Supplementary Materials
Exposure to Formaldehyde Perturbs the Mouse Gut Microbiome Junhui Guo 1,2§,4, Yun Zhao 1, Xingpeng Jiang 3,2§, Rui Li 1,2§, Hao Xie 4, Leixin Ge 1, Bo Xie 1,2§, Xu Yang 1,* and Luoping Zhang 2,* 1
2
3 4
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California, USA School of Computer, Central China Normal University, Wuhan 430079, China School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
§: As a visiting scholar at UC Berkeley. * Correspondence: Luoping Zhang, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California, USA. E-mail:
[email protected], Tel.: +1 510 334 5959; and Xu Yang, School of Life Sciences, Central China Normal University, Wuhan 430079, China. E-mail:
[email protected], Tel.: +86 27 6786 6997.
Genes 2018, 9, 192; doi:10.3390/9040192
www.mdpi.com/journal/genes
Genes 2018, 9, 192
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Supplementary Materials: Figure S 1. 1200
OTUs
900
600 No additives 0.1 ng/ml MeOH 0.3 ng/ml MeOH 1.0 ng/ml FA 3.0 ng/ml FA
300
0
0
5000
10000
15000
20000
25000
30000
Sequences per sample
Figure S 1. The rarefaction curves for the FA or MeOH treated samples.
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Figure S 2. (B) 1500
50
1200
40
Phylogenetic Diversity
Chao1 Index
(A)
900
600
300
0
s OH OH A A ditive ng/ml Me ng/ml Me ng/ml F ng/ml F 1.0 3.0 0.1 0.3
No ad
30
20
10
0
s OH OH A A ditive ng/ml Me ng/ml Me ng/ml F ng/ml F 1.0 3.0 0.1 0.3
No ad
Figure S 2. The richness (Chao1 index) and phylogenetic diversity analysis of the FA or MeOH treated samples.
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Figure S 3.
(A)
(B)
f_S24-7
g_Coprococcus g_Desulfovibrio
o_Clostridiales
g_[Ruminococcus]
g_Bacteroides
f_F16
f_Lachnospiraceae
g_Adlercreutzia
f_Rikenellaceae
f_Desulfovibrionaceae g_Turicibacter
g_Lactobacillus
g_Clostridium
f_Ruminococcaceae
g_Anaerostipes
g_[Prevotella]
g_Dorea
g_Oscillospira
g_Dehalobacterium f_Erysipelotrichaceae
g_Ruminococcus g_Prevotella g_Parabacteroides 0.1
o_YS2
No additives 0.1 ng/ml MeOH 0.3 ng/ml MeOH 1.0 ng/ml FA 3.0 ng/ml FA
1
10
o_RF39 0.01
100
Relative Abundance (%)
(C)
No additives 0.1 ng/ml MeOH 0.3 ng/ml MeOH 1.0 ng/ml FA 3.0 ng/ml FA
g_Helicobacter
0.1
1
10
Relative Abundance (%)
(D)
g_Roseburia
o_Clostridiales
f_Clostridiaceae
g_Streptococcus
Unassigned
g_Achromobacter
f_[Mogibacteriaceae]
f_Gemellaceae
o_Bacteroidales
g_Coprobacillus
g_Candidatus Arthromitus
f_Caulobacteraceae
g_Mucispirillum f_Coriobacteriaceae
f_Peptococcaceae g_Serratia
g_Lactococcus g_Bacillus
f_Lachnospiraceae
g_Solibacillus
f_Prevotellaceae
f_Christensenellaceae
f_Enterobacteriaceae g_Anaeroplasma
g_Delftia 0.001
g_Microcystis
No additives 0.1 ng/ml MeOH 0.3 ng/ml MeOH 1.0 ng/ml FA 3.0 ng/ml FA
f_Desulfovibrionaceae
0.01
0.1
Relative Abundance (%)
No additives 0.1 ng/ml MeOH 0.3 ng/ml MeOH 1.0 ng/ml FA 3.0 ng/ml FA
f_Ruminococcaceae f_Bacillaceae
1
0.001
0.01
0.1
Relative Abundance (%)
Figure S 3. The relative abundance of bacterial community composition at the genus level. (A), dominant genera; (B), common genera; (C) and (D), rare genera.
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Figure S 4.
Figure S 4. Differential PICRUSt predicted KEGG pathways between untreated and MeOH treated mice detected by STAMP software [34]. (A) Differential KEGG pathways between untreated and the 0.3 ng/ml MeOH treated mice. (B) Differential KEGG pathways between untreated and the 0.1 ng/ml FA treated mice.
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Table S1: Summary of sequence data Num samples
21
Num observations
1197
Total count
699775
Table density (fraction of non-zero values)
0.723
Counts/sample summary Min
29276
Max
38178
Median
33092
Mean
33322.62
Std. dev.
2793.643
Sample Metadata Categories
None provided
Observation Metadata Categories
taxonomy
Counts/sample detail p3.24.Y3.3
29276
0.24.Y1.3
29438
p1.24.Y4.1
29650
p10.24.Y4.2
30338
p30.24.Y7.1
30450
p30.24.Y5.3
31165
0.24.Y6.3
31402
0.24.Y6.2
31409
p10.24.Y4.1
31947
0.24.Y6.1
31999
p1.24.Y2.1
33092
p1.24.Y2.3
33961
p30.24.Y7.2
34536
p30.24.Y5.2
34915
p30.24.Y7.3
35349
p3.24.Y3.2
35802
p1.24.Y2.2
35934
p3.24.Y3.1
36462
p30.24.Y5.1
36722
0.24.Y1.1
37750
0.24.Y1.2
38178
