# Microbe

> Use when the user has a 16S or ITS feature table plus taxonomy and metadata and needs alpha/beta diversity, composition bars, differential abundance, co-occurrence networks, random-forest biomarkers, or a taxonomy tree. Drive the microbe MCP tools with local Rscript.

- Skill: `minimax-ai/microbe` (Agent Skill)
- Install (CLI): `npx skillmds@latest add minimax-ai/microbe`
- Raw SKILL.md: https://api.skillmd.com/api/skills/minimax-ai/microbe/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: MiniMax AI (https://skillmd.com/u/minimax-ai)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/minimax-ai/microbe

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# microbe

Use the `microbe` MCP tools. Do not reimplement vegan/DESeq2 plots in Python.

## Typical order

1. `microbe_env`
2. `microbe_alpha`, `microbe_beta`
3. `microbe_composition`, `microbe_diff`
4. `microbe_network`, `microbe_rf`, `microbe_corr`, `microbe_tree` as requested

Expected columns: `feature_id` + sample counts; taxonomy ranks or a QIIME semicolon string; `sample_name` + `group`.

Missing R or packages: return the tool's repair command. This Plugin does not go from raw reads to ASVs.