An accurate and efficient experimental approach for characterization of the complex oral microbiota

• DOI: 10.1186/s40168-015-0110-9
• Publication Date: 2015-10-05T10:08:20Z
• Authors: Wei Zheng; Maria Tsompana; Angela Ruscitto; Ashu Sharma; Robert Genco; Yijun Sun; Michael J. Buck
• Keywords: UniFrac; Hypervariable region; Pyrosequencing; Oral Microbiome; Jaccard index

Currently, taxonomic interrogation of microbiota is based on amplification 16S rRNA gene sequences in clinical and scientific settings. Accurate evaluation the depends heavily primers used, genus/species resolution bias can arise with non-representative genomic regions. The latest Illumina MiSeq sequencing chemistry has extended read length to 300 bp, enabling deep profiling large number samples a single paired-end reaction at fraction cost. An increasingly researchers have adopted this technology for various microbiome studies targeting V3–V4 hypervariable region. To expand applicability powerful platform further descriptive functional studies, we standardized tested an efficient, reliable, straightforward workflow amplification, library construction, V1–V3 region using new 2 × platform. Our analysis involved 11 subgingival plaque from diabetic non-diabetic human subjects suffering periodontitis. efficiency reliability our experimental protocol was compared data same samples. Comparisons were measures observed richness species evenness, along Procrustes analyses beta(β)-diversity distance metrics. As control, also analyzed total eight technical replicates regions synthetic community known bacterial operon counts. We show that accurately true composition. unweighted UniFrac β-diversity metrics depicted significant correlation between oral composition However, phylotype higher region, suggesting offers deeper assessment population diversity ecology complex microbiota. This study provides valuable evidence selection appropriate amplicons future studies. expect framework will be widely applicable other types microbiota, allowing robust, time-efficient, inexpensive examination thousands population, phylogenetic, crossectional longitutidal