PXD006281

PXD006281 is an original dataset announced via ProteomeXchange.

Title	Meta-Proteomics profiling of a four species biofilm
Description	Microbial biofilms are omnipresent and implicated in a wide spectrum of areas ranging from bioremediation, food production and biomedical applications. To date little is understood about how biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we ap-ply a meta-proteomics approach to investigate the mechanism driving biofilm formation in a microbial model consortium of four bacterial soil isolates of Steno-trophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paeni-bacillus amylolyticus. The protein abundances between community and the single species biofilms were compared to describe how different metabolic pathways were influenced by inter-species interactions. Our results indicate that community development is dependent on interactions between community members facilitat-ing surface attachment and cross-feeding on specific amino acids. Opposite regu-lation patterns of fermentation and nitrogen pathways in Paenibacillus amylolyticus and Xanthomonas retroflexus may, however, also indicate that competition for lim-ited resources affects community development. Overall our results demonstrate the multitude of pathways characterizing biofilm formation in mixed communities. In order to obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for removing peptide sequences shared between community members from the ref-erence proteomes used for spectral database searches. This pipeline can readily be applied to other microbial communities.
HostingRepository	PRIDE
AnnounceDate	2017-12-06
AnnouncementXML	Submission_2017-12-06_07:48:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jakob Herschend
SpeciesList	scientific name: Paenibacillus amylolyticus; NCBI TaxID: 1451; scientific name: Microbacterium oxydans; NCBI TaxID: 82380; scientific name: Stenotrophomonas rhizophila; NCBI TaxID: 216778; scientific name: Xanthomonas retroflexus; NCBI TaxID: 305959;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-04-10 05:35:16	ID requested
⏵ 1	2017-12-06 07:48:49	announced

Herschend J, Damholt ZBV, Marquard AM, Svensson B, S, ø, rensen SJ, H, ä, gglund P, Burm, ø, lle M, A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community. Sci Rep, 7(1):16483(2017) [pubmed]

curator keyword: Metaproteomics, Biological

submitter keyword: LC-MS/MS, Biofilm, Soil Isolates, metaproteomics, drip flow reactor

Mette Burmølle
contact affiliation	University of Copenhangen, Section of Microbiology
contact email	burmolle@bio.ku.dk
lab head
Jakob Herschend
contact affiliation	University of Copenhagen
contact email	jakob.herschend@bio.ku.dk
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/2017/12/PXD006281

PRIDE project URI

• PRIDE
  1. PXD006281
     1. Label: PRIDE project
     2. Name: Meta-Proteomics profiling of a four species biofilm