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Supporting Information
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Mucosal microbiota differ according to presence/absence of cecal contents
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Differences between the cecal mucosal communities in mice lacking or containing
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luminal contents may reflect a lack of recent food intake and/or an influence of the
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luminal contents on mice with recent food intake. Among the major phyla we found
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significant differences in Bacteroidetes (mean for mice with contents 47.34%, without
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contents 36.99%, ANOVA P = 0.0497). Among the genera with average abundances
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>1%, we found significant differences in Bacteroides (with contents 34.79%, without
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contents 22.6%, ANOVA P = 0.0228), Helicobacter (with contents 19.32%, without
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contents 28.72%, ANOVA P = 0.0489), Alistipes (with contents average 1.06%,
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without contents 3.10%, ANOVA P = 0.0072), and Dorea (with contents 0.95%,
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without contents 1.95%, ANOVA P = 0.0023). Beta-diversity measures also display
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significant differences, although only a small proportion of variation is explained
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(Adonis for Bray-Curtis dissimilarities: r2 = 0.01326, P = 0.007, Jaccard: r2 =0.0111,
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P = 0.004, weighted UniFrac: r2 = 0.02774, P = 0.024, unweighted UniFrac: r2 =
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0.01151, P = 0.239; Fig. S2).
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Fig. S1. NeighbourNet network of 121 mitochondrial D-loop sequences. The
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network was generated using “SplitsTree” under the default settings. Colors indicate
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the geographic sampling location. The numbering of the haplogroups (indicated by
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grey ovals) corresponds to that of Bonhomme et al. (2011).
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Fig S2. Constrained analysis of principle coordinates of Bray-Curtis distance
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based on presence (with) or absence (without) of cecal contents. CAP1 is the axis
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from the constrained analysis of principle coordinates (“capscale”, see Methods) and
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MDS1 is the first axis of the unconstrained analysis. Each of the eight geographic
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sampling locations is indicated by a unique color; abbreviations for the sampling
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locations (e.g. “AN” for Angers) are given in Table 1. **Represents significance from
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the “anova.cca” test with respect to presence/absence of cecum content as a
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categorical variable with 1000 permutations (see Methods; P < 0.01).
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Fig S3. (a) Chao1 index and (b) Shannon diversity measures based on genus level
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composition in mucosa communities. Abbreviations are listed in Table 1 and
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geographical locations can be found in Fig 1.
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Fig S4. Constrained analysis of principle coordinates of Bray-Curtis dissimilarity
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based on mucosa vs. content communities. CAP1 is the axis from the constrained
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analysis of principle coordinates (“capscale”, see Methods) and MDS1 is the first axis
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of the unconstrained analysis. Each of the eight geographic sampling locations is
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indicated by a unique color; abbreviations for the sampling locations (e.g. “AN” for
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Angers) are given in Table 1. **Represents significance from the “anova.cca” test
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with respect to content/mucosa as a categorical variable with 1000 permutations (see
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Methods; P < 0.01).
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Geographical distance (Ln transformed)
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Between Sites
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Within Site
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-1
Between Sites
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Within Site
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Geographical distance (Ln transformed)
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Between Sites
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Within Site
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Between Sites
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Within Site
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Bacterial Community Similarity (Jaccard, Ln transformed)
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Bacterial Community Similarity (Bray-Curtis, Ln transformed)
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Bacterial Community Similarity (Jaccard, Ln transformed)
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Bacterial Community Similarity (Bray-Curtis, Ln transformed)
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Geographical distance (Ln transformed)
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Geographical distance (Ln transformed)
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Fig S5. Similarity-distance decay in bacterial communities in a) mucosa and b)
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content. The red dashed lines denote regression based on the whole data set, green
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solid lines denote regression at a local scale (within sampling locations/regions) and
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blue
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locations/regions). Details are provided in Table S6.
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lines
denote
regression
at
a
continental
scale
(between
sampling