design: Total DNA was extracted from stool samples following the manufacturers protocols using either the FastDNA Spin Kit (MP Biomedicals) or the Maxwell RSC PureFood GMO and Authentication Kit (Promega). Extracted DNA concentrations were quantified using a Qubit 2.0 fluorometer (Invitrogen). Sequencing libraries were prepared with the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (NEB) according to the manufacturers protocol. Shotgun sequencing was conducted at CJ Bioscience, Inc., using either an Illumina NextSeq or NovaSeq system.