PXD073583

PXD073583 is an original dataset announced via ProteomeXchange.

Title	LFQ values with shared and unique peptides - Community context reshapes microbial proteomes and reduces functional overlap
Description	Microbial coexistence in complex communities requires mechanisms that minimize competition and optimize resource use. Here, we show that bacteria modulate protein abundance in response to specific community members, reducing functional redundancy and promoting metabolic complementarity. Using synthetic gut-derived consortia exposed to distinct carbon sources, we systematically profiled proteomic responses of individual species across isolate, pairwise, and four-member communities. We found that biotic interactions, rather than abiotic conditions, were the dominant drivers of proteomic variation. These interactions led to reproducible, partner-specific expression shifts that significantly reduced functional overlap and were frequently associated with increased community productivity. Our findings reveal that microbes dynamically reshape their realized niche through protein abundance plasticity, enabling them to partition metabolic space and stabilize community structure. This study provides a mechanistic link between microbial interaction networks, regulatory flexibility, and coexistence, offering a generalizable framework for understanding and engineering functional microbial ecosystems.
HostingRepository	PRIDE
AnnounceDate	2026-02-19
AnnouncementXML	Submission_2026-02-19_06:39:17.158.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anke Trautwein-Schult
SpeciesList	scientific name: Faecalibacterium prausnitzii; NCBI TaxID: NEWT:853; scientific name: Xylanibacter ruminicola; NCBI TaxID: NEWT:839; scientific name: Butyrivibrio fibrisolvens DSM 3071; NCBI TaxID: NEWT:1121131; scientific name: Anaerobutyricum hallii DSM 3353; NCBI TaxID: NEWT:411469; scientific name: Roseburia intestinalis L1-82; NCBI TaxID: NEWT:536231; scientific name: Megasphaera elsdenii DSM 20460; NCBI TaxID: NEWT:1064535; scientific name: Marvinbryantia formatexigens DSM 14469; NCBI TaxID: NEWT:478749;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; LTQ Orbitrap; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-26 12:08:36	ID requested
⏵ 1	2026-02-19 06:39:18	announced

Dataset with its publication pending

submitter keyword: None

Prof. Dr.
contact affiliation	Institut für Mikrobiologie, Universität Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald
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/2026/02/PXD073583

PRIDE project URI

• PRIDE
  1. PXD073583
     1. Label: PRIDE project
     2. Name: LFQ values with shared and unique peptides - Community context reshapes microbial proteomes and reduces functional overlap