Genomic DNA was converted to sequencing libraries with unique dual indexed adapters to ensure that reads and/or organisms are not misaligned (Transnetyx Inc., Cordova, TN, USA). DNA extraction is performed using the Qiagen DNeasy 96 PowerSoil Pro QIAcube HT extraction kit and protocol. Genomic DNA is converted to sequencing libraries with unique dual indexed adapters to ensure that reads and/or organisms are not misaligned. Library preparation is performed using the Watchmaker DNA library preparation with fragmentation protocol. Sequencing is performed using the Illumina NovaSeq instrument and protocol at a depth of 2 million 2 x 150 bp read pairs. Raw data (in the form of FASTQ files) was analyzed using the One Codex analysis software using the One Codex database consisting of more than 127,000 whole microbial reference genomes22. Comparing a microbial sample against the One Codex Database consists of three sequential steps: 1) Every individual sequence is compared against the database by exact alignment using k-mers where k=3123,24; 2) Sequence artifacts are filtered out based on the relative frequency of unique k-mers; 3)