Microbiology
The Microbiology area is a web workspace for microbial community and pathogen research. Upload feature tables or processed profiles; run QC, taxonomic and community profiling, alpha/beta diversity with PERMANOVA, compositional differential abundance, and functional pathway analysis; compare cohorts; and generate AI-assisted interpretation grounded in computed metrics — with reference-database provenance for every step.
Start from a research scenario
Guided workflows map common questions to data requirements, analysis steps, and documentation — pick the scenario closest to your study.
Community profiling
Research question: Which taxa dominate each sample and cohort, how prevalent are they, and how much of the community remains unclassified at the chosen rank?
Profile which microbes are present and how abundant they are across samples, starting from a processed feature table and an optional taxonomy map.
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Diversity comparison
Research question: Do communities differ in alpha diversity or overall composition between groups, and is any separation statistically supported rather than a depth artifact?
Compare within-sample and between-sample diversity across groups, with the sequencing-depth confound kept visible.
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Core microbiome
Research question: Which taxa are reliably present across this cohort or environment, and how does the answer change as prevalence and abundance thresholds shift?
Identify which taxa are consistent, recurring members of a community — present above a chosen prevalence and abundance threshold — rather than incidental or rare detections.
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Differential abundance
Research question: Which taxa are differentially abundant between two groups once compositionality and sparsity are accounted for, and how prevalent and how large is each difference?
Identify taxa that differ between two cohorts using compositional-data-aware methods, with prevalence and effect size reported alongside significance.
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Longitudinal community analysis
Research question: How does community diversity change within each subject over time, and is there a statistically supported overall trend once repeated measures per subject are accounted for?
Track how a community changes within subjects over time — trajectories, timepoint-to-timepoint shifts, and a repeated-measures trend test — instead of collapsing a longitudinal design into a single cross-sectional comparison.
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Functional profiling
Research question: Which microbial pathways or gene families differ between communities, and are those functions measured directly or inferred from taxonomy?
Compare microbial pathway and gene-family abundance across cohorts, keeping measured functions distinct from inferred functional potential.
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Genomic relatedness
Research question: Which isolates in this collection are genomically close enough to suggest a shared source or lineage, and what clusters does that relatedness form at a given distance threshold?
Compute pairwise genetic distance between sequenced isolates from an alignment and group closely related isolates into clusters — a minimal, license-safe relatedness signal, not full phylogenetics.
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Cross-area microbiome
Research question: How do microbial community or functional features relate to host response, immune state, or clinical outcomes measured in another Gradient Biotech area?
Connect microbial community findings to host, immune, or clinical results through shared sample identity, without duplicating another area's pipeline.
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Platform features
Everything available in the Microbiology workspace today — pipelines, explorers, exports, and provenance.
- Study workspaces with sample manifests, datasets, saved cohorts, and run history
- Feature-table, taxonomy, tree, and pathway-table ingestion with reference-database provenance
- Microbial QC: per-sample depth, feature retention, prevalence, and low-depth flags
- Stacked relative abundance bar charts by taxonomy rank (phylum through species) with per-sample views
- Alpha rarefaction curves for sequencing-depth adequacy assessment
- Alpha diversity (Shannon, Simpson, observed features, Chao1) with group significance testing (Kruskal-Wallis, pairwise Wilcoxon)
- Beta diversity (Bray-Curtis or Jaccard), PCoA ordination, PERMANOVA, and betadisper dispersion test
- ANCOM-BC differential abundance with sampling-fraction correction, 95% CI, and BH correction; CLR + Mann-Whitney also available
- Core microbiome analysis with an interactive prevalence x abundance scatter and live threshold sliders
- Longitudinal community analysis: within-subject trajectories, first-differences, and a repeated-measures linear mixed-effects trend test
- Functional pathway abundance and cohort comparison with measured-vs-inferred distinction
- Grounded AI interpretation citing computed metrics, with associational (non-causal) guardrails
- Async job polling with downloadable artifacts and reference-database versioning per run