Dynamics of phage-host interactions in Bacteroides fragilis resolved by single-cell transcriptomics [bulk RNA-Seq data]

Success of phage therapies is limited by bacterial defenses against phages. While a variety of anti-phage defense mechanisms has been characterized, how expression of these systems is distributed across individual cells and how their combined activities translate into protection from phages has not been studied. Using bacterial single-cell RNA sequencing, we profiled the transcriptomes of ~50,000 cells from cultures of a human pathobiont, Bacteroides fragilis, infected with a lytic bacteriophage. We quantified the asynchronous progression of phage infection in single bacterial cells and reconstructed the infection timeline, characterizing both host and phage transcriptomic changes as infection unfolded. We discovered subpopulations of bacteria that remained uninfected and heterogeneously expressed protective factors. Each cell's vulnerability to phage infection was defined by combinatorial expression of multiple genetic loci, including phase-variable capsular polysaccharide (CPS) biosynthesis pathways, restriction-modification systems (RM), and a novel operon predicted to encode fimbrial genes. Acting in concert, these heterogeneously expressed anti-phage defense mechanisms create a phenotypic landscape where distinct protective combinations enable the survival and re-growth of bacteria expressing these phenotypes without acquiring additional mutations. The emerging model of complementary action of multiple protective mechanisms heterogeneously expressed across an isogenic bacterial population showcases the potent role of phase variation and stochasticity in bacterial anti-phage defenses. Overall design: Exponentialy growing Bacteroides fragilis NCTC 9343 culture was cultivated in chopped meat carbohydrate (CMC) media and either infected or not with Bf12P1 phage. Total RNA was extracted and sequenced.