PXD055395

PXD055395 is an original dataset announced via ProteomeXchange.

Title	Kamrad et al Interspecies interactions drive proteome reorganization and emergent metabolism in gut bacteria"
Description	Inter-species interactions shape the function and dynamics of microbial communities. Yet, the understanding of how these interactions influence the molecular physiology of interacting species remains surprisingly limited. Here, we assembled 104 synthetic pairwise co-cultures of 15 diverse gut bacteria in vitro and examined responses using meta-proteomics and metabolomics. We detect a diversity of ecological interactions with an overall dominance of competition, amensalism and exploitation, yet with a circa 18% overall prevalence of positive interactions. The growth changes were accompanied by strong molecular changes, with typically more than 60% of the proteome of a species changing in response to at least one partner. We find that the magnitude of the proteome responses is influenced by proteome size, species abundance, and pH of the co-culture. Small-molecule transport and carbon metabolism are among the most responsive processes indicating pervasive metabolic interactions. Using metabolomics we identified likely cross-fed metabolites, emergent polyamine metabolism, and niche partitioning in amino acid utilization in co-cultures. Notably, many yet uncharacterized proteins were differentially abundant in co-cultures, suggesting a role of the ‘dark proteome’ in inter-species interactions. Clustering of these proteins with those with known biological function indicates an approach to leverage species interactions for functional genomics. Overall, our systematic approach demonstrates how bacterial interactions profoundly affect the physiology of participating cells, advancing our molecular understanding of ecological interactions.
HostingRepository	PRIDE
AnnounceDate	2025-05-12
AnnouncementXML	Submission_2025-05-12_12:34:21.156.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stephan Kamrad
SpeciesList	scientific name: Agathobacter rectalis; NCBI TaxID: 39491; scientific name: Clostridium sporogenes; NCBI TaxID: 1509; scientific name: Clostridioides difficile; NCBI TaxID: 1496; scientific name: Lactobacillus acidophilus; NCBI TaxID: 1579; scientific name: Collinsella aerofaciens; NCBI TaxID: 74426; scientific name: Segatella copri; NCBI TaxID: 165179; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Parabacteroides merdae; NCBI TaxID: 46503; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Bacteroides thetaiotaomicron; NCBI TaxID: 818; scientific name: Phocaeicola vulgatus; NCBI TaxID: 821; scientific name: Bacteroides uniformis; NCBI TaxID: 820; scientific name: Klebsiella aerogenes; NCBI TaxID: 548; scientific name: Lactobacillus gasseri; NCBI TaxID: 1596; scientific name: [Clostridium] saccharolyticum; NCBI TaxID: 84030; scientific name: Ruminococcus gnavus; NCBI TaxID: 33038;
ModificationList	iodoacetamide derivatized residue
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-30 09:13:25	ID requested
⏵ 1	2025-05-12 12:34:21	announced

Dataset with its publication pending

submitter keyword: C. difficile, Metaproteomics,Microbiome

Kiran Patil
contact affiliation	MRC Toxicology Unit, University of Cambridge
contact email	kp533@mrc-tox.cam.ac.uk
lab head
Stephan Kamrad
contact affiliation	The Francis Crick Institute
contact email	stephan.kamrad@gmail.com
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/2025/05/PXD055395

PRIDE project URI

• PRIDE
  1. PXD055395
     1. Label: PRIDE project
     2. Name: Kamrad et al Interspecies interactions drive proteome reorganization and emergent metabolism in gut bacteria"