Extended Data Fig. 3: Bacterial DNA is found in the thymus after early-life colonization.
a, b, h–j, Mice were colonized with SFB or E. coli at weaning (young) or at 12 weeks of age (adult) and one week later were compared to age-matched control mice. a, b, SFB-specific qPCR in faecal pellets (FP) (a; young: CTRL, SFB n = 8; adult: CTRL, SFB n = 6); and MLNs (b; young: CTRL, SFB n = 9; adult: CTRL, SFB n = 7). h–j, E. coli-specific qPCR in the thymus (h; young: CTRL n = 10, EC n = 15; adult: CTRL, EC n = 15), MLNs (i; young: CTRL, EC n = 8; adult: CTRL, EC n = 7) and faecal pellets (j; young: CTRL, EC n = 8; adult: CTRL, EC n = 10). Mice were colonized with SFB at weaning and compared one week later to age-matched control mice. c, e, SFB-specific qPCR (c; n = 6 per group) and 16S qPCR (e) in the thymus, MLNs, liver, spleen, heart and lungs (in e, thymus, MLNs: CTRL, SFB n = 12; liver, SPL, heart, lungs: CTRL, SFB n = 6). d, g, Mice were colonized with SFB at weaning and analysed up to three weeks later. SFB-specific PCR (d) and 16S qPCR (g) in the thymus, MLNs and faecal pellets (n = 5 per group). f, Mice were colonized with SFB at 12 weeks of age and compared one week later to age-matched control mice. 16S qPCR in thymus and MLNs (thymus: CTRL n = 16, SFB n = 11; MLNs CTRL, SFB n = 7). k, Mice were euthanized at 4 weeks of age, tissues were collected, DNA was isolated and 16S rDNA sequencing was performed. Bacterial phyla and class relative abundance in the thymus, MLNs and caecum (n = 5 per group; thymus and MLNs were pooled). l–n, Mice were treated with antibiotics at weaning and compared one week later to age-matched control mice. 16S qPCR in the thymus (l; n = 7 (CTRL), n = 8 (ABX)); MLNs (m; n = 16 (CTRL), n = 9 (ABX)) and faecal pellets (n; n = 10 per group). Each replicate is a biologically independent sample. Data are shown as mean ± s.e.m. (d, g) or as individual values and mean; P values by two-tailed unpaired t-test (l–n) or two-way ANOVA with Tukey’s (a, b, f, h–j), Sidak’s (c, e) or Fisher’s LSD (e) post hoc test.
