Automated Microbiome DNA Extraction and Sequencing

The University of California Microbiome Core performed nucleic acid extractions using previously published protocols (D’Amato et al. 2020 (link)). Briefly, extractions and purifications were performed using the MagMAX Microbiome Ultra Nucleic Acid Isolation Kit (Thermo Fisher Scientific, USA) and automated on KingFisher Flex robots (Thermo Fisher Scientific, USA). Blank controls and mock communities (Zymo Research Corporation, USA) were carried through all downstream processing steps. Input DNA was quantified using a PicoGreen fluorescence assay (Thermo Fisher Scientific, USA) and metagenomic libraries were prepared with Illumina DNA Prep kits (Illumina Incorporated, USA) following the manufacturer’s instructions and automated on epMotion automated liquid handlers (Eppendorf, Germany). Sequencing was performed on the Illumina NovaSeq 6000 sequencing platform with paired-end 150 base pair cycles at the Institute for Genomic Medicine (IGM) at the University of California San Diego.