1 Supporting Information 2 3 Mucosal microbiota differ according to presence/absence of cecal contents 4 Differences between the cecal mucosal communities in mice lacking or containing 5 luminal contents may reflect a lack of recent food intake and/or an influence of the 6 luminal contents on mice with recent food intake. Among the major phyla we found 7 significant differences in Bacteroidetes (mean for mice with contents 47.34%, without 8 contents 36.99%, ANOVA P = 0.0497). Among the genera with average abundances 9 >1%, we found significant differences in Bacteroides (with contents 34.79%, without 10 contents 22.6%, ANOVA P = 0.0228), Helicobacter (with contents 19.32%, without 11 contents 28.72%, ANOVA P = 0.0489), Alistipes (with contents average 1.06%, 12 without contents 3.10%, ANOVA P = 0.0072), and Dorea (with contents 0.95%, 13 without contents 1.95%, ANOVA P = 0.0023). Beta-diversity measures also display 14 significant differences, although only a small proportion of variation is explained 15 (Adonis for Bray-Curtis dissimilarities: r2 = 0.01326, P = 0.007, Jaccard: r2 =0.0111, 16 P = 0.004, weighted UniFrac: r2 = 0.02774, P = 0.024, unweighted UniFrac: r2 = 17 0.01151, P = 0.239; Fig. S2). 18 19 20 21 22 Fig. S1. NeighbourNet network of 121 mitochondrial D-loop sequences. The 23 network was generated using “SplitsTree” under the default settings. Colors indicate 24 the geographic sampling location. The numbering of the haplogroups (indicated by 25 grey ovals) corresponds to that of Bonhomme et al. (2011). 26 27 28 29 30 31 32 Fig S2. Constrained analysis of principle coordinates of Bray-Curtis distance 33 based on presence (with) or absence (without) of cecal contents. CAP1 is the axis 34 from the constrained analysis of principle coordinates (“capscale”, see Methods) and 35 MDS1 is the first axis of the unconstrained analysis. Each of the eight geographic 36 sampling locations is indicated by a unique color; abbreviations for the sampling 37 locations (e.g. “AN” for Angers) are given in Table 1. **Represents significance from 38 the “anova.cca” test with respect to presence/absence of cecum content as a 39 categorical variable with 1000 permutations (see Methods; P < 0.01). 40 41 42 43 Fig S3. (a) Chao1 index and (b) Shannon diversity measures based on genus level 44 composition in mucosa communities. Abbreviations are listed in Table 1 and 45 geographical locations can be found in Fig 1. 46 47 48 Fig S4. Constrained analysis of principle coordinates of Bray-Curtis dissimilarity 49 based on mucosa vs. content communities. CAP1 is the axis from the constrained 50 analysis of principle coordinates (“capscale”, see Methods) and MDS1 is the first axis 51 of the unconstrained analysis. Each of the eight geographic sampling locations is 52 indicated by a unique color; abbreviations for the sampling locations (e.g. “AN” for 53 Angers) are given in Table 1. **Represents significance from the “anova.cca” test 54 with respect to content/mucosa as a categorical variable with 1000 permutations (see 55 Methods; P < 0.01). 56 9 10 11 12 13 -1 -2 -3 14 7 8 Geographical distance (Ln transformed) 60 Between Sites -4 -3 -4 -5 8 Within Site -5 -1 Between Sites -2 Within Site 7 9 10 11 12 13 14 Geographical distance (Ln transformed) 8 9 10 11 12 13 14 -1 -2 Between Sites -3 -3 -4 -5 7 Within Site -4 Between Sites -2 Within Site -5 -1 Bacterial Community Similarity (Jaccard, Ln transformed) b. Bacterial Community Similarity (Bray-Curtis, Ln transformed) 61 Bacterial Community Similarity (Jaccard, Ln transformed) a. Bacterial Community Similarity (Bray-Curtis, Ln transformed) 57 58 59 7 Geographical distance (Ln transformed) 8 9 10 11 12 13 14 Geographical distance (Ln transformed) 62 63 64 Fig S5. Similarity-distance decay in bacterial communities in a) mucosa and b) 65 content. The red dashed lines denote regression based on the whole data set, green 66 solid lines denote regression at a local scale (within sampling locations/regions) and 67 blue 68 locations/regions). Details are provided in Table S6. 69 70 71 72 73 lines denote regression at a continental scale (between sampling