Single-cell bacterial sequencing of invertible loci reveals promoter inversion rates as a strong determinant of population heterogeneity

Population heterogeneity can promote bacterial fitness in response to unpredictable environmental conditions. Human gut symbiont Bacteroides spp., displays variability in single cell surface architectures by combinatorial regulation of promoter inversions that drive expression of capsular polysaccharides (CPS). Using high-throughput single-cell sequencing, we reveal population heterogeneity generated through combinatorial promoter inversion and show that B. fragilis populations can access diverse CPS promoter states. Combining our data with stochastic computational modeling, we demonstrate that the rates of promoter inversion regulated by a broadly conserved serine recombinase are a major mechanism shaping population heterogeneity. Exploiting control over the expression of the recombinase, we devise a method for creating phase-locked variants and show that populations with different initial compositions converge to a similar steady-state composition over time. Our approach can be used to interrogate single-cell phase variable states of diverse microbes including bacterial pathogens. Summary sentenceHigh-throughput single cell sequencing of phase variation reveals regulation as a major driver of population diversification