PXD057336

PXD057336 is an original dataset announced via ProteomeXchange.

Title	Transcriptional, Proteomic, and Metabolic Adaptations of Gut Bacteroides and Parabacteroides Hosts to Persistent Bacteriophage Infection In Vitro
Description	The mechanisms underlying the coexistence of crAss-like phages and other types of phages infecting Bacteroidales are not well understood. This study examines potential mechanisms that promote phage coexistence in the Bacteroidales order through RNA-seq and proteomic analysis. The analysis was performed on anaerobic bacterial cultures co-cultured with phages over a period of 5 days and corresponding control cultures without phage, with daily subculturing into FAB (Fastidious Anaerobe Broth) fresh media. The study focuses on four individual phage-bacteria pairs: Bacteroides intestinalis APC919/174-crAss001, Bacteroides xylanisolvens APCS1/XY-crAss002, Bacteroides thetaiotaomicron VPI-5482 tdk-acapsular mutant (cps) - DAC15, and Parabacteroides distasonis APCS2/PD-PDS1. Each phage-host pair used had 4 biological replicates. The samples for the analysis were collected during the bacterial mid-log phase (OD600= ~0.3) on the fifth day of co-culture, which occurred between 5-7 hours after subculture. Bacterial cultures were centrifuged at 4,500 x g for 15 min at 4 °C. Immediately after centrifugation, the supernatant was transfer to a new tube and stored at -80 °C and the pellet was carefully dried to remove any remaining liquid and also stored at -80 °C. All samples were processed for proteomics analysis in which proteins differentially expressed in control or infected sample conditions were of interest due to their potential involvement during crAss-like phage infection.
HostingRepository	PRIDE
AnnounceDate	2024-12-09
AnnouncementXML	Submission_2024-12-09_12:19:27.886.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jessie Maier
SpeciesList	scientific name: Parabacteroides distasonis; NCBI TaxID: 823; scientific name: Bacteroides intestinalis; NCBI TaxID: 329854; scientific name: Bacteroides xylanisolvens; NCBI TaxID: 371601; scientific name: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); NCBI TaxID: 226186; scientific name: Crassvirales; NCBI TaxID: 1978007;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-29 22:33:37	ID requested
⏵ 1	2024-12-09 12:19:28	announced

Cort, é, s-Mart, í, n A, Buttimer C, Maier JL, Tobin CA, Draper LA, Ross RP, Kleiner M, Hill C, Shkoporov AN, Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages. bioRxiv, ():(2024) [pubmed]

10.1101/2024.11.17.624012;

submitter keyword: Bacteroides, Parabacteroides, gut microbiome, phage-bacteria interaction,bacteriophages, crAssphages, cohabitation

Manuel Kleiner
contact affiliation	Plant and Microbial Biology Department, Kleiner Lab, North Carolina State University, USA
contact email	manuel_kleiner@ncsu.edu
lab head
Jessie Maier
contact affiliation	North Carolina State University
contact email	jlmaier@ncsu.edu
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/2024/12/PXD057336

PRIDE project URI

• PRIDE
  1. PXD057336
     1. Label: PRIDE project
     2. Name: Transcriptional, Proteomic, and Metabolic Adaptations of Gut Bacteroides and Parabacteroides Hosts to Persistent Bacteriophage Infection In Vitro