Transcriptomic comparative analysis of duodenal samples from SSc patients treated with FMT or placebo between weeks 2 and 16. Bulk RNA sequencing was performed on duodenal biopsies from SSc placebo (n = 4) vs FMT (n = 5) patients. (A) The heat map and (B–D) pathway analysis of significantly upregulated and downregulated genes. The analysis was performed with the comprehensive gene set enrichment web server EnrichR for Pathways [database: (A) Reactome 2016, (B) Human Phenotype Oncology, (C) Jensen DISEASES] of significantly upregulated genes in samples from SSc patients treated with FMT at weeks 2 and 16 (P ≤ 0.05, log2 ratio ≥ 0.5). Arrows indicate upregulated expression of MMP1. FMT: faecal microbiota transplantation