design: DNA was extracted from community samples using a Qiagen DNeasy PowerSoil Pro Kit (cat # 47016) according to manufacturer's instructions with the following noted change. Samples were heated for 10 min at 100 C after addition of lysis buffer and prior to vortexing. Following extraction, DNA was quantified with Qubit dsDNA, high sensitivity (ThermoFisher cat # Q32851) and normalized to 0.2 ng/uL. Shotgun metagenomic sequencing libraries were prepared using the Nextera XT DNA Library kit with 1 ng DNA input, according to manufacturers instructions (Illumina cat # FC-131-1096 and FC-131-2001). Libraries were quantified using a Qubit as indicated above and normalized to 2 ng/l for sequencing.