Longitudinal sampling of patient gut microbiomes at indicated timepoints in LC cohort, along with samples from patients with CD, healthy participants, or irC patients from CVC cohort (validation). (A–C) Longitudinal alpha diversity (A) and observed richness (B) using 16S rRNA sequencing data and microbiota density (C) at distinct irC disease stages (pre-irC, irC-initial, irC-late, and post-irC) (n = 13 irC patients). Linear mixed model fit by restricted maximum likelihood with P value estimations using Satterthwaite’s method “lmerModLmerTest.” Comparison of values at pre-irC versus irC-initial (A, P = 0.0042; B P = 0.0019; C, P = 0.036), irC-late (A, P = 0.039; B, P = NS; C, P = NS), post-irC (A, P = NS; B, P = NS; C, P = NS). (D) Intrapatient metagenomic microbiota profiles change (Bray-Curtis distance) over time within either irC patients (red) or non-irC patients (blue). Intrapatient comparison of microbiotas in eight non-irC patients (blue) with paired stool samples collected at pre-ICI and follow-up (4–7 wk post-ICI initiation). For irC microbiomes (red), intrapatient comparison of paired stool samples collected at (1) pre-irC and active irC (in nine irC patients) or (2) pre-irC and post-irC (in three irC patients). Mann-Whitney compared the dissimilarity of non-irC paired samples against that of irC paired samples (pre-irC versus irC, P = 0.14, q = 0.28; pre-irC versus post-irC, P = 0.78, q = 0.78). (E) Comparison of alpha diversity between pre-irC metagenomic microbiomes profiles of irC patients (red), patients with CD (purple), and healthy individuals (green). Mann-Whitney (P value) and BH adjustment (q-value) to compare alpha diversity between groups (pre-irC versus CD: P = 0.046, q = 0.092; pre-irC versus healthy P = 0.93, q = 0.93). (F) Comparison of alpha diversity between irC-initial metagenomic microbiome profiles of irC patients (from LC and CVC) (red), patients with CD (purple), and healthy individuals (green). Mann-Whitney (P value) and BH adjustment (q-value) to compare alpha diversity between groups (irC-initial versus CD: P = 0.99, q = 0.99; irC-initial versus healthy P = 0.13, q = 0.27). Mann-Whitney P values in E and F were adjusted for multiple comparisons (q-value) by the BH method. *P < 0.05, **P < 0.01; P value estimations using Satterthwaite’s method “lmerModLmerTest.”
Figure 3.

Longitudinal sampling of patient gut microbiomes at indicated timepoints in LC cohort, along with samples from patients with CD, healthy participants, or irC patients from CVC cohort (validation). (A–C) Longitudinal alpha diversity (A) and observed richness (B) using 16S rRNA sequencing data and microbiota density (C) at distinct irC disease stages (pre-irC, irC-initial, irC-late, and post-irC) (n = 13 irC patients). Linear mixed model fit by restricted maximum likelihood with P value estimations using Satterthwaite’s method “lmerModLmerTest.” Comparison of values at pre-irC versus irC-initial (A, P = 0.0042; B P = 0.0019; C, P = 0.036), irC-late (A, P = 0.039; B, P = NS; C, P = NS), post-irC (A, P = NS; B, P = NS; C, P = NS). (D) Intrapatient metagenomic microbiota profiles change (Bray-Curtis distance) over time within either irC patients (red) or non-irC patients (blue). Intrapatient comparison of microbiotas in eight non-irC patients (blue) with paired stool samples collected at pre-ICI and follow-up (4–7 wk post-ICI initiation). For irC microbiomes (red), intrapatient comparison of paired stool samples collected at (1) pre-irC and active irC (in nine irC patients) or (2) pre-irC and post-irC (in three irC patients). Mann-Whitney compared the dissimilarity of non-irC paired samples against that of irC paired samples (pre-irC versus irC, P = 0.14, q = 0.28; pre-irC versus post-irC, P = 0.78, q = 0.78). (E) Comparison of alpha diversity between pre-irC metagenomic microbiomes profiles of irC patients (red), patients with CD (purple), and healthy individuals (green). Mann-Whitney (P value) and BH adjustment (q-value) to compare alpha diversity between groups (pre-irC versus CD: P = 0.046, q = 0.092; pre-irC versus healthy P = 0.93, q = 0.93). (F) Comparison of alpha diversity between irC-initial metagenomic microbiome profiles of irC patients (from LC and CVC) (red), patients with CD (purple), and healthy individuals (green). Mann-Whitney (P value) and BH adjustment (q-value) to compare alpha diversity between groups (irC-initial versus CD: P = 0.99, q = 0.99; irC-initial versus healthy P = 0.13, q = 0.27). Mann-Whitney P values in E and F were adjusted for multiple comparisons (q-value) by the BH method. *P < 0.05, **P < 0.01; P value estimations using Satterthwaite’s method “lmerModLmerTest.”

This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal