Functional divergence in gastrointestinal microbiota in physically-separated
genetically identical mice
Authors: G. B. Rogers1,2*, J. Kozlowska2 J. Keeble2, K. Metcalfe3, M. Fao3, S. E. Dowd4, A. J.
Mason2, M. A. McGuckin1, K. D. Bruce2
1 Immunity,
Infection, and Inflammation Program, Mater Research Institute – University of
Queensland, Translational Research Institute, Woolloongabba, Australia.
2 King's
College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
3Charles
River UK, Manston Rd. Margate, Kent CT9 4LT UK
4 Molecular
Research MR DNA, Shallowater, TX 79363, USA
Supplementary information
Supplementary information
Chao1
Sample
Mean
Room 1
257.84
Std.
deviation
27.03
Room 2
282.94
58.7
B
Room 3
311.44
88.59
B
Room 4
168.43
18.52
A
significance
B
OTU richness
Sample
Mean
Room 1
354.80
Std.
deviation
17.00
Room 2
421.40
151.13
B
Room 3
706.40
342.38
B
Room 4
208.00
23.67
A
significance
B
Shannon index
Room 1
7.74
Std.
deviation
2.23
Room 2
10.23
1.71
B
Room 3
9.10
1.22
B
Room 4
4.45
0.38
A
Sample
Mean
significance
B
Supplementary Table 1. Bacterial alpha diversity assessed using the Chao1 richness estimate, OTU
richness, and Shannon Index, with Kruskall-Wallis test of K samples with a controlled multiple pairwise comparison. Significant differences in measures are indicated using standard notation; samples
that share a letter are not significantly different, while samples that do not share a letter are
significantly different. In this table, we see room 4 is significantly different than rooms 1, 2 and 3 for all
measures (p<0.001).
Phylum
Genus
Bacteroidetes
Firmicutes
Bacteroidetes
Bacteroidetes
Firmicutes
Firmicutes
Bacteroidetes
Bacteroidetes
Firmicutes
Firmicutes
Bacteroidetes
Firmicutes
Firmicutes
Proteobacteria
Bacteroidetes
Proteobacteria
Proteobacteria
Proteobacteria
Firmicutes
Firmicutes
Prevotella
Coprococcus
Bacteroides
Parabacteroides
Lactobacillus
Oscillospira
Alistipes
Tannerella
Clostridium
Roseburia
Pedobacter
Ruminococcus
Blautia
Sutterella
Sphingobacterium
Rhodospirillum
Novispirillum
Nautilia
Butyrivibrio
Eubacterium
Mean abundance (percentage)
38.96
16.37
7.07
6.39
4.38
3.82
3.55
3.54
3.47
1.91
1.86
1.52
1.41
0.72
0.63
0.50
0.50
0.45
0.34
0.27
Supplementary Table 2. The 20 genera identified with the highest mean abundance in the faecal
samples studied.
Group
Prevotella
Group
Pedobacter
Group
Alistipes
Group
Novispirillum
1
16.013
A
1
0.905
A
1
5.032
B
1
0
2
32.46
AB
2
4.513
B
2
4.949
B
2
0.409
A
3
43.529
B
3
2.009
A
3
3.696
AB
3
1.595
B
63.838
C
0
A
0.539
A
0
A
4
Group
Coprococcus
4
Group
Ruminococcus
4
Group
Tannerella
4
Group
A
Eubacterium
1
41.323
B
1
3.501
B
1
1.788
A
1
0.188
AB
2
11.891
A
2
0.779
A
2
5.674
C
2
0.092
A
3
7.908
A
3
1.191
AB
3
4.485
BC
3
0.03
A
4.37
A
0.616
A
2.203
AB
0.78
B
4
Group
Bacteroides
4
Group
Sutterella
4
Group
Clostridium
4
Group
Porphyromonas
1
5.575
AB
1
0
A
1
5.655
B
1
0.177
2
11.537
C
2
1.826
B
2
2.196
A
2
0.547
B
3
9.835
BC
3
1.074
AB
3
1.923
A
3
0.331
AB
4
1.324
A
4
0
A
4
4.124
AB
4
0
Group
Parabacteroides
Group
Sphingobacterium
Group
Roseburia
Group
AB
A
Anaerotruncus
1
3.359
A
1
0.243
A
1
4.16
B
1
0.297
B
2
11.02
B
2
1.032
B
2
0.803
A
2
0.035
A
3
8.179
B
3
1.249
B
3
0.688
A
3
0.069
A
4
2.988
A
4
0
A
4
1.973
AB
4
0.067
A
Supplementary Table 3. Controlled ANOVA tests identified genera whose relative abundance
differed significantly between room groups (cont p < 0.05). Based upon controlled ANOVA using least
square means this table lists significantly different genera between groups (p < 0.05). The LS mean
for each genera and group is provided. Group indicates which room group. Each genus with
significant differences is indicated along with their LS mean and their relative significance. Groups
which share a letter are not significantly different from each other while groups which do not share a
letter (A, B, C) are significantly different (thus, a group which has A is significantly different from a
group which only has letter B, while a group with letter A is not significantly different from a group
which has AB).
Supplementary Figure 1. Variation in microbiota phyla