Transcriptional and metabolic adaptations of gut Bacteroides and Parabacteroides hosts to persistent bacteriophage infection in vitro

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 analysis. The analysis was performed on bacterial cultures co-cultured with phages over a period of 5 days, with daily subculturing into 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.