01 v/v/v (eluent B). Linear gradient elution was as follows: 0– 2 min from 40 to 43% eluent B, 2–12 min from 50 to 54% eluent B, 12-18 min from 70 to 99% eluent B, and 18–20 min 40% eluent B.. The column temperature was set at 55 °C, and the flow rate was 0.4 mL/min. One μL of sample was loaded to MaXis plus high-resolution QTof mass spectrometer (Bruker, Bremen, Germany), Lipids were detected by electrospray ionization in positive (ESI+) and negative mode (ESI-).

Sample Preparation:

Sampleprep ID:SP002074
Sampleprep Summary:F. prausnitzii A2-165 (DSM 17677) was inoculated in YCFAG medium (Lopez-Siles et al, 2012), without (CP0) and with 0.01 mg/mL CP (CP2) (Wang et al., 2021) in an anaerobic chamber (80% N2, 12% CO2, and 8% H2) and incubated in the same chamber at 37°C.

Combined analysis:

Analysis ID AN003238 AN003239
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Bruker maXis Impact qTOF Bruker maXis Impact qTOF
Ion Mode POSITIVE NEGATIVE
Units peak area Peak area

Chromatography:

Chromatography ID:CH002388
Chromatography Summary:The diluted lipid solution was separated using a Zorbax Eclipse Plus C18 column (1.8 μm, 50 × 2.1 mm) on an Acquity UPLC system (Waters, Manchester, UK). Mobile phases consisted of 10 mM ammonium formate in water/acetonitrile/formic acid 2:3:0.005 v/v/v (eluent A) and 10 mM ammonium formate in isopropanol/acetonitrile/formic acid 9:1:0.01 v/v/v (eluent B). Linear gradient elution was as follows: 0– 2 min from 40 to 43% eluent B, 2–12 min from 50 to 54% eluent B, 12-18 min from 70 to 99% eluent B, and 18–20 min 40% eluent B.. The column temperature was set at 55 °C, and the flow rate was 0.4 mL/min. One μL of sample was loaded to MaXis plus high-resolution QTof mass spectrometer (Bruker, Bremen, Germany), Lipids were detected by electrospray ionization in positive (ESI+) and negative mode (ESI-).
Instrument Name:Waters Acquity
Column Name:Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
Column Temperature:55
Flow Gradient:0- 2 min from 40 to 43% eluent B, 2-12 min from 50 to 54% eluent B, 12-18 min from 70 to 99% eluent B, and 18-20 min 40% eluent B.
Flow Rate:0.4 mL/min
Solvent A:40% water/60% acetonitrile; 0.005% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.01% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS003011
Analysis ID:AN003238
Instrument Name:Bruker maXis Impact qTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Peak detection and statistics. The MSConvert (Version: 3.0.18234) tool from the ProteoWizard package was used to convert the raw files from the Bruker QToF into .mzML files.
Ion Mode:POSITIVE
  
MS ID:MS003012
Analysis ID:AN003239
Instrument Name:Bruker maXis Impact qTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Peak detection and statistics. The MSConvert (Version: 3.0.18234) tool from the ProteoWizard package was used to convert the raw files from the Bruker QToF into .mzML files.
Ion Mode:NEGATIVE
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