Of the 163 samples that underwent 16S rRNA gene amplicon sequencing, an average of >16,000 sequences per sample were recovered, accounting for a total of 2646 OTUs. When rarefied to 10,000 sequences per sample to give a more accurate picture of the data, curves indicated that the NP swabs and sequencing depth adequately displayed microbial species richness.

Syracuse University

"Total nucleic acids were extracted from a frozen specimen without a buffer using the DNeasy UltraClean DNA Extraction Kit (Qiagen) and quantified using the Qubit™ assay (Invitrogen) from one of the four aliquots prepared from the original sample. The 16S rRNA gene V4–V5 region was amplified using a modified 515F–806R primer pair.20 Sequencing of amplicons was completed using the Illumina MiSeq platform to generate 2 × 250 paired-end reads."

Method for 16S rRNA gene amplicon sequencing with NP Swab

Lopez, S.M.C., Martin, J.M., Johnson, M. et al. A method of processing nasopharyngeal swabs to enable multiple testing. Pediatr Res 86, 651–654 (2019). https://doi-org.libezproxy2.syr.edu/10.1038/s41390-019-0498-1
https://www.nature.com/articles/s41390-019-0498-1

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