Longitudinal Taxonomic and Predicted Functional Gut Microbiome Responses to Tirzepatide and Semaglutide: An Exploratory Secondary Analysis of the OMDOT ‐1 Randomized Controlled Trial

Aims Glucagon‐like peptide‐1‐based therapies improve metabolic outcomes, but longitudinal gut microbiome dynamics remain poorly characterized. We compared taxonomic and predicted functional microbiome responses to tirzepatide and semaglutide in Type 2 diabetes. Materials and Methods This exploratory secondary analysis included 36 participants from a randomized controlled trial comparing tirzepatide, semaglutide and conventional treatment. Faecal samples were collected at five time points over 16 weeks and analyzed by 16S rRNA gene sequencing. Genus‐level features were screened using MaAsLin2, and candidate genera were further evaluated using longitudinal mixed‐effects models. Predicted microbial functions were inferred using PICRUSt2 and analyzed using MaAsLin2. Primary analyses were adjusted for baseline body mass index, with exploratory sensitivity analyses additionally adjusted for changes in body weight and haemoglobin A1c. Results No significant between‐group differences in beta diversity were observed. Alpha diversity increased predominantly in the tirzepatide group, with a significant time‐by‐treatment interaction versus control. Longitudinal trajectories relative to the control group differed for several genera, including Romboutsia_B , Barnesiella and Ruminococcus_E with both treatments and Vescimonas with tirzepatide ( q < 0.05). Across 2106 predicted EC features, longitudinal effects were positively correlated between tirzepatide and semaglutide (67.1% concordant direction; Pearson r = 0.450, p < 0.001). Treatment‐versus‐control analyses identified predicted functional changes involving energy and carbohydrate metabolism. Conclusions Tirzepatide and semaglutide were associated with partially distinct taxonomic changes, accompanied by broadly similar predicted functional patterns. These longitudinal findings complement, while remaining distinct from, Week‐16 shotgun metagenomic endpoint analyses. Trial Registration Japan Registry of Clinical Trials (jRCT), jRCT1051240017