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PXD042954-1

PXD042954 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIntegration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge
DescriptionMulti-omics has the promise to provide a detailed molecular picture for biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimum structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community. Kefir grain, a microbial community that ferments milk and creates kefir, represents a self-renewing, stable, natural microbial community. Kefir has been shown to associate with a wide range of health benefits. We obtained a controlled bacterial community using the two most abundant and well-studied species in kefir grains: Lentilactobacillus kefiri and Lactobacillus kefiranofaciens. We applied growth temperatures of 30°C and 37°C, and ob-tained transcriptomic, metabolomic, and proteomic data for the same 20 samples (10 samples per temperature). We obtained a multi-omics interaction network, which generated insights that would not have been possible with single-omics analysis. We identified interactions among transcripts, proteins, and metabolites suggesting active toxin/antitoxin systems. We also observed multifarious interactions that involved the shikimate pathway. These observations helped explain bacterial adaptation to different stress conditions, co-aggregation, and increased activation of L. kefiranofa-ciens at 37°C.
HostingRepositoryPRIDE
AnnounceDate2023-08-18
AnnouncementXMLSubmission_2023-08-18_05:16:16.034.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSopheAlvarez
SpeciesList scientific name: Lactobacillus kefiranofaciens; NCBI TaxID: 267818; scientific name: Lactobacillus kefiri; NCBI TaxID: 33962;
ModificationListmonohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Eclipse
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-06-13 12:56:59ID requested
12023-08-18 05:16:16announced
22023-11-14 07:03:26announced2023-11-14: Updated project metadata.
Publication List
Keyword List
submitter keyword: Lactobacillus,proteomics, metabolomics, Lentilactobacillus, kefir
Contact List
SophieAlvarez
contact affiliationProteomics and Metabolomics Facility, University of Nebraska - Lincoln
contact emailsalvarez@unl.edu
lab head
SopheAlvarez
contact affiliationUniversity of Nebraska - Lincoln
contact emailsalvarez@unl.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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