Related Experiment Video
Updated: Mar 29, 2026

Cefoperazone-treated Mouse Model of Clinically-relevant Clostridium difficile Strain R20291
Published on: December 10, 2016
Characterization of the Gut Microbiome of Patients with Clostridioides difficile Infection and Healthy Individuals in
Dimitra Mougiou1, Georgia Gioula1, Lemonia Skoura2
1Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
Background/Objectives:
The gut microbiome plays an important role in the colonization of an individual by Clostridioides difficile and in the development of Clostridioides difficile infection (CDI). The main purpose of this study was to compare the gut microbiomes of patients with CDI and healthy individuals.
Methods:
We prospectively included 48 individuals: 32 patients with CDI and 16 healthy individuals. Microbiomes were analyzed by sequencing the hypervariable regions of the 16S rRNA gene using an Ion GeneStudio™ S5 System. Further statistical analysis of microbiome data was performed with the open-source programming language R version 3.5.2.
Results:
Among the CDI patients, Firmicutes and Proteobacteria were the most abundant phyla, while Enterobacteriaceae and Enterococcaceae were the most abundant families. Genus-level analysis showed that Enterococcus was the dominant genus in CDI patients; in contrast, in healthy individuals, Faecalibacterium was the most abundant. The MaAsLin2 tool revealed that members of the family Enterococcaceae and the genus Enterococcus were more abundant in patients with CDI than in healthy individuals. Alpha and beta diversity did not reveal differences between the two study groups.
Conclusions:
We observed differences in microbiome patterns between healthy individuals and CDI patients that were consistent with the literature. Further studies are needed.
Related Concept Videos
Microbiota of the Stomach and Small Intestine
Microbiota of the Large Intestine
Functions of the Gut Microbiota
Introduction to the Human Microbiota
Development of Human Microbiota
Bacterial Flora of the Large Intestine
The normal gut flora of the colon plays a critical role in generating essential vitamins such as vitamins K, B5, and B7.

