Dataset including clinical features related to Parkinson's disease and lifestyle habits of three groups of individuals: 1) individuals with manifest Parkinson’s disease, 2) non-manifesting GBA1 variant carriers (individuals who are at increased risk of developing Parkinson’s disease because carriers of GBA1 genetic variants), and 3) healthy controls. This dataset has been generated as part of a cross-sectional study comparing the gut (fecal) microbiome composition, analyzed thorough shotgun metagenomic sequencing of the three groups. The study has evaluated associations between gut microbiome alterations and clinical features suggestive of Parkinson’s disease, in both Parkinson’s disease and non-parkinsonian individuals (GBA1 variant carriers and healthy controls).