DOI: 10.1101/497792Dec 17, 2018Paper

Highly reproducible 16S sequencing facilitates measurement of host genetic influences on the stickleback gut microbiome

BioRxiv : the Preprint Server for Biology
Clayton M SmallWilliam A Cresko

Abstract

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. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach consisting of tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Individual abundance estimates for rare OTUs, however, showed much lower reproducibility. We found that the stickleback gut microbiome was highly variable, even among siblings housed together, but that an effect o...Continue Reading

Related Concepts

DNA
Environment
Experimental Design
Sticklebacks
Evaluation
Isolation Aspects
Gut
High Throughput Analysis
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