Supplemental Figure 1 : Box and Whiskers plot of the median lengths of viral contigs assembled in each subject and time point. The gray boxes represent the third quartile, the black boxes represent the first quartile, and the second quartile (median) is represented at the intersection of the gray and black boxes. The error bars represent the minimum and maximum of all data points. The median length is demonstrated on the Y-axis, and each
Subject#1-8 is demonstrated on the X-axis. The time points from Day 1 AM to Day 60
AM left to right are represented by each consecutive bar for all subjects.
Supplemental Figure 2 : Box and Whiskers plot of the median GC content for viral contigs assembled in each subject and time point. The gray boxes represent the third quartile, the black boxes represent the first quartile, and the second quartile (median) is represented at the intersection of the gray and black boxes. The error bars represent the minimum and maximum of all data points. The median GC content is demonstrated on the
Y-axis, and each Subject#1-8 is demonstrated on the X-axis. The time points from Day 1
AM to Day 60 AM left to right are represented by each consecutive bar for all subjects.
Supplemental Figure 3 : Plots of percentage of contigs in each subject with viral homologues in the NCBI database. The percentage of significant homologues is demonstrated on the Y-axis, and each Subject#1-8 is demonstrated on the X-axis. The time points from Day 1 AM to Day 60 AM left to right are represented by consecutive colored bars for all subjects.

Supplemental Figure 4 : Plots of percentage of contigs in each subject that have multiple viral homologues along their lengths. The percentage of contigs with multiple homologues is demonstrated on the Y-axis, and each Subject#1-8 is demonstrated on the X-axis. The time points from Day 1 AM to Day 60 AM left to right are represented by consecutive colored bars for all subjects.
Supplemental Figure 5 : Plots demonstrating the breakdown of phage genes identified in contigs from Subject#1 Day 1 AM (Panel A), Subject #1 Day 1 PM (Panel B), and Subject
#1 Day 7 AM (Panel C). Each column represents an individual contig identified with homologous sequences to viruses in the NCBI non-redundant database. Red denotes sequences homologous to structural components of bacteriophage, purple represents virulence-associated phage genes, and yellow denotes replication machinery and transposases. The number of contigs studied in each subject and time point is demonstrated above each panel.
Supplemental Figure 6 : Bar plots demonstrating the percentage of beta lactamase homologues that were homologous to plasmid beta lactamases (Panel A) or TEM beta lactamases (Panel B).
Supplemental Figure 7 : Bar graph demonstrating the percentage of contigs (± standard error) generated from different time points across all subjects. Significance testing was determined by two-tailed t-test.

Supplemental Figure 8
: Bar graphs (± standard error) demonstrating the relative contribution of each time point to contigs formed from all 11 time points (Panel B).
Subjects#1-8 are shown consecutively in Panels A-H.
Supplemental Figure 9 : Heatmap demonstrating the recruitment of all reads to globally assembled contigs constructed from the reads of every subject and time point. Each column represents an individual time point for each subject from Day 1AM to Day 60AM left to right. Each row represents a globally assembled contig. The ‘matrix-like’ appearance of the heatmap is due to the relatively high number of reads from individual subjects across time that were used in the construction of the contigs.
Supplemental Figure 10 : Rarefaction analysis based on chao1 estimates of bacterial
OTUs present for each subject at all time points. Panel A – Subject #1, Panel B – Subject
#2, Panel C – Subject #3, Panel D – Subject #4, Panel E – Subject #5, Panel F – Subject
#6, Panel G – Subject #7, and Panel H – Subject #8.
Supplemental Figure 11 : Bar plots of bacterial taxonomy based on 16S rRNA at the
Phylum level. The percentage of OTUs identified belonging to the observed phyla is demonstrated on the Y-axis and each subject and consecutive time point from Day 1 AM to Day 60 AM left to right is demonstrated on the X-axis.
Supplemental Figure 12 : Heatmap of taxonomic assignments for bacterial OTUs based on 16S rRNA sequences. The heatmap is organized by subject and time point, where the

subject# is denoted along each axis, and the individual time points are denoted by each column consecutively from Day 1 AM to Day 60AM left to right for each subject. Each row represents an individual taxonomic assignment.
Supplemental Table 1 : Virome reads from all subjects.
Supplemental Table 2 : Recruitment of reads to contigs within and between subjects and sexes.
Supplemental Table 3 : 16S rRNA reads from all subjects.
Supplemental Table 4 : Shared 16S rRNA OTUs between subjects and sexes.
Supplemental Table 5 : Primer sequences used in this study.