Pi
c
Sp ov
ir
o
Au un ina
to av e
g i
N rap rina
4− h e
lik ivi
H e v rina
p1 ir e
u
93 T7− like se
6 lik vir s
la e us
ct v
G oco irus
ok c e
* M us cal s
ho ph
Ph u−li vir ag
i2 ke ina es
9 v e
T1 −lik iru
e s
Ph −lik vi es
iC e v r u s
D ir e s
Pe 119 use
d li s
P u ke
* L 2− ovi viru
am like rina s
b d vi e
a ru
PB −li se
ke s
I3 1lik vi
Ph −lik evir rus
iK e v us es
Z − ir u
li s
T ke es
SP ec vir
6− tivir use
lik us s
e
vi
ru
se
s
1
2
3
4
5
total log10 sum abundance per Gbp across the samples
Supplementary Figures
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Figure S1 – Total Sum Abundance of all Phage Taxa Across 252 Samples.
The asterix besides Mu-like and Lambda-like viruses indicates that their marker
genes do not detected all of the genomes in the genera (ie. recall < 85%) and thus
do not accurately reflect the abundance of those taxa.
4−
lik
Pi e v
co iru
H viri ses
p1 n
93 Sp like ae
6 ou vi
la n a r u
c
s
Ph toc viri
i2 oc na
* M 9−li cal e
u− ke pha
l vi g
Pe ike rus es
Au du viru es
to ov s
Ph gra irin es
iC ph ae
D
G 1 1 ivir i
ok 9 na
l
T7 ush ikev e
−l ov iru
P2 ike irin s
−l vir ae
I3 ike use
Ph −lik viru s
e
* L iKZ vi ses
−
am li rus
b ke es
SP da− vir
6− lik use
T1 like e v s
−l v irus
ik ir
e
PB e v use s
1l irus s
i
Te kev es
c t ir u
iv s
ir u
s
N
0
20
40
60
80
Percentage of Samples Taxa is Present In
100
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ubiquitous
taxa
●
moderately
prevalent
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rare taxa
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●
Figure S2 – Prevalence of all Phage taxa in the 252 Samples.
The asterix besides Mu-like and Lambda-like viruses indicates that their marker
genes do not detected all of the genomes in the genera (ie. recall < 85%) and thus
do not accurately reflect the abundance of those taxa.
8
6
4
2
Number of Non−overlaping Phage taxa
Denmark
Spain
USA
Figure S3 – Number of Non-overlapping Phage Taxa Per Sample, Grouped
by Country of Residence of the Subject. Subfamilies with representative
genera were not included in this analysis. For example, Autographivirinae was
not included as a taxon, as it is represented by the T7-like and SP6-like genera.
Pi
N cov
4 − ir
l in
Sp ike ae
o u vir
u
H nav se
p 1 ir s
Pe like inae
v
G d u o ir u
ok v s
i
Au us rin
to ho a e
Ph gr vir
iK aph ina
Z iv e
I3 −lik irin
− e a
S lik v e
93 P6 e v irus
6 −li iru es
la ke se
ct
o v s
T1 co irus
c
−
Ph lik cal es
i2 e v ph
* 9−l iru ag
* L Mu ike ses es
a m − lik vir
bd e v use
P2 a− iru s
l s
Ph −lik ike es
e
iC v vir
D ir u s
1 u
PB 19 se es
li s
T7 1lik kev
e
−l v iru
ik iru s
e
Te vir s
ct us
iv es
iru
s
−3
−2
−1
0
1
median log10 abundance per Gbp in each sample
2
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Figure S4 – Median Abundance Per Sample for of all Phage Taxa detected.
The asterix besides Mu-like and Lambda-like viruses indicates that their marker
genes do not detected all of the genomes in the genera (ie. recall < 85%) and thus
do not accurately reflect the abundance of those taxa.
●
●
●
0.0
1
●
0.5
●
●
−0.5
−1.5
−1.0
log10abundance per Gbp
−2.0
0
−1
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5
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●
10
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●
−3.0
−3
−2.5
−2
log10abundance per Gbp
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15
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5
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●
10
phage taxa
2
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15
phage taxa
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0
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●
−3
−2
−1
−1
0
log10abundance per Gbp
●
−2
log10abundance per Gbp
1
1
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●
−3
●
5
10
phage taxa
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●
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●
●
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●
15
5
10
15
phage taxa
Figure S5 – Example Rank Abundance Curves for 4 random samples.
On the y-axis is the log10 abundance of the taxon and the x-axis indicates the
rank of the taxon. These are for non-overlapping taxa as explained above.
number of scaftig prophage regions
2500
2400
2300
2200
2100
2000
1900
1800
1700
1600
1500
1400
1300
1200
1100
1000
900
800
700
600
500
400
300
200
100
0
●
present
PtoH>5
PtoH>10
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●
1
2
5
25
50
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●
75
100
125
150
175
200
225
252
number of samples
Figure S6 – Number of Scaftig-predicted prophages identified.
The -axis indicates the number of predicted prophages detected, and the x-axis
indicates the number of samples the prophage was detected in. The orange and
red points indicates prophages that were deemed to be active based on their
PtoH ratio.
●
present
PtoH>5
PtoH>10
450
400
number of refGenome prophage regions
●
350
300
250
●
●
●
●
●
200
●
150
●
●
●
●
100
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●
●
50
●
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●
●
●
●
●
0
1
2
5
25
50
75
100
125
150
175
200
225
252
number of samples the reference genome prophage is present in
Figure S7 - Number of refG-predicted prophages identified.
The Y-axis indicates the number of predicted prophages detected, and the x-axis
indicates the number of samples the prophage was detected in. The orange and
red points indicates prophages that were deemed to be active based on their
PtoH ratio.