Abstract
We present a detailed protocol for Pseudomonas-specific 16S rRNA gut-microbiome profiling of brown planthopper (BPH) populations collected across changing climates and geographical locations using next-generation sequencing. We provide a technique for comparative analysis of Pseudomonas species structure and composition across BPH populations. Additionally, using qPCR we quantify the titers of Pseudomonas species in BPH. This protocol can be adopted for analyzing microbiome dynamics and monitoring populations of other pests, a crucial aspect for understanding their biodiversity, speciation, and adaptations. For complete details on the use and execution of this protocol, please refer to Gupta et al. (2022).1.