Table 2

Similarity of percentages (SIMPER) analysis of microbial community dissimilarity (Bray–Curtis) between core species groups for (A) CD and siblings, (B) healthy controls and siblings and (C) CD and healthy cohorts

A
NameMean abundance in the CD cohortMean abundance in the siblings cohort% ContributionCumulative %
Faecalibacterium prausnitzii22.424.220.720.7
Escherichia fergusonii21.49.715.936.6
Shigella flexneri13.67.210.747.3
Ruminococcus gnavus13.15.28.956.2
Bacteroides vulgatus13.27.67.864.0
Eubacterium rectale9.86.46.670.6
Oscillospira guilliermondii08.05.976.5
Escherichia coli6.504.581.0
Sutterella wadsworthensis06.04.585.5
Bacteroides dorei05.74.289.6
Roseburia faecis04.02.992.6
B
NameMean abundance in the healthy cohortMean abundance in the siblings cohort% ContributionCumulative %
Faecalibacterium prausnitzii30.924.218.918.9
Escherichia fergusonii4.19.710.629.5
Sutterella wadsworthensis8.76.09.438.9
Shigella flexneri3.67.28.447.3
Bacteroides vulgatus8.07.68.455.7
Eubacterium rectale9.96.47.062.8
Oscillospira guilliermondii8.58.07.069.8
Bacteroides dorei05.75.475.2
Ruminococcus gnavus4.15.24.179.3
Bacteroides uniformis2.92.03.182.4
Roseburia faecis2.44.03.085.4
Coprococcus eutactus2.302.287.7
Shigella dysenteriae2.102.189.8
Blautia producta2.01.81.891.6
C
NameMean abundance in the CD cohortMean abundance in the healthy cohort% ContributionCumulative %
Faecalibacterium prausnitzii22.430.922.422.4
Escherichia fergusonii21.44.114.436.7
Shigella flexneri13.63.69.346.0
Ruminococcus gnavus13.14.18.654.6
Bacteroides vulgatus13.28.08.062.7
Eubacterium rectale9.89.97.470.1
Sutterella wadsworthensis08.76.476.5
Oscillospira guilliermondii08.56.282.8
Escherichia coli6.504.487.2
Bacteroides uniformis02.92.189.3
Roseburia faecis02.41.891.1
  • Given is mean per cent abundance of sequences for core species only across the samples each was observed to occupy and the average dissimilarity between samples (overall mean (A)=73.4% and (B)=55.0%, (C)=73.0%). Percentage contribution is the mean contribution divided by mean dissimilarity across samples. The list of species is not exhaustive, so cumulative per cent value does not sum to 100%. Species level identities of detected taxa are reported here. However, given the length of the ribosomal sequences analysed, these identities should be considered putative.

  • CD, Crohn's disease.