Erik Larsson, Valentina Tremaroli, Ying Shiuan Lee, Omry Koren, Intawat Nookaew,. Ashwana Fricker, Jens Nielsen, Ruth E. Ley, Fredrik Bäckhed. Contents:.
Supplementary material to:
Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88
Erik Larsson, Valentina Tremaroli, Ying Shiuan Lee, Omry Koren, Intawat Nookaew, Ashwana Fricker, Jens Nielsen, Ruth E. Ley, Fredrik Bäckhed
Contents: Figures S1-6 Tables S1,4,5
Figure S1
10 0
CXCL10
B
*
15 10 5 0
1.5
SPRR1a
Relative expression
20
*
20
1.0 0.5 0
6 4 2 0
4
MUC2
*
3 2 1 0
Colon 1.5 1.0 0.5 0
CXCL10
Relative expression
8
Relative expression
Relative expression
Colon CCL5
8 6 4 2 0
SPRR1a
*
Relative expression
CCL5
GF CONV-R
Ileum Relative expression
30
Relative expression
A
Relative expression
Ileum
2.0 1.5
MUC2
*
1.0 0.5 0
Figure S1. qRT-PCR analysis of (A) chemokines and (B) genes involved in mucosa fortification in epithelial cells isolated from the ileum and colon of GF and CONV-R mice. n = 4 mice/group. * P < 0.05; Mann Whitney U-test.
C
O N
R
V-
G F
5
OAS1a
4
***
3
2
1
0
N VM R yd 88 M yd -/88 G -/F C O N VR
0
N VM R yd 88 M yd -/88 G -/F C O N VR
*
O
1
C
O
G
F N VM R yd 88 M yd -/88 G -/F C O N VR
W T
30
O
2
F
3
G
IRF9
C
***
W T
4
F
IRF7
relative expression
0
relative expression
***
W T
***
W T
O N
G F
VM R yd 88 M yd -/88 G -/F C O N VR
C
4
10
relative expression
V-
R yd 88 M yd -/88 G -/F C O N VR
M
O N
W T
relative expression
***
G
0 6
15
C
2
W T
CCL5
W T
4 8
W T
6
R yd 88 M yd -/88 G -/ F C O N VR
***
M
IFIT2
V-
8
O N
0
G F
2 2
C
4
W T
***
G F
6
relative expression
F
0
W T
O
G
N VM R yd 88 M yd -/88 G -/F C O N VR
C
relative expression 5
C
R
V-
W T
W T
***
W T
O N
G F
relative expression 10
relative expression
C
yd 88 yd -/88 G -/F C O N VR
M
M
W T
W T
RSAD2
W T
relative expression 15
yd 88 yd -/ 88 G -/F C O N VR
M
M
W T
W T
Figure S2
CXCL10
IFI44
15
OASL2
***
10 5
0
*
***
20
10 0
***
5
0
Figure S2. qRT-PCR validation of antiviral gene expression in the proximal colon of CONV-R wildtype and Myd88-/- mice. n = 4-6/group. * P < 0.05; *** P < 0.0001; ANOVA.
Figure S3
2 1
2 0
T W
yd 8
M
M
OASL2
yd 8 M
5 0
8/-
W
10
yd 8
8/-
0
*
15
T
5
20
W
10
Relative expression
*
15
T
Relative expression
IFIT2
M
W
4
8/-
0
6
8/-
3
*
8
yd 8
*
4
Relative expression
CXCL10
5
T
Relative expression
IRF7
Figure S3. qPCR analysis of antiviral gene expression in epithelial cells isolated from the colon of CONV-R wildtype and Myd88-/- mice. n = 4/group. * P < 0.05; Mann-Whitney U-test.
Figure S4
6 4 2 0
REG3γ
*
10 5 0
B
2.0
NOX1
1.5 1.0 0.5 0
10 5 0
*
50 40 30 20 10 0
REG3γ
*
Relative expression
15
Relative expression
Relative expression
20
REG3β
40
NOS2
*
30 20 10 0
Colon
Colon 25
Relative expression
*
8
15
2.5 2.0 1.5 1.0 0.5 0
NOX1
Relative expression
REG3β
Relative expression
10
Relative expression
Relative expression
A
GF CONV-R
Ileum
Ileum
80 60
NOS2
*
40 20 0
Figure S4. qRT-PCR analysis of antimicrobial genes in epithelial cells isolated from ileum and colon of GF and CONV-R mice. n = 4 mice/group. * P < 0.05; Mann Whitney U-test.
Figure S5. Relative abundance of the different phyla in individual mice (Myd88 +/+ or -/-) along the length of the gut.
Figure S6
0.7
Myd88+/+
UniFrac difference (average)
0.6
Myd88-/-
0.5 0.4 0.3 0.2 0.1 0
Duodenum
Jejunum
Ileum
Cecum & colon
Figure S6. Mean unweighted UniFrac distances derived from the different sections of the gut. P-values were corrected for multiple comparisons using the Bonferroni correction; *** p
