Core microbiome
Identify which taxa are consistent, recurring members of a community — present above a chosen prevalence and abundance threshold — rather than incidental or rare detections.
Research question
Which taxa are reliably present across this cohort or environment, and how does the answer change as prevalence and abundance thresholds shift?
Who this is for
- Microbiome researchers describing the stable, shared community members of a cohort or environment
- Teams comparing "core" membership across studies or timepoints
- Analysts who want to explore threshold sensitivity without re-running the pipeline
Data requirements
| Data | Required | Purpose |
|---|---|---|
| Feature table (taxa × samples) | Yes | Per-taxon prevalence and abundance |
| Taxonomy map | No | Collapse to the selected rank before thresholding |
Workflow
Upload feature table (+ taxonomy) → Run Core microbiome
→ Explore prevalence/abundance thresholds interactively
→ Review the core-taxa table
→ AI interpretation
Step 1 — Run Core microbiome
The Core microbiome analysis computes, for every taxon at the selected rank, the fraction of samples it was detected in (prevalence) and its mean and median relative abundance, then classifies taxa as "core" at a default prevalence/abundance threshold pair.
Step 2 — Explore thresholds interactively
The result view plots prevalence against log-scale mean abundance for every taxon, with two live threshold sliders. Dragging a slider reclassifies which taxa count as core directly in the browser — no re-run is needed to test a stricter or looser definition of "core."
Expected outputs
- Full prevalence/abundance table per taxon (display capped, but core counts and fractions reflect the entire table)
- Prevalence-vs-abundance scatter plot with adjustable threshold lines
- Core-taxa list and count at the current thresholds