Fig. 1

SFB abundance correlates with ileitis severity in SPF-house Tnf ^ΔARE mice. A Ileitis scores of SPF-housed Tnf ^ΔARE mice at the age of 3–4, 8, 12, and 18 weeks of age. Color-code represents severity of inflammation as described above. Cecal content of SPF-housed WT mice with undetectable SFB counts was introduced into germ-free Tnf ^ΔARE mice and littermate WT controls. B Quantitative analysis of SFB abundance in Tnf ^ΔARE and matching WT mice overtime. CT value > 30 is regarded as non-specificity threshold. C Representative H&E-stained tissue sections from distal ileum, caecum, and proximal colon of Tnf ^ΔARE mice showing no (NR), low (LR), and high grade (R) of inflammation in the ileum as described above. D Analysis of bacterial localization in distal ileum of inflamed (R) and non-inflamed (NR) Tnf ^ΔARE mice from F1 generation by performing FISH staining with eubacterial 16S probe (red) and DAPI for nuclear visualization. E Quantitative analysis of Tnf and Il-17A mRNA expression in distal ileum of non-inflamed (NR) and inflamed (R Tnf ^ΔARE mice and WT controls. F Correlation analysis between Ileitis score and SFB abundance in intestinal contents and fecal pellets in the full cohort of 18-week-old Tnf ^ΔARE mice and G in 12 10-week-old (mild ileitis) and 12 > 24-week-old (severe ileitis) SAMP1/YitFc mice, respectively. We replaced all data points below the detection limit (threshold of Ct > 30) by a fixed minimal value Ct = 30 in (F, G). This illustrates the dataset more clearly than excluding the values under the detection limit completely from the analysis. Statistical significance was assessed by One-way-ANOVA followed by Tukey multiple comparison test. *p < 0.05; **p < 0.01; ***p < 0.001 was considered statistically significant