Cryptic Insect Microbiome Compositions Unveiled with Full-Length 16S Sequencing

Abstract

Insects have interconnected relationships with gut microorganisms which can have impacts on behavior and survival. Understanding foundational ecological principles of the insect-associated microorganisms is important to understand how insects utilize microbes to cope with stress and different environments. Common microbiome surveys of insect microbiomes utilize 16S rRNA sequencing of metagenomic DNA. For amplicon-based surveys of insect microbiome, fragment length and 16S rRNA subunit choice may have unintended biases, and some primer combinations may under-represent genus or species richness. Contemporary solutions target sequencing of the entire 16S rRNA fragment. Here, we illustrate the benefit of full-length 16S rRNA sequencing in improving sample resolution compared to V4 which provides new insight into the gut microbiome community composition of an invasive insect. We evaluated the gut microbiome of mass-reared medfly males (Mediterranean fruit fly, Ceratitis capitata) that were collected across a nine-month sampling period. Full-length 16S rRNA PCR products of samples were prepared into a Kinnex 16S rRNA library, sequenced on a PacBio Revio system, and the resulting HiFi amplicon data was processed into amplicon sequence variants (ASVs). Our findings reveal substantial differences in bacterial compositions across different medfly cohorts when sampling the full-length amplicons which were not detectible when only considering the V4 regions. Strain-level gut microbiome variation were supported with genomes assembled from shotgun metagenomic sequencing. Our findings support that long-read sequencing of full-length 16S rRNA amplicon uncover ecologically important interactions between host and gut microbiomes and serve as a bridge between short-fragment sequencing and shotgun metagenomics.