5 Microbiome: methods, evidence, and claims

5.1 Learning objective

Evaluate the scientific reasoning, reproducibility, and interpretation of a microbiome analysis.

5.2 Case specification

Support level: Partially guided.

Planned scenario: A synthetic microbial community study with a feature table, taxonomy, sample metadata, and repeated observations.

Evaluation question: Do the analytical choices support the reported community differences?

This is an original case design. Data and scientific conclusions have not yet been generated or validated.

5.3 Planned evidence package

See cases/microbiome/case-specification.md. The completed package will contain a data dictionary, input data, supplied response, code, output tables, and an independently verified reference analysis.

5.4 Review priorities

Sample alignment and filtering decisions
Experimental unit and repeated observations
Choice of transformation and comparison
Limits of relative-abundance and causal claims

5.5 Learner workflow

Read the question and inventory the supplied evidence.
Extract claims from the supplied response.
Mark each claim supported, incorrect, unsupported, or uncertain.
Run or inspect the relevant verification checks.
Update your judgment and explain any correction.
Complete the evidence log and self-assess with the rubric.

5.6 Checkpoint

Which conclusions survive verification, and which require correction or additional evidence?

5.7 Deliverable

A case review using templates/evaluation-report.qmd and templates/evidence-log.csv.

5.8 Worked explanation

To be authored after the reference workflow and expected outputs have been verified. Include valid reasoning as well as errors, and discuss defensible alternative interpretations.