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

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 defenses. Among the most abundant phages in the gut are the crAss-like phages that infect members of the order Bacteroidales, in particular, genus <i>Bacteroides</i>. In this study, we explored some of the mechanisms enabling the co-existence of four phage-Bacteroidales host pairs <i>in vitro</i> using a multi-omics approach (transcriptomics, proteomics and metabolomics). These included three <i>Bacteroides</i> species paired with three crAss-like phages (<i>Bacteroides intestinalis</i> and фcrAss001, <i>Bacteroides xylanisolvens</i> and фcrAss002, and an acapsular mutant of <i>Bacteroides thetaiotaomicron</i> with DAC15), and <i>Parabacteroides distasonis</i> paired with the siphovirus фPDS1. We show that phase variation of individual capsular polysaccharides (CPSs) is the primary mechanism promoting phage co-existence in Bacteroidales, but this is not the only strategy. Alternative resistance mechanisms, while potentially less efficient than CPS phase variation, can be activated to support bacterial survival by regulating gene expression and resulting in metabolic adaptations, particularly in amino acid degradation pathways. These mechanisms, also likely regulated by phase variation, enable bacterial populations to persist in the presence of phages, and <i>vice versa</i>. An acapsular variant of <i>B. thetaiotaomicron</i> demonstrated broader transcriptomic, proteomic, and metabolomic changes, supporting the involvement of additional resistance mechanisms beyond CPS variation. This study advances our understanding of long-term phage-host interaction, offering insights into the long-term persistence of crAss-like phages and extending these observations to other phages, such as фPDS1. Knowledge of the complexities of phage-bacteria interactions is essential for designing effective phage therapies and improving human health through targeted microbiome interventions.