Detecting Changes in the Gut Microbiome following Human Biotherapy via Pyrosequencing of the 16S rRNA Gene

Date

2013-04-25

Authors

Pinder, Shaun

Journal Title

Journal ISSN

Volume Title

Publisher

University of Guelph

Abstract

Human biotherapy (HBT) or fecal transplants have been shown to be an effective treatment for patients with recurrent Clostridium difficile infection (CDI). This study examines the microbial populations present in CDI patients pre- and post-HBT by extracting bacterial DNA from stool samples and performing pyrosequencing of the 16S rRNA gene. We then compared these microbial populations to those of the donors. We examined 19 pairs of patient samples, of which 14 were clinically cured of CDI, and 5 patients were failures. The successful treatment of CDI was associated with an increase in diversity and richness of the patient's fecal microbiome. The majority of those cured showed an increase in the proportion of Firmicutes and decrease in the proportion of Proteobacteria, although varying antibiotic exposure and innate variability between patients was observed.

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Keywords

Clostridium difficile, 16S rRNA, pyrosequencing, mothur, fecal transplant, human biotherapy, gut microbiome, exact logistic regression via MCMC, Roche 454 DNA sequencing

Citation