Fig. 5: Association of fecal microbiome diversity and composition with responses to neoadjuvant Nivo+CT or Ipi+Nivo+CT.
Fecal samples collected before Nivo+CT (n = 19) or Ipi+Nivo+CT (n = 18) treatments were characterized via 16S V4 RNA gene profiling. a, Fecal microbiome profiles of patient samples from the two treatment groups and MPR status are represented by compositional plots showing the relative abundance at the order level. b, Differentially abundant taxa (cutoff of P < 0.1, two-sided DESeq2 likelihood ratio test) aggregated at the genus level between MPR (n = 7) and no MPR (n = 12) in the Nivo+CT arm (left panel) and box-and-whisker plot (right panel) of DESeq2 normalized abundances. c, Differentially abundant taxa (cutoff of P < 0.1, two-sided DESeq2 likelihood ratio test) aggregated at the genus level between MPR (n = 8) and no MPR patients (n = 10) in the Ipi+Nivo+CT arm (left panel) and box-and-whisker plot (right panel) of DESeq2 normalized abundances. d, Differentially abundant taxa (cutoff of P < 0.1, two-sided DESeq2 likelihood ratio test) aggregated at the genus level (or last known taxon) associated with the Nivo+CT and Ipi+Nivo+CT treatment responses—that is, MPR (n = 15) and no MPR (n = 22). e, Box-and-whisker plot of DESeq2 normalized abundances evaluating differentially abundant taxa associated with MPR status for the same taxa as shown in d. For box-and-whisker plots (b,c,e), the box includes data within first (Q1) and third (Q3) quartiles. The horizontal line represents the median. Length of whiskers represents minima (Q1 − [1.5 × IQR], where IQR means interquartile range) and maxima (Q3 + [1.5 × IQR]). Data points outside of whiskers are considered outliers. For differential abundance analyses (b,c,d), P values for each feature are provided in a source data file. Source data for a–e are provided in a source data file.
