Figure 1.
Vancomycin administration results in tuft cell hyperplasia and increased IL-25 concentrations in the proximal colon and leads to the enrichment of B. thetaiotaomicron in the microbiome. (A) Following the approach from Buonomo et al. (2016) IL-25 was measured by ELISA in the proximal colon of C57BL/6 WT mice treated with various antibiotics via oral gavage. Protein concentration in the lysate (pg/ml) was normalized by total protein in the sample (in mg) as in Buonuomo et al. (2016). Data are representative of independent experiments repeated twice, using n = 4–6 female mice per treatment group. ANOVA with Tukey post-hoc test was run to determine significant differences. Statistical significance was estimated at FDR of 0.05. (B) IL-25 mRNA expression was measured by RT-qPCR in the proximal colon of C57BL/6 WT mice treated with different antibiotics. Data are representative of independent experiments repeated twice using n = 4–6 female mice per treatment group. ANOVA with Tukey post-hoc test was run to determine significant differences. Statistical significance was estimated at an FDR of 0.05. (C) TC percentages were estimated by quantifying the percentage of DCLK1+ EPCAM+ cells compared with total cells in C57BL/6 WT mice treated with various antibiotics or untreated. Data are representative of independent experiments repeated twice, using n = 4–6 female mice per treatment group. ANOVA with Tukey post-hoc test was run to determine significant differences. Statistical significance was estimated at FDR of 0.05. (D) TC hyperplasia was confirmed via IHC by enumerating the number of DCLK1-expressing cells in the field of view (FOV). The white bar indicates a scale of 100 μm. Data are representative of independent experiments repeated twice, using n = 4–6 female mice per treatment group. ANOVA with Tukey post-hoc test was run to determine significant differences. Statistical significance was estimated at an FDR of 0.05. (E) Fecal pellets from vancomycin-treated mice and untreated mice were profiled for microbial composition via 16S rRNA sequencing at day 0, 1 and, 10 after antibiotic treatment and showed enrichment in B. thetaiotaomicron in the samples after vancomycin treatment. (F) Principal coordinate analysis of Bray-Curtis distance demonstrates sample segregation according to antibiotic treatment and (vancomycin versus PBS) and treatment time (Day 0, 1, 10). The top four informative component loadings are shown as arrows, each represented by a corresponding microbiome SV. (G) Differential analysis for samples at day 10 was performed using DESeq2 and indicates a statistically significant enrichment of B. thetaiotaomicron (SVs) and S. xylosus in vancomycin-treated mice compared to untreated. Significance was determined based on FDR of 0.05. Note: Animals assigned to different antibiotic treatments were first co-housed to homogenize the microbiome and then separated according to treatment.

Vancomycin administration results in tuft cell hyperplasia and increased IL-25 concentrations in the proximal colon and leads to the enrichment of B. thetaiotaomicron in the microbiome. (A) Following the approach from Buonomo et al. (2016) IL-25 was measured by ELISA in the proximal colon of C57BL/6 WT mice treated with various antibiotics via oral gavage. Protein concentration in the lysate (pg/ml) was normalized by total protein in the sample (in mg) as in Buonuomo et al. (2016). Data are representative of independent experiments repeated twice, using n = 4–6 female mice per treatment group. ANOVA with Tukey post-hoc test was run to determine significant differences. Statistical significance was estimated at FDR of 0.05. (B) IL-25 mRNA expression was measured by RT-qPCR in the proximal colon of C57BL/6 WT mice treated with different antibiotics. Data are representative of independent experiments repeated twice using n = 4–6 female mice per treatment group. ANOVA with Tukey post-hoc test was run to determine significant differences. Statistical significance was estimated at an FDR of 0.05. (C) TC percentages were estimated by quantifying the percentage of DCLK1+ EPCAM+ cells compared with total cells in C57BL/6 WT mice treated with various antibiotics or untreated. Data are representative of independent experiments repeated twice, using n = 4–6 female mice per treatment group. ANOVA with Tukey post-hoc test was run to determine significant differences. Statistical significance was estimated at FDR of 0.05. (D) TC hyperplasia was confirmed via IHC by enumerating the number of DCLK1-expressing cells in the field of view (FOV). The white bar indicates a scale of 100 μm. Data are representative of independent experiments repeated twice, using n = 4–6 female mice per treatment group. ANOVA with Tukey post-hoc test was run to determine significant differences. Statistical significance was estimated at an FDR of 0.05. (E) Fecal pellets from vancomycin-treated mice and untreated mice were profiled for microbial composition via 16S rRNA sequencing at day 0, 1 and, 10 after antibiotic treatment and showed enrichment in B. thetaiotaomicron in the samples after vancomycin treatment. (F) Principal coordinate analysis of Bray-Curtis distance demonstrates sample segregation according to antibiotic treatment and (vancomycin versus PBS) and treatment time (Day 0, 1, 10). The top four informative component loadings are shown as arrows, each represented by a corresponding microbiome SV. (G) Differential analysis for samples at day 10 was performed using DESeq2 and indicates a statistically significant enrichment of B. thetaiotaomicron (SVs) and S. xylosus in vancomycin-treated mice compared to untreated. Significance was determined based on FDR of 0.05. Note: Animals assigned to different antibiotic treatments were first co-housed to homogenize the microbiome and then separated according to treatment.

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