# microbe-mcp

> microbe-mcp — presisitence-microbe-mcp. Use this tool when you need to analyze microbiome or amplicon data, and want to perform tasks such as calculating alpha and beta diversity, identifying differential abundance, and constructing networks. The microbe-mcp tool takes in microbiome data and outputs visualizations in PNG or PDF formats, providing insights into complex microbial communities. It is particularly useful for researchers and scientists working with 16S or ITS data and seeking to understand the composition and interactions within microbial ecosystems.

Canonical page: https://skillsregistry.net/skills/presisitence-microbe-mcp  
JSON: https://api.skillsregistry.net/v1/skills/presisitence-microbe-mcp

## Description

An MCP server that wraps R scripts for microbiome and amplicon (16S/ITS) analysis, providing tools for alpha/beta diversity, differential abundance, networks, and more, with PNG/PDF outputs.

## Trust

- **Trust score (0–1):** 0.69
- **Verification tier:** scanned
- **Last scanned:** 2026-08-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-08-28

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/n7ff2odb5n)
- **Repository:** <https://github.com/Presisitence/microbe-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "presisitence-microbe-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/presisitence-microbe-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/presisitence-microbe-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt