Table 1.
Study population demographics and disease phenotype.
Figure 1.
Total Bacteroidales (cfu/biopsy) by cohort and degree of inflammation.
Biopsies were grouped by cohort: CD (Crohn Disease), UC (ulcerative colitis) and Control and degree of inflammation: no and mild inflammation (no/mild) or moderate to severe inflammation (mod/svr). N is equivalent to the number of biopsies in each group. Column level represents mean Bacteroidales log cfu/biopsy. Error bars represent inter-quartile ranges A. Entire cohort. There were no significant differences detected between cohorts. B Includes only biopsies from newly diagnosed subjects.
Table 2.
Total Bacteroidales [cfu/biopsy) and number of different Bacteroidales species detected per biopsy by diagnoses and degree of inflammation in entire cohort.
Figure 2.
Heatmaps of Bacteroidales species distribution and concentration by cohort.
A. Control cohort. B. UC cohort. C. CD cohort. Bacteroidales species are labeled at the top of the figure. Subject numbers are listed on the left. Each row represents the species detected on that subject's biopsy (In cases where more than one biopsy of the same degree of inflammation was present, the detected species levels (cfu/biopsy) from each biopsy was averaged and all detected species from both biopsies were included). The degree of inflammation of the biopsy is indicated to the right of the biopsy (N: Non-inflamed, Mild, Mod: Moderate, or Svr: Severe). White lines demarcate biopsies from one subject.
Figure 3.
Bacteroidales species diversity by degree of inflammation.
The median number of species per IBD biopsy detected from biopsies with no or mild inflammation (No/Mild) compared to IBD biopsies with moderate to severe inflammation (Mod/Svr). Error bars represent inter-quartile ranges. N equals the number of biopsies in each group. *P = 0.02.
Table 3.
Comparison of Bacteroidales species, by disease status (IBD vs. controls) and study group (CD, UC, and controls).
Figure 4.
PCR analysis of bft from B. fragilis isolates.
Lane one contains a bft containing strain (086 care of C. Sears, MD). Lane two contains a B. fragilis strain without bft (9343). Lane three contains an isolate from the terminal ileum (TI) of subject 34. Lanes four and five contain isolates from TI and ascending colon biopsies from control subject 43. Lane 6 contains an isolate from the non-inflamed terminal ileum of a subject 71 with CD. Lane 7 contains an isolate from an inflamed TI biopsy of subject 64 with CD. Lanes 8 and 9 contains isolates from non-inflamed rectal and inflamed ascending colon biopsies of a subject 74 with CD. Lanes 10 and 11 are isolates from non-inflamed TI and inflamed descending colon biopsies of a subject 39 with UC. Lanes 12 and 13 are isolates from an non-inflamed cecal biopsy and inflamed rectal biopsy from subject 62 with UC.
Table 4.
Number of biopsies with B. fragilis where bft or PSA was present.
Figure 5.
PSA analysis of B. fragilis isolates.
A Western blot of PSA from B. fragilis isolates grown in vitro after isolation from control, CD and UC (inflamed (I) a non-inflamed (NI) biopsies. Panel A: Lanes 1–6 contain B. fragilis isolates from the biopsies control subjects (4, 6, 13, 34, 68, and 1). Lanes 7–8 contain isolates from non-inflamed and inflamed biopsies from subject 23 with UC. Lanes 9–11 contain isolates from inflamed and uninflamed biopsies from subjects with UC: 32, 29 and 77. Panel B: Lane 1 contains B. fragilis type strain 9343 as a positive control. Lanes 2 and 3 contain isolates from a non-inflamed and then an inflamed biopsy from subject 47 with CD. Lanes 4–8 contain B. fragilis isolates from inflamed biopsies of subjects 26, 56, 64, 14, and 85 with CD.