Gut microbiota from threespine stickleback hosts Raw sequence reads. Gasterosteus aculeatus

Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same lab environment. We sampled guts from 42 fish to address technical and biological sources of variation in 16S-based estimates of microbial diversity.