design: Genomic DNA from samples was extracted using the Omega Biotek Mag-Bind Blood & Tissue DNA HDQ 96 Kit (4x96 Preps) (Cat. No. / ID: M6399-01) according to the manufacturers protocol. Whole (25mm or 47mm) filters were used for genomic DNA extraction. The extraction protocol was automated and completed using a Hamilton Microlab Starlet. Genomic DNA was eluted into 100 l and frozen at -20 C. Forward primer: GTGYCAGCMGCCGCGGTAAReverse primer: GGACTACNVGGGTWTCTAATPrimer notes: 515F and 806R.                                                                                                                A portion of mitochondrial 16S rDNA gene was PCR amplified from each genomic DNA sample. Both forward and reverse primers contained a 5 adaptor sequence to allow for subsequent indexing and Illumina sequencing. Each 25 L PCR reaction was mixed according to the Promega PCR Master Mix specifications (Promega catalog # M5133, Madison, WI) which included 12.5ul Master Mix, 0.5 l of each primer, 1.0 l of gDNA, and 10.5 l DNase/RNase-free H2O. DNA was PCR amplified using the following conditions: initial denaturation at 95 C for 5 minutes, followed by 35 cycles of 45 seconds at 95 C, 1 minute at 50 C, and 90 seconds at 72 C, and a final elongation at 72 C for 10 minutes. Sample library pools were prepped for sequencing on an Oxford Nanopore Technologies MinION (Oxford, England) using the Ligation Sequencing Kit V14 (cat# SQK-LSK114). Final basecalling was completed using AWS Batch and EC2 g5.xlarge instances running ONT's dorado software (v0.7.1) in super high accuracy mode using the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 basecalling model.