QIAamp PowerFecal Pro DNA Kit (50)

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Publication protocol

Stool samples were collected using the OMNIgene®•GUT collection kit (DNAgenoTekTM, Ottawa, ON, Canada), and microbial DNA was extracted from the samples using the QIAamp PowerFecal Pro DNA Kit (QIAGEN, Valencia, CA, USA). The DNA extracts were quantified using the QuantiFluor® ONE dsDNA System and QuantusTM Fluorometer (Promega, Madison, WI, USA) and subsequently prepared for shotgun metagenomic sequencing using the NexteraTM DNA Flex Library Preparation Kit (Illumina, San Diego, CA, USA). The DNA libraries were normalized prior to pooling to ensure equal library representation, and the pooled libraries were sequenced using the Illumina NextSeq 550 System (Illumina, San Diego, CA, USA). Sequencing read depth ranged from 13.1 M to 15.4 M total reads in the four samples. Raw sequence reads (FASTQ files) were trimmed and analyzed using One Codex (https://www.onecodex.com/) to assess alpha diversity (as measured by the Shannon index) and to identify relative microbial abundances within the gut microbiome of each participant. Institutional Review Board (IRB) approval for human subject research was granted by the New England IRB #120190096 (Approval 8/26/2019). Written consent was obtained for each study participant.

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