Amplicon sequencing reads for WISH-tag barcoded bacterial strains
Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that are not captured when recording strain abundances using conventional amplicon sequencing and require intra-strain resolution. To approach this, we have chosen host microbiomes as an example and developed a novel genomic tagging system, termed WISH-tags that allows enumeration by both quantitative PCR and next-generation sequencing. We experimentally validated the performance of 62 tags and showed that they enable their differentiation with a dynamic range of at least five orders of magnitude with high precision and without background DNA amplification. We introduced WISH-tags into a set of model and non-model bacteria of the mouse and plant microbiota, respectively, and confirmed equal fitness of barcoded strains compared to untagged wild type strains. We then investigated intra-strain priority effects using isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. Our findings reveal a resistance to colonization by late arriving strains of Salmonella Typhimurium in the mouse gut, whereas the phyllosphere accommodated latecomers of Sphingomonas in a proportional manner to their presence at the late inoculation timepoint. This illustrates how WISH-tags can serve as a valuable resource for deciphering the population dynamics underlying microbiome assembly, including bottlenecks, and can be applied across biological systems