Summary of Study ST002431

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 PR001564. The data can be accessed directly via it's Project DOI: 10.21228/M8J41M 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 IDST002431
Study TitleMS profiling of the Long Term Evolution Experiment
Study SummaryThe metabolome of a cell is the integration point of an organism's environment, genetics, and gene expression pattern. The metabolic phenotype can be under selection and is known to contribute to adaption. However, the metabolome's inherent networked and convoluted nature makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the Long Term Evolution Experiment (LTEE) as a model to understand how mutations can transduce themselves through a cellular network, eventually affecting metabolism and perhaps fitness. We used mass-spectropscopy to broadly survey the metabolomes of both ancestors and all 12 evolved lines and combined this with genomic and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work brings the field closer to a complete genotype-phenotype map for the LTEE and a better understanding of how mutations might affect fitness through the metabolome. We used mass-spectroscopy to profile metabolic changes in the Long Term Evolution Experiment and link these change to upstream changes in gene expression and mutations.
Institute
Rutgers University
DepartmentGenetics
LaboratoryShah
Last NameFavate
First NameJohn
Address145 Bevier Road, Piscataway, NJ, 08854
Emailjohn.favate@rutgers.edu
Phone7325894642
Submit Date2022-12-01
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-02-16
Release Version1
John Favate John Favate
https://dx.doi.org/10.21228/M8J41M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001564
Project DOI:doi: 10.21228/M8J41M
Project Title:Linking genetic and phenotypic changes in the long term evolution experiment using metabolomics
Project Type:MS
Project Summary:The metabolome of a cell is the integration point of an organism's environment, genetics, and gene expression pattern. The metabolic phenotype can be under selection and is known to contribute to adaption. However, the metabolome's inherent networked and convoluted nature makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the Long Term Evolution Experiment (LTEE) as a model to understand how mutations can transduce themselves through a cellular network, eventually affecting metabolism and perhaps fitness. We used mass-spectropscopy to broadly survey the metabolomes of both ancestors and all 12 evolved lines and combined this with genomic and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work brings the field closer to a complete genotype-phenotype map for the LTEE and a better understanding of how mutations might affect fitness through the metabolome.
Institute:Rutgers University
Department:Genetics
Laboratory:Shah
Last Name:Favate
First Name:John
Address:145 Bevier Road, Piscataway, NJ, 08854
Email:john.favate@rutgers.edu
Phone:7325984642

Subject:

Subject ID:SU002520
Subject Type:Bacteria
Subject Species:Escherichia coli
Taxonomy ID:562

Factors:

Subject type: Bacteria; Subject species: Escherichia coli (Factor headings shown in green)

mb_sample_id local_sample_id age growth_phase
SA242941rel607_e_r1ancestral exponential
SA242942rel606_e_r1ancestral exponential
SA242943rel606_e_r2ancestral exponential
SA242944rel607_e_r2ancestral exponential
SA242945rel606_s_r2ancestral stationary
SA242946rel607_s_r2ancestral stationary
SA242947rel607_s_r1ancestral stationary
SA242948rel606_s_r1ancestral stationary
SA242949ap4_e_r2evolved exponential
SA242950ap4_e_r1evolved exponential
SA242951ap5_e_r2evolved exponential
SA242952ap6_e_r1evolved exponential
SA242953am1_e_r1evolved exponential
SA242954ap6_e_r2evolved exponential
SA242955ap3_e_r2evolved exponential
SA242956ap5_e_r1evolved exponential
SA242957ap3_e_r1evolved exponential
SA242958am4_e_r1evolved exponential
SA242959am4_e_r2evolved exponential
SA242960am3_e_r1evolved exponential
SA242961am2_e_r2evolved exponential
SA242962am1_e_r2evolved exponential
SA242963am2_e_r1evolved exponential
SA242964am5_e_r1evolved exponential
SA242965am3_e_r2evolved exponential
SA242966ap2_e_r1evolved exponential
SA242967am5_e_r2evolved exponential
SA242968ap1_e_r2evolved exponential
SA242969ap2_e_r2evolved exponential
SA242970ap1_e_r1evolved exponential
SA242971am6_e_r2evolved exponential
SA242972am6_e_r1evolved exponential
SA242973ap4_s_r1evolved stationary
SA242974ap3_s_r1evolved stationary
SA242975ap3_s_r2evolved stationary
SA242976ap4_s_r2evolved stationary
SA242977ap6_s_r1evolved stationary
SA242978ap2_s_r2evolved stationary
SA242979ap6_s_r2evolved stationary
SA242980ap5_s_r2evolved stationary
SA242981ap5_s_r1evolved stationary
SA242982am1_s_r1evolved stationary
SA242983am3_s_r2evolved stationary
SA242984am4_s_r1evolved stationary
SA242985am3_s_r1evolved stationary
SA242986am2_s_r2evolved stationary
SA242987am1_s_r2evolved stationary
SA242988am2_s_r1evolved stationary
SA242989am4_s_r2evolved stationary
SA242990am5_s_r1evolved stationary
SA242991ap1_s_r1evolved stationary
SA242992ap1_s_r2evolved stationary
SA242993am6_s_r2evolved stationary
SA242994am6_s_r1evolved stationary
SA242995am5_s_r2evolved stationary
SA242996ap2_s_r1evolved stationary
Showing results 1 to 56 of 56

Collection:

Collection ID:CO002513
Collection Summary:Bacterial cells were grown in DM25 medium and collected via vacuum filtration at 2hr and 24hr timepoints.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR002532
Treatment Summary:No treatment was applied to the samples. The samples consist of the ancestral strains of the LTEE, REL606 and REL607, and clones from each of the evolved lines, designated Ara-1:6 and Ara+1:6

Sample Preparation:

Sampleprep ID:SP002526
Sampleprep Summary:Samples were prepared using the 40:40:20 acetonitrile:methanol:water protocol.

Combined analysis:

Analysis ID AN003957 AN003958
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap Thermo Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002928
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:25
Flow Gradient:0 min, 100% B; 3 min, 100% B; 3.2 min, 90% B; 6.2 min, 90% B; 6.5 min, 80% B; 10.5 min, 80% B; 10.7 min, 70% B; 13.5 min, 70% B; 13.7 min, 45% B; 16 min, 45% B; 16.5 min, 100% B; and 22 min, 100% B
Flow Rate:0.3mL/min
Solvent A:95% water/5% acetonitrile; 20 mM acetic acid; 40 mM ammonium hydroxide, pH 9.4
Solvent B:20% water/80% acetonitrile; 20 mM acetic acid; 40 mM ammonium hydroxide, pH 9.4
Chromatography Type:HILIC

MS:

MS ID:MS003692
Analysis ID:AN003957
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:EL-MAVEN
Ion Mode:POSITIVE
  
MS ID:MS003693
Analysis ID:AN003958
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:EL-MAVEN
Ion Mode:NEGATIVE
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