PXD002838

PXD002838 is an original dataset announced via ProteomeXchange.

Title	The effect of microbial colonization on the host proteome varies by gastrointestinal location
Description	Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum, and proximal colon under three colonization states: germ-free, monocolonized with Bacteroides thetaiotaomicron, and conventionally raised. Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal tract. Unsupervised clustering showed that host protein abundance primarily depended on gastrointestinal location rather than colonization state and specific proteins and functions that defined these locations were identified by random forest classifications. K-means clustering of protein abundance across locations revealed substantial differences in host protein production between conventionally raised mice relative to germ-free and monocolonized mice. Finally, comparison to fecal proteomic datasets suggested that the identities of stool proteins are not biased to any region of the gastrointestinal tract, but are substantially impacted by the microbiota in the distal colon.
HostingRepository	PRIDE
AnnounceDate	2015-11-25
AnnouncementXML	Submission_2015-11-25_02:54:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joshua Elias
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-02 01:38:02	ID requested
⏵ 1	2015-11-25 02:54:15	announced

Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE, The effect of microbial colonization on the host proteome varies by gastrointestinal location. ISME J, 10(5):1170-81(2016) [pubmed]

curator keyword: Biological

submitter keyword: mouse gut microbiome host-centric proteomics

Joshua E Elias
contact affiliation	Department of Chemical & Systems Biology, Stanford University, Stanford, CA
contact email	josh.elias@stanford.edu
lab head
Joshua Elias
contact affiliation	Chemical & Systems Biology
contact email	josh.elias@stanford.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD002838

PRIDE project URI

• PRIDE
  1. PXD002838
     1. Label: PRIDE project
     2. Name: The effect of microbial colonization on the host proteome varies by gastrointestinal location