PXD008288

PXD008288 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of Fusobacterium nucleatum and Porphyromonas gingivalis biofilms and planktonic cultures when grown as mono- or dual-species models
Description	Bacterial cells in biofilms adopt a profoundly different phenotype than their planktonic counterparts. The Gram-negative bacteria Fusobacterium nucleatum and Porphyromonas gingivalis are pathogens associated with oral biofilm and periodontal disease. In this study, we identified and functionally characterized the proteome of F. nucleatum and P. gingivalis cells grown either as biofilms or in planktonic cultures by high-resolution liquid chromatography-tandem mass spectrometry. We used proteomic analysis for identification and label-free quantification of proteins, and sequence-based functional characterization for their classification. In F. nucleatum biofilm five proteins showed changes from planktonic condition, including proteins involved in vitamin B metabolic processes. Forty proteins were changed in P. gingivalis biofilm, 30 increased and 10 decreased. Putative cell division trigger factor and riboflavin biosynthesis proteins were the most increased in this biofilm. To describe interactions between the two species at the protein level, we grew the bacteria either individually or together. In the mixed species biofilm culture, 112 proteins showed significant changes, with 72 proteins derived from F. nucleatum and 40 proteins from P. gingivalis. By comparing dual-species to mono-species in biofilm and in planktonic growth conditions, P. gingivalis showed more proteins with decreased level in the dual species conditions.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:29:30.054.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marwan Mansoor Ali Mohammed
SpeciesList	scientific name: Fusobacterium nucleatum subsp. nucleatum ATCC 25586; NCBI TaxID: 190304; scientific name: Porphyromonas gingivalis ATCC 33277; NCBI TaxID: 431947;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-24 03:25:40	ID requested
1	2021-09-22 04:42:45	announced
2	2021-09-24 00:03:14	announced	2021-09-24: Updated project metadata.
⏵ 3	2024-10-22 05:29:31	announced	2024-10-22: Updated project metadata.

10.1016/j.anaerobe.2021.102449;

Ali Mohammed MM, Pettersen VK, Nerland AH, Wiker HG, Bakken V, Label-free quantitative proteomic analysis of the oral bacteria Fusobacterium nucleatum and Porphyromonas gingivalis to identify protein features relevant in biofilm formation. Anaerobe, 72():102449(2021) [pubmed]

curator keyword: Biological

submitter keyword: Bacterial biofilms, Label-free quantitative proteomics., Biofilm phenotype, Planktonic bacteria, Fusobacterium nucleatum, Porphyromonas gingivalis

Vidar Bakken
contact affiliation	The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
contact email	Vidar.Bakken@uib.no
lab head
Marwan Mansoor Ali Mohammed
contact affiliation	University of Sharjah, College of Dental Medicine, Department of Oral and Craniofacial Health Sciences
contact email	drmarwan98@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/2021/09/PXD008288

PRIDE project URI

• PRIDE
  1. PXD008288
     1. Label: PRIDE project
     2. Name: Proteomic analysis of Fusobacterium nucleatum and Porphyromonas gingivalis biofilms and planktonic cultures when grown as mono- or dual-species models