Fig. 4: Global transcriptional response to antibiotics in non-responder phenotypes.
From: Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut
A Principal component analysis (PCA) of RNA-seq samples based on abundances of orthologous protein clusters. Percentages in brackets denotes explained variance. Symbol fill denotes sampling time relative to antibiotic treatment and colors denotes response type. Ellipses denote 95% confidence interval from a Student’s t-distribution. Dashed ellipse describes samples taken before antibiotic exposure. B, C Volcano plots of pre-treatment responder vs. non-responder samples (B) and non-responder samples during treatment vs. untreated samples (C). Each dot denotes a differential abundance test for a distinct SEED cluster of orthologous proteins. Percentages for each day denote positive tests rate (number of significant tests/total tests) and colors denote the day the samples were taken (days 20 and 25 were before and day 29 was during antibiotic treatment). Tests with FDR q values < 0.05 are shown as larger dots, whereas non-significant results are shown as small dots.
