Abstract
G A A b st ra ct s study we investigated the applicability of rectal swabs for gut microbiota profiling in a clinical routine setting. We analysed optimal storage and processing of rectal swabs for clinical routine, reproducibility of profiles from rectal swabs and similarity to microbial profiles from fecal and mucosal samples. Methods Rectal swabs, mucosal biopsies, mucosal washings and fecal samples from 38 subjects were prospectively collected and analysed by IS-pro, a high-throughput molecular fingerprinting method. Two rectal swabs were stored in RTF buffer at room temperature for two hours before freezing at -20°C and one was immediately snap frozen. These samples were used to evaluate reproducibility of rectal swabs and effect of storage at room temperature. IS-profiles from rectal swabs were further compared to mucosal and fecal samples. All data analysis was performed with in-house developed software tools in combination with the Spotfire software package (TIBCO, Palo Alto, USA). Results IS-profiles from the two rectal swabs stored in RTF buffer at room temperature were highly similar (estimated correlation coefficients of IS-profiles .90%) and were equally similar to the snap frozen rectal swab. Correlation of rectal swabs to feces was low (estimated correlation coefficients of IS-profiles 40-60%) and correlations to mucosal samples were slightly higher (50-70%). Correlations of fecal samples to mucosal samples were low (4060%). Conclusion We find that rectal swabs give highly reproducible microbiota profiles that resemble mucosal adherent microbiota more closely than feces. Storage of swabs in RTF buffer of up to two hours at room temperature does not affect the results of subsequent microbiota analysis, making reproducible routine sampling in a clinical setting feasible.
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