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In this latest release, GMrepo v3 has been expanded to 890 projects and 118\u2009965 runs\/samples, including 87\u2009048 16S rRNA and 31\u2009917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in \u226510 projects, 143 were consistently enriched in healthy controls (MCI &amp;gt; 75%), while 85 were enriched in diseases (MCI &amp;lt; 25%). A marker-centric interface enables users to explore marker behavior across diseases. 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