Pooled genomic sequencing of mixed cultures of Coccidioides posadasii strains at 37C and RT

Next generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains a bottleneck for exploiting this information, particularly for pathogens that are difficult to manipulate. Here, we establish a method for high-throughput phenotyping of mixed cultures, in which the pattern of naturally occurring single-nucleotide polymorphisms in each isolate is used as intrinsic barcodes which can be read out by sequencing. We demonstrate that our method can correctly deconvolute strain proportions in simulated mixed-strain pools. As an experimental test of our method, we infer the strain compositions for large mixed pools of natural isolates of Coccidioides posadasii after competition at 37C and room temperature. We validate the results of these selection experiments by recapitulating the temperature-specific enrichment results in smaller pools.