Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection

We present bacterial 16S rRNA gene datasets derived from stool samples of 44 patients with diarrhea indicative of a Clostridioides difficile infection. Patients originated from Germany, Ghana, and Indonesia. After hospitalization and diagnosis, stool samples were taken and subjected to DNA isolation. DNA isolations of stool samples from 35 asymptomatic control individuals were performed. The bacterial community structure was assessed by 16S rRNA gene analysis (V3-V4 region). Metadata from patients and asymptomatic control individuals include gender, age, country, presence or absence of diarrhea, concomitant diseases, and results of the microbiological tests to diagnose C. difficile presence. We also provide initial data analysis and an overview of the entire dataset. After processing of raw paired-end sequencing data, reads were merged, quality-filtered, primer sequences removed, reads truncated to 400 bp and dereplicated. Singletons were removed and remaining sequences were sorted by cluster size, clustered at 97% sequence similarity and chimeric sequences were discarded. Taxonomy to each operational taxonomic units (OTU) was assigned by BLASTn searches against Silva database 123.1 and an OTU table was constructed.