Borrowing it
Nothing to install: this file belongs to monarch-initiative/dismech. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/monarch-initiative/dismech/main/.claude/skills/microbiome-curation/SKILL.mdgit clone --depth 1 https://github.com/monarch-initiative/dismechWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/monarch-initiative/dismech/microbiome-curation)<a href="https://agentmods.dev/skills/monarch-initiative/dismech/microbiome-curation"><img src="https://agentmods.dev/badge/skills/monarch-initiative/dismech/microbiome-curation/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/monarch-initiative/dismech/microbiome-curation"><img src="https://agentmods.dev/badge/skills/monarch-initiative/dismech/microbiome-curation.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00085 | $0.02831 |
| Opus 5.5 | $0.00034 | $0.01132 |
| Sonnet 5.5 | $0.00017 | $0.00566 |
| Haiku 4.5 | $0.00009 | $0.00283 |
Grade A, and why
microbiome-curation scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 335 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Microbiome Curation Skill
Overview
Curate microbiome-related pathophysiology entries with ecological depth beyond simple taxa +/- lists. Focus on:
- Ecological concepts (diversity, stability, keystone taxa)
- Causal chains from dysbiosis to clinical manifestations
- Metabolic consequences (SCFA, bile acids)
- Integration with BugSigDB and primary literature
When to Use
- Adding microbiome dysbiosis entries to disorders
- Curating pathophysiology for IBD, C. diff, obesity, metabolic diseases
- Decomposing "microbiome dysbiosis" into causal graph nodes
- Adding ecological concepts (Anna Karenina, colonization resistance)
- Linking microbial metabolites to host pathophysiology
Key Principle: Graph Structure Over Monolithic Entries
DO NOT create single entries bundling all microbiome effects:
# BAD - monolithic entry
- name: Microbiome Dysbiosis
description: >
Reduced diversity with depletion of Firmicutes and expansion of pathobionts,
leading to decreased SCFA and barrier dysfunction.
DO decompose into atomic nodes with downstream edges:
# GOOD - causal graph
- name: Loss of Microbial Diversity
downstream:
- target: Loss of Keystone SCFA Producers
- target: Increased Microbial Community Instability
- name: Loss of Keystone SCFA Producers
downstream:
- target: Decreased Butyrate Production
- name: Decreased Butyrate Production
downstream:
- target: Impaired Colonocyte Energy Metabolism
- name: Impaired Colonocyte Energy Metabolism
downstream:
- target: Epithelial Barrier Dysfunction
This enables:
- Shared nodes across disorders
- Explicit feedback loops
- Targeted therapeutic entry points
- Evidence on specific causal steps
Ecological Dimensions of Dysbiosis
Beyond Taxa +/-
BugSigDB captures increased/decreased taxa, but ecology is richer:
| Dimension | What it captures | Example |
|---|---|---|
| Taxonomic | Which species +/- | Faecalibacterium, E. coli |
| α-Diversity | Richness/evenness | Shannon index |
| β-Diversity | Inter-individual variability | Anna Karenina effect |
| Functional | Pathway capacity | Butyrate synthesis genes |
| Metabolic | Actual output | Fecal SCFA concentrations |
| Network | Community structure | Keystone taxa, modularity |
| Stability | Resilience | Alternative stable states |
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 335 lines · 85 tokens per session scan A 7f80da06a97a
microbiome-curation is a skill published in the GitHub repository monarch-initiative/dismech (69 stars, last pushed today), licensed BSD-3-Clause. It adds 85 tokens to every session and 2,831 once invoked, about $0.0003 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-15.
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