Dataset Information

Transcriptional, Proteomic, and Metabolic Adaptations of Gut Bacteroides and Parabacteroides Hosts to Persistent Bacteriophage Infection In Vitro

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Bacteroides Intestinalis Bacteroides Xylanisolvens Crassvirales Bacteroides Thetaiotaomicron (strain Atcc 29148 / Dsm 2079 / Nctc 10582 / E50 / Vpi-5482) Parabacteroides Distasonis

SUBMITTER: Jessie Maier

LAB HEAD: Manuel Kleiner

PROVIDER: PXD057336 | Pride | 2024-12-09

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	BI_S_1_1_4_140_1000ng_run2_20240318125004.msf	Msf
	BI_S_1_1_4_140_1000ng_run2_20240318125004.raw	Raw
	BI_S_C_1_3_140_1000ng_run2_20240318055858.msf	Msf
	BI_S_C_1_3_140_1000ng_run2_20240318055858.raw	Raw
	BI_S_C_2_29_140min_15ul_run3.msf	Msf

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Publications

Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages.

Cortés-Martín Adrián A Buttimer Colin C Maier Jessie L JL Tobin Ciara A CA Draper Lorraine A LA Ross R Paul RP Kleiner Manuel M Hill Colin C Shkoporov Andrey N AN

bioRxiv : the preprint server for biology 20241117

<h4>Background</h4>Bacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where bacteria employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies to overcome these defences. Among the most abundant phages in the gut are the crAss-like phages that infect members of the Bacteroidales, in particular <i>Bacteroides.</i> In this study, we explored some of ...[more]

PMID: 39605433

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