microbe-mcp

Downstream microbiome / amplicon (16S · ITS) analysis MCP. Wraps R scripts such as vegan / DESeq2 / edgeR / igraph / Hmisc / randomForest / ggtree into tools, producing png + pdf via the local Rscript.

Charts align with two public papers (for easy layout replication, without their raw data):

• Liu et al. 2023, Nature Microbiology — rice false smut phyllosphere microbiota

• Zhou et al. 2022, Nature Communications — cross-kingdom synthetic microbiota for tomato Fusarium wilt

R engine

Priority: MICROBE_RSCRIPT → Rscript on PATH → C:\Program Files\R\... / registry.

$env:MICROBE_RSCRIPT = "C:\Program Files\R\R-4.5.1\bin\Rscript.exe"
uv run microbe-cli

Related MCP server: methods-mcp

Data contract (3 CSVs)

Tools (9)

microbe_env microbe_alpha microbe_beta microbe_composition microbe_diff microbe_network microbe_rf microbe_corr microbe_tree

Does not include reads → ASV (DADA2/QIIME2). A feature table is all that's needed to connect.

Testing

python tests/prep_test.py   # 合成扩增子表，无真实样本
python tests/smoke.py

Registration

{
  "mcpServers": {
    "microbe": {
      "command": "uv",
      "args": ["run", "--directory", "/absolute/path/to/microbe-mcp", "server.py"],
      "env": { "MICROBE_RSCRIPT": "/path/to/Rscript" }
    }
  }
}

License

MIT.