MassIVE MSV000085860

Partial Public

MetaboLights MTBLS525 - GNPS A synthetic community system for probing microbial interactions driven by exometabolites

Subscribe Comment Reanalyze Spectra Add Reanalysis

Description

Despite that most microorganisms live as part of community, we have modest knowledge about the interactions among microbial community members in nature, and the implications of those interactions for emergent community properties or ecosystem-relevant functions. To facilitate advances in understanding microbial interactions, we describe a straightforward synthetic community system for interrogating the extracellular interactions among microbial community members. The laboratory-scale system physically separates microbial populations within the community, but allows for chemical interactions via a shared media reservoir. Community goods, including small molecules, extracellular enzymes, and antibiotics, can be assayed using sensitive mass spectrometry, and community member outcomes can be assayed, for example, using flow cytometry, biomass measurements, and transcript analyses. The synthetic community design allows for determining the causes and consequences of community diversity and functional outcomes given manipulation of community membership or structure, abiotic stressors, or temporal dynamics. Because it is versatile to accommodate any artificial or environmental microbiome members, scalable to high-throughput capacity, flexible to an array of experimental designs, and accessible to a variety of laboratories because no specialized or costly components are required, this synthetic community system has the potential to practically advance knowledge of microbial interactions within both natural and artificial communities. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: GNPS Metabolomics MetaboLights

Contact

Principal Investigators:
(in alphabetical order) 		John Chodkowski, Michigan State University, Department of Microbiology & Molecular Genetics
Submitting User: caceves
Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
Browse Metadata
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.