Microbial Clinical Atlas

Background

Microbiome studies increasingly generate taxonomic profiles linked to host phenotypes, yet interpretation remains fragmented across heterogeneous literature, inconsistent terminology, and resource-specific formats. Clinically relevant taxa are often reported without standardized annotation of ecological context, molecular features, or supporting evidence, making comparisons across studies difficult and limiting reproducibility. As multi-omic datasets expand, there is a growing need for a structured framework that connects microbial taxa to clinically and biologically interpretable knowledge.

Objective

This project develops the Microbial Clinical Atlas (MCA), a curated knowledge base that organizes microbial taxa into standardized Taxon Passports linked to clinical associations, evidence, and molecular context. By integrating literature curation with microbiome, metabolomic, and immune profiling frameworks, we aim to support rigorous interpretation of clinically relevant microbiome signals.

Aims

• Curate standardized Taxon Passports that capture microbial identity, ecology, clinical relevance, and evidence-linked associations using a transparent and versioned framework.
• Develop a structured evidence model that links taxa to clinical associations, literature support, and molecular context, including metabolite- and pathway-relevant annotations.
• Build and share an accessible web resource with searchable entries, downloadable exports, and reproducible data structures to support microbiologists and researchers beginning microbiome analysis.

Through this work, we aim to establish a reusable framework for translating microbiome readouts into interpretable biological and clinical knowledge. The resulting resource will support cross-study comparison, improve consistency in microbiome interpretation, and facilitate the generation of mechanism-informed hypotheses in translational microbiome research.