Stage-specific gut microbiome shifts across the Type 2 Diabetes Mellitus spectrum: A systematic review and meta-analysis

AimsThe gut microbiome has been implicated in type 2 diabetes progression, but reproducible biomarkers across studies remain limited due to technical and population heterogeneity. This study investigated whether specific gut microbiome shifts occur progressively across stages of type 2 diabetes. MethodsWe systematically reanalysed 16S rRNA datasets from 12 published studies (n=1,247 samples) after quality control, examining five groups (healthy controls, prediabetes (PD), new-onset type 2 diabetes, established type 2 diabetes, and type 2 diabetes with complications. Sequencing reads were quality-filtered, denoised, and resolved into amplicon sequence variants with genus-level taxonomic assignments using the SILVA database. Centered log-ratio (CLR)-transformed abundance data were analysed using PERMANOVA, meta-analysis with leave-one-study-out validation, differential abundance testing (Wilcoxon and ANCOM), and Random Forest classification. Eligible studies were identified through comprehensive searches of PubMed, Ovid Medline and Web of Science from June 2010 - June 2025 using predefined inclusion and exclusion criteria following PRISMA 2020 guidelines. Studies were investigated by two independent reviewers and included if they provided 16S rRNA data on adults across diabetes stages. Study quality was assessed based on metadata completeness and raw data availability. This systematic review and meta-analysis was registered in the Open Science Framework (OSF; registration https://osf.io/eth7a; embargoed until October 2026) and conducted according to PRISMA guidelines. ResultsEarly disease transitions showed minimal microbiome alterations, with only 4 genera, (notably enrichment of Allisonella and Escherichia-Shigella) were significantly different between healthy and PD (q < 0.05), and no significant genera between PD and new-onset type 2 diabetes. Advanced disease exhibited robust dysbiosis, with 9 genera differentially abundant in type 2 diabetes vs complicated type 2 diabetes and 5 genera in healthy vs complicated type 2 diabetes comparisons. Complicated type 2 diabetes was characterised by enrichment of Hungatella and [Clostridium] innocuum group and depletion of Faecalibacterium and compared to both uncomplicated type 2 diabetes and healthy controls. Random Forest classification achieved poor performance for early contrasts (AUC [&le;] 0.79) but strong discrimination for advanced disease (type 2 diabetes vs complicated type 2 diabetes: AUC = 0.89; Healthy vs complicated type 2 diabetes: AUC = 0.96). ConclusionGut microbiome alterations are subtle and inconsistent in early dysglycemia but become pronounced and reproducible with diabetic complications, suggesting microbiome-based biomarkers may be most clinically useful for identifying disease progression rather than early detection. Limitations include heterogeneity of sequencing methods and reliance on 16S rRNA data, which may restrict taxonomic and functional resolution. To our knowledge, this is the first meta-analysis to systematically evaluate gut microbiome alterations across multiple clinical stages of type 2 diabetes progression.