A Comparison of 16S Amplicons in Microbial Community Standards & Environmental Samples

In the evolving field of bacterial metagenomics, many researchers choose to use variable regions of the 16S rRNA gene to understand which bacteria are present and how many bacteria are present in a sample. The expanding... [ view full abstract ]

In the evolving field of bacterial metagenomics, many researchers choose to use variable regions of the 16S rRNA gene to understand which bacteria are present and how many bacteria are present in a sample. The expanding number of next generation sequencing options and platforms provides many possibilities for 16S sequencing, from looking at one variable domain to combinations of variable domains. The variable regions of the 16S gene offer differential ability to discriminate bacteria from each other and from environmental contaminants. Here, we show the performance of four different options of next generation 16S rRNA sequencing: 16S V1-V3, 16S V3-V4, 16S V4, and 16S V5-V6.  Each region was tested on both a known community of bacteria and on environmental samples. The known communities show the relative representation and performance of each primer set.  The environmental samples demonstrate the performance and challenges these primers sets face in samples similar to those used by metagenomics researchers. The environmental samples were analyzed and classified using the One Codex pipeline and database.