Included are the following files1) Assembly files (47) in the form of .fasta for each of the 47 different samples (8 participants x 5 or 6 time points). This is the results of the assembly from hybrid long read data (all Pacbio Revio + ONT Promethion > Q20). Assemblies performed using metaMDBG. This file includes all contigs from the pipeline described in the manuscript and will include both high-quality and complete MAGs. "hybrid_assemblies.tar.gz"2) Assembly files (40) in the form of .fasta for the short read metaspades and tell-seq assembly methods"SR_tellseq_assemblies.tar.gz""SR_metaspades_assemblies.tar.gz" 3) Assembly files from sub-sampling experiment: 3 samples (A6, D5, and H6) were deep sequenced with both PB Revio and ONT Promethion lsk114 R10.4.1 SUP400. Data was randomly subsampled to various depths (1, 5, 10, 20, 30, 40 Gbp, and all) and then assembled with both metaMDBG and metaFlye. -A6: total of 26 files (PB was less than 40 Gbp thus no 40 Gbp subsampling depth)-D5: total of 28 files-H6: total of 28 files-total: 82 files"LR_ONTPB_sub_assemblies.tar.gz" 4) Tar file of all circular contigs from assemblies. This will include 47 separate fasta files (1 for each participant and time point). This data was used for the viral and plasmid analyses. "Hsap_circ_contigs_47_assemblies.tar.gz"5) File containing all of the 985 cMAGs with annotations generated using prokka "985cMAGs_prokkaannotation.tar.gz 6) Deep taxonomic profiling feature table: Pacbio samples (45) with features classified using the GTDB and 985 cMAGs custom database"PB_985cMAG-sourmash_45s_2162f" #feature table"mapping-file_PB45s_2162f_deID.txt" #mapping file, deidentified