tooluniverse-microbiome-research

Analyze microbiome studies, taxonomic profiles, and genome quality using MGnify, GTDB, ENA, and EuropePMC.

1.7k|254|Updated Mar 3, 2025

Search Tags:#literature review #metagenomics #gtdb #microbiome #dysbiosis #mgnify #taxonomic profiling

Ready to run

npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-microbiome-research

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: tooluniverse-microbiome-research
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-microbiome-research
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-microbiome-research

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Microbiome research requires querying scattered databases like MGnify, GTDB, ENA, and literature archives, each with different APIs and identifier schemes. This Skill unifies study discovery, taxonomic profiling, functional annotation, and literature review into guided workflows with a reasoning framework for interpreting results.

Core Features & Use Cases

Study Discovery by Biome: Search MGnify metagenomics studies using the biome hierarchy (e.g., human gut, soil, marine) and ENVO ontology terms via OLS.
Taxonomic and Functional Profiling: Retrieve community composition, GO terms, and InterPro domains from MGnify analyses, cross-referenced with GTDB taxonomy.
Genome Quality Assessment: Evaluate metagenome-assembled genomes (MAGs) for completeness, contamination, and N50 metrics.
Use Case: A researcher investigating gut dysbiosis in IBD can find relevant MGnify studies, extract taxonomic profiles, identify depleted taxa like Faecalibacterium, and pull supporting literature from EuropePMC in one workflow.

Quick Start

Ask the AI to find gut microbiome studies in MGnify and retrieve the taxonomic composition for one of the returned analyses.

Frequently Asked Questions about tooluniverse-microbiome-research

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I find metagenomics studies for a specific biome?▼

Use MGnify_list_biomes to browse the biome hierarchy, then pass a lineage string like root:Host-associated:Human:Digestive system to MGnify_search_studies. You can also search ENVO ontology terms with ols_search_terms for environment metadata.

How do I get the taxonomic composition of a metagenomics sample?▼

Call MGnify_list_analyses with a study accession (MGYS*) to find analysis accessions (MGYA*), then call MGnify_get_taxonomy with the analysis accession. It returns organisms with lineage, abundance counts, and taxonomy rank.

What is the difference between MGnify and GTDB taxonomy?▼

MGnify provides taxonomic profiles from metagenomics analyses, while GTDB offers a standardized bacterial and archaeal genome taxonomy that may reclassify NCBI names, such as splitting Firmicutes into multiple phyla. Cross-reference both for consistent naming.

Can I analyze drug-microbiome interactions with this approach?▼

Yes, combine MGnify study searches with PubChem for drug identity, CTD for chemical-gene interactions, KEGG for microbial metabolic pathways, and Reactome for host pathway enrichment. Use single-keyword MGnify searches since multi-word queries may timeout.

Why does my MGnify search time out or return no results?▼

The MGnify API can be slow for broad or multi-word queries. Use concise single-keyword searches like metformin, and keep the size parameter at 100 or fewer results per page.

When should I use taxonomic versus functional analysis?▼

Use taxonomic analysis alone when asking which organisms are present or whether composition differs between groups. Add functional analysis with GO terms and InterPro when asking what metabolic capabilities differ or why a taxonomic shift matters.