16S Amplicon Sequencing
Isolation of total DNA from stool samples and analysis by Illumina MiSeq 16S rRNA bacterial amplicon sequencing were performed in the UNC Microbiome Core Facility following standard Illumina sequencing protocols. Data sequencing output was converted to fastq format and demultiplexed using Illumina Bcl2Fastq 2.20.0 . The resulting paired-end reads were processed with the QIIME ver.2.2020.6  wrapper for DADA2 including merging paired ends, quality filtering, error correction, and chimera detection. Amplicon sequencing units from DADA2 were assigned taxonomic identifiers using the Silva database.