Invasive arthropods can harbor a variety of microbial symbionts. Some of these microbial symbionts are vertically transmitted from parent to offspring, while others are environmentally acquired. The use of different host resources can influence the microbial composition of insect herbivores, as we previously found for aphids feeding on sugarcane versus those feeding on sorghum. Here the microbial composition of aphids feeding on commercial sorghum and invasive Johnson grass were compared. Whole genome sequencing data of aphids was mined for microbial sequences using the Kraken pipeline. We compare our results to one of our previous studies that used 16s RNA to target the microbial composition of sorghum aphids feeding on sorghum and sugarcane. Using this approach we show how mining existing genomic sequencing data allows for the analysis of samples for population genetics studies, while still providing high quality that contain reads from microbial symbionts.
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