This dataset is related to "Resolution of Long-Term Severe Irritable Bowel Syndrome Following Fecal Microbiota Transplantation: A Case Report and Microbiota Analysis" (Elena Montenegro-Borbolla, Wakim El-khoury Jeanine, Claire Bertelli, Schoepfer Alain, Benoît Guery, Tatiana Galperine). The dataset includes the R Markdown (.Rmd) file and the corresponding .html output, which lists the R packages and versions used plus the code used to generate the figures presented in the paper. Additionally, the necessary phyloseq object and a .csv file containing read counts are provided to enable replication of our case report results. These data were generated using the zAMP pipeline (Scherz et al., 2025, BioRxiv) with sequencing reads available in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB81207.