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Genomic DNA was extracted from nasopharyngeal swab and saliva samples using the zymoBIOMICS DNA Miniprep Kit (Zymo Research, Irvine, California) according to the manufacturers instructions. 16S rRNA sequencing libraries were prepared by amplifying and barcoding the V1-V2 region of the 16S rRNA gene using the Quick-16S NGS Library Prep Kit (Zymo Research) according to the manufacturers instructions. Samples were pooled and sequenced on an Illumina platform with 2  250 base pair standard run.