Figure 1.
Two subject groups were sampled.
Group A: 38 subjects who underwent an elective colonoscopy. Feces was collected at home two to five days before. Rectal swabs and biopsies were taken during the procedure. Two swabs were stored for two hours at room temperature and at −20°C afterwards, one swab was immediately snap frozen. The mucosal biopsy was washed in PBS and snap frozen. Group B: 10 patients with IBD. This group collected feces and one rectal swab at home. Feces was stored in a sterile container and the rectal swab in RTF buffer, both at at −20°C. A second rectal swab was obtained at the outpatient clinic and stored in the same fashion as the first swab.
Figure 2.
The x-axis represents IS fragment length, the y-axis represents relative abundance of fragments. Colours of fragments correspond to bacterial phyla. Blue peaks represent AFFV group, red peaks represent Bacteroidetes. Each peak may be regarded as an operational taxonomic unit (OTU).
Figure 3.
Diversity analysis of samples that were either directly lysed or underwent bead-beating prior to DNA isolation.
Shannon diversity indices are generally lower for bead-beated samples for the phylum Bacteroidetes (pink), the AFFV group (blue) and consequently for all phyla combined (green).
Figure 4.
Comparisons of microbiota profiles of the colonoscopy group expressed as R squared.
All comparisons have been done separately for AFFV group (left) and Bacteroidetes (right). Figures show comparisons of all profiles. Red dots represent comparisons of samples of the same subject (intra-subject correlation). Yellow box plots are based on all correlations, red box plot on intra-subject correlations only. A: Duplicate swab profiles stored in RTF buffer. B: Swab stored in RTF buffer versus snap frozen swabs. C: Swabs stored in buffer versus mucosal biopsies. D: Swabs stored in buffer versus fecal samples. E: fecal samples versus mucosal biopsies.
Table 1.
Median R squared and Inter Quartile Range (IQR) values for all comparisons.
Figure 5.
Comparisons of microbiota profiles in the IBD outpatient group expressed as R squared.
All comparisons have been done separately for AFFV group (left) and Bacteroidetes (right). Figures show comparisons of all profiles. Red dots represent comparisons of samples of the same subject (intra-subject correlation). Yellow box plots are based on all correlations, red box plots on intra-subject correlations only. A: Swabs taken by patients at home versus swabs taken by the physician at the polyclinic. B: Swabs versus fecal samples.
Figure 6.
Diversity analysis of the different sample types.
Shannon diversity indices are highly similar between duplicate swabs and snap frozen swabs for all phyla. Diversity is lower for the AFFV group in mucosal biopsies and fecal samples compared to rectal swabs.
Figure 7.
Comparisons of microbial diversity in prepped versus unprepped subjects.
Diversity in fecal samples is similar in both groups. For rectal swab samples, diversity seems to be somewhat higher in the unprepped group, and distribution of diversity indices are somewhat smaller than in the prepped group. AFFV diversity can be seen to be higher in rectal swabs than in fecal samples.
Figure 8.
Principal coordinate analysis depicting the different sample types.
Rectal swabs, fecal samples and mucosal biopsies may sometimes be very similar, but on a whole, these three sample types seem to harbor more or less distinct microbiota.