Shannon variety indices are extremely related between duplicate swabs and snap frozen swabs for all phyla. Diversity is lower for the AFFV group in mucosal biopsies and fecal samples in comparison with rectal swabs. Finally, rectal swabs, fecal samples and mucosal biopsies have been in contrast by correlation of profiles.

First, we in contrast swab samples to mucosal biopsy samples taken by colonoscopy in 32 subjects. These correlations have been generally low, particularly for the AFFV group. Bacteroidetes profiles showed a somewhat larger similarity with a large distribution of values for R2 .

For rectal swab samples, diversity seems to be somewhat larger within the unprepped group, and distribution of range indices are somewhat smaller than within the prepped group. AFFV variety could be seen to be higher in rectal swabs than in fecal samples.

Bacteroidetes typically had a barely greater correlation than AFFV . In the IBD outpatient group, correlations had been markedly greater, particularly for the Bacteroidetes, which had a median R2 just like that found for duplicate swab profiles . These data confirmed that fecal profiles resembled swab profiles, particularly for the phylum Bacteroidetes, however not in people who underwent bowel prepping.

Next, rectal swab profiles have been in comparison with fecal profiles in nineteen topics of the colonoscopy group and in all ten topics of the IBD outpatient group. In the colonoscopy group, correlations between swab and fecal profiles had been usually low, similar to the correlation of swab samples to mucosal biopsy samples in this prepped affected person group.

Comparisons between all samples have been made by calculating squared correlation coefficients for all attainable pairs of samples. When duplicate swabs stored in RTF from the colonoscopy group had been in comparison with different samples, averaged profiles of the duplicate swabs have been used. DNA was isolated from feces or mucosal biopsies as described beforehand . In short, for mucosal samples, the first step consisted of lysis of tissue and bacteria with the QIAamp DNA mini Kit followed by DNA extraction with the NucliSENS easyMag automated DNA isolation machine (Biomérieux, Marcy l'Etoile, France).