This paper presents a method to quantify host-microbe interactions by tracking bacterial lineages with barcoding and high-throughput sequencing.5[7] This technology analyzes the dynamics of microbial populations in the host, including stages of infection initiation, population bottleneck development, and cell spreading.5 Barcoding identifies host and microbial factors that determine susceptibility to infection through quantification of the infectious bottleneck.[The study reveals how dominant lineages evolve during infection or tumor growth.The technique allows the exploration of population bottlenecks, dissemination, and evolution of microbes in the host.The findings have implications for understanding host response, vaccination, and therapeutic options with respect to founder effects.Published in Science, Volume 391, Issue 6780, Pages 34-40, January 2026.[5] The findings have implications for understanding the host response, vaccination, and therapeutic options with respect to founder effects.