PXD033418-1

PXD033418 is an original dataset announced via ProteomeXchange.

Title	Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits
Description	The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we reveal that many microbial populations show divergent proteome production in function of the feed efficiency state. Thus, proteomic data serve as a strong indicator of host feed efficiency state phenotype, overpowering predictions based on genomic and taxonomic information. We highlight protein production of specific phylogenies associated with each of the feed efficiency states. We also find remarkable plasticity of the proteome both in the individual population and at the community level, driven by niche partitioning and competition. These mechanisms result in protein production patterns which exhibit functional redundancy and checkerboard distribution that are tightly linked to the host feed efficiency phenotype. By linking microbial protein production and the ecological mechanisms that act within the microbiome feed efficiency states, our present work reveals a layer of complexity that bears immense importance to the current global of food security and sustainability.
HostingRepository	PRIDE
AnnounceDate	2022-08-25
AnnouncementXML	Submission_2022-08-25_03:32:37.393.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anke Trautwein-Schult
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-24 12:29:54	ID requested
⏵ 1	2022-08-25 03:32:37	announced
2	2023-11-14 08:56:09	announced	2023-11-14: Updated project metadata.

10.1038/S41396-022-01295-8;

submitter keyword: rumen metaproteome, feed efficient animal, rumen microbiome, LC-MS/MS

Dörte Becher
contact affiliation	University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
contact email	dbecher@uni-greifswald.de
lab head
Anke Trautwein-Schult
contact affiliation	University of Greifswald
contact email	anke.trautwein-schult@uni-greifswald.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/2022/08/PXD033418

PRIDE project URI

• PRIDE
  1. PXD033418
     1. Label: PRIDE project
     2. Name: Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits