PXD006070

PXD006070 is an original dataset announced via ProteomeXchange.

Title	Rumen metaproteome - A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments
Description	The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal’s feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, squeezed solid and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more abundant in the corn silage whereas oligosaccharide transporters showed a higher abundance in the fiber-rich diets. Proteins involved in carbon metabolism were detected in high numbers and identification of metabolites like short-chain fatty acids, methylamines and phenylpropionate by NMR enabled linkage between producers and products. This study forms a solid basis to retrieve deeper insight into the complex network of gut microbial adaptation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:08:51.286.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jana Seifert
SpeciesList	scientific name: Archaea; NCBI TaxID: 2157; scientific name: Bacteria; NCBI TaxID: 2;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-10 05:58:41	ID requested
1	2017-08-15 02:58:46	announced
2	2017-09-11 06:10:31	announced	Updated publication reference for PubMed record(s): 28883813.
⏵ 3	2024-10-22 04:08:59	announced	2024-10-22: Updated project metadata.

10.3389/fmicb.2017.01605;

Deusch S, Camarinha-Silva A, Conrad J, Beifuss U, Rodehutscord M, Seifert J, A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments. Front Microbiol, 8():1605(2017) [pubmed]

curator keyword: Metaproteomics

submitter keyword: rumen, metaproteomics, LC-MS/MS

Jana Seifert
contact affiliation	University of Hohenheim (Germany), Institute of Animal Science
contact email	jseifert@uni-hohenheim.de
lab head
Jana Seifert
contact affiliation	University of Hohenheim
contact email	jseifert@uni-hohenheim.de
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/2017/08/PXD006070

PRIDE project URI

• PRIDE
  1. PXD006070
     1. Label: PRIDE project
     2. Name: Rumen metaproteome - A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments