Figure S1. Changes in body weights of mice over six-week study calculated as increase
or decrease in body weight as a percentage of initial body weight at Day 0. Data are
shown as mean ± S.E.M. Two-way ANOVA was performed on percent changes in
weight between groups on each day; for all comparisons p > 0.05. Two-way ANOVA
was performed within groups comparing percent changes on different days. For baseline
LF mice, * = P < 0.05; for baseline MF mice, + = P < 0.05.
Figure S2. Relative abundance plots of phylum-level taxonomic classification from 16S
rRNA gene amplicon analysis. Standardized mean relative abundances of phyla
distribution from samples within each treatment group from the indicated day are shown.
1
A
B
Figure S3. Analysis of bacterial community structure through 16S rRNA amplicon
analysis. Mean relative abundances of order level taxa in fecal bacterial communities
present at > 1% in A) baseline LF and B) baseline MF mice. Data are shown as mean ±
S.E.M.
2
Figure S4. Distances of bacterial communities from baseline communities (based on the
third principle coordinate axis of Bray-Curtis PCOA plot in Fig. 3F). Mean pairwise
distances ± S.E.M of baseline LF and baseline MF communities of individual mice
between each time point and Day 0. The asterisk represents significant differences at each
time point relative to Day 0 (P-value: * < 0.05, Two-way ANOVA, Bonferroni correction
for multiple comparisons).
3
Figure S5. NMDS of Bray-Curtis distances of sequence abundances in BAC, IND, and
VLP metagenomes (NMDS Stress 0.1380967). Sample colors represent fraction of
origin, and sample shapes represent different treatment groups.
4
Figure S6. Similarity hierarchical clustering (Bray-Curtis distances of relative
abundances) of contigs that changed significantly over the experiment. These contigs
shared sequence similarity to known proteins associated with phage, prophages,
transposable elements, and plasmids.
5
Baseline MF IND Assembled Contig ID
282627_15745_VLP
1568425_102182_IND
3398_3397_VLP
189_188_IND
1395_1394_VLP
11392_11391_IND
278888_15308_VLP
268318_14671_VLP
11577_11576_IND
279518_15392_VLP
1460_1459_VLP
9169_9168_IND
6233_6232_IND
8182_8181_IND
11573_11572_IND
81561_11054_VLP
2281_2280_VLP
11500_11499_IND
1541036_99683_IND
1301_1300_VLP
345_344_IND
3314_3313_VLP
47_46_IND
11895_11894_IND
485381_86166_IND
2052_2051_IND
9619_9618_IND
8233_8232_IND
1546282_100483_IND
11070_5415_VLP
1168485_95035_IND
11495_11494_IND
-log2(Abundance)
20
15
10
5
0
1
22
43
Experimental Day
Figure S7. Estimated abundances of contigs that were present in baseline MF IND
samples (averaged for all replicate samples). Group I and Group II clustered contigs are
shown in red and blue, respectively.
6
Baseline MF VLP Assembled Contig ID
282627_15745_VLP
1568425_102182_IND
3398_3397_VLP
189_188_IND
1395_1394_VLP
11392_11391_IND
278888_15308_VLP
268318_14671_VLP
11577_11576_IND
279518_15392_VLP
1460_1459_VLP
9169_9168_IND
6233_6232_IND
8182_8181_IND
11573_11572_IND
81561_11054_VLP
2281_2280_VLP
11500_11499_IND
1541036_99683_IND
1301_1300_VLP
345_344_IND
3314_3313_VLP
47_46_IND
11895_11894_IND
485381_86166_IND
2052_2051_IND
9619_9618_IND
8233_8232_IND
1546282_100483_IND
11070_5415_VLP
1168485_95035_IND
11495_11494_IND
-log2(Abundance)
20
15
10
0
1
22
43
Experimental Day
Figure S8. Estimated abundances of contigs that were present in baseline MF VLP
samples (averaged for all replicate samples). Group I and Group II clustered contigs are
shown in red and blue, respectively.
7
Baseline LF IND Assembled Contig ID
282627_15745_VLP
1568425_102182_IND
3398_3397_VLP
189_188_IND
1395_1394_VLP
11392_11391_IND
278888_15308_VLP
268318_14671_VLP
11577_11576_IND
279518_15392_VLP
1460_1459_VLP
9169_9168_IND
6233_6232_IND
8182_8181_IND
11573_11572_IND
81561_11054_VLP
2281_2280_VLP
11500_11499_IND
1541036_99683_IND
1301_1300_VLP
345_344_IND
3314_3313_VLP
47_46_IND
11895_11894_IND
485381_86166_IND
2052_2051_IND
9619_9618_IND
8233_8232_IND
1546282_100483_IND
11070_5415_VLP
1168485_95035_IND
11495_11494_IND
-log2(Abundance)
20
15
10
0
1
22
43
Experimental Day
Figure S9. Estimated abundances of contigs that were present in baseline LF IND
samples (averaged for all replicate samples). Group I and Group II clustered contigs are
shown in red and blue, respectively.
8
Baseline LF VLP Assembled Contig ID
282627_15745_VLP
1568425_102182_IND
3398_3397_VLP
189_188_IND
1395_1394_VLP
11392_11391_IND
278888_15308_VLP
268318_14671_VLP
11577_11576_IND
279518_15392_VLP
1460_1459_VLP
9169_9168_IND
6233_6232_IND
8182_8181_IND
11573_11572_IND
81561_11054_VLP
2281_2280_VLP
11500_11499_IND
1541036_99683_IND
1301_1300_VLP
345_344_IND
3314_3313_VLP
47_46_IND
11895_11894_IND
485381_86166_IND
2052_2051_IND
9619_9618_IND
8233_8232_IND
1546282_100483_IND
11070_5415_VLP
1168485_95035_IND
11495_11494_IND
-log2(Abundance)
20
15
10
0
1
22
43
Experimental Day
Figure S10. Estimated abundances of contigs that were present in baseline LF VLP
samples (averaged for all replicate samples). Group I and Group II clustered contigs are
shown in red and blue, respectively.
9