Modeling prebiotic interventions on luminal and mucosa-associated microbiota without and with Clostridium difficile infection in vitro.
Libraries for whole-genome sequencing were prepared using the Illumina DNA prep protocol according to the instructions of Illumina (Illumina DNA Prep Reference Guide, 1000000025416v10). DNA concentrations were standardized across samples. After the tagmentation and clean-up steps, PCR-mediated standard indexed i5 and i7 adapters were added and the library was amplified. Next, the libraries were cleaned-up and pooled. Whole-genome sequencing was performed using the Illumina NextSeq sequencer applying NextSeq V3 chemistry.