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. 2018 Nov 5;8:16321. doi: 10.1038/s41598-018-34294-x

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Overall workflow of the study. Mock community samples consisting of five oral strains were sequenced via six DNA extraction methods and followed by amplification of three 16S rRNA gene target regions. The results of subsequent 16S rDNA sequencing on the MiSeq platform were quantitatively compared. For each of the six samples (each of which underwent one of the six DNA extraction method), triple biological replicates (“Bio. replicates”) for each of the amplification regions were sequenced. In addition, for the amplification region of V3-V4 (P2), one technical replicate (“Tech. replicate”) for each of the six samples was sequenced. All the 54 biological samples were processed by the same experimenter (Experimenter A) and sequenced on the same sequencing batch (Batch A), while six technical replicates were processed by the other experimenter (Experimenter B) and on the other batch (Batch A).