Taxonomy reports, abundance profiles, diversity indices, distance matrices, and differentially abundant taxa.

Each tool returns taxonomy reports, abundance profiles, diversity indices and distance matrices, or a table of differentially abundant taxa with statistics. These let you take the next step: an abundance profile feeds diversity and differential-abundance testing, differentially abundant taxa point to microbiome-disease associations, and abundant species can hand off to genomics for functional annotation.

Interpreting Metagenomics outputs

Metagenomics Classify output

Field	Type	Description
`sample_id`	string	Sample identifier
`total_reads`	number	Total reads processed
`classified_reads`	number	Reads successfully classified
`classification_rate`	number	Fraction of reads classified (0-1)
`taxa`	array	Taxonomic hits, sorted by abundance

Taxa entry fields

Field	Type	Description
`taxon_id`	number	NCBI taxonomy ID
`name`	string	Taxonomic name
`rank`	string	Taxonomic rank (kingdom, phylum, class, order, family, genus, species)
`abundance`	number	Relative abundance (0-1)
`read_count`	number	Number of reads assigned
`confidence`	number	Classification confidence (0-1)

Classification rate interpretation

Classification rate	Interpretation
> 80%	Good classification rate for human gut metagenomes
50-80%	Typical for environmental samples (soil, ocean)
20-50%	Many novel/uncharacterized organisms
< 20%	Consider host contamination or database mismatch

Metagenomics Profile output

Field	Type	Description
`sample_id`	string	Sample identifier
`richness`	number	Number of distinct taxa detected
`evenness`	number	Pielou evenness index (0-1)
`dominant_taxon`	string	Most abundant taxon name
`dominant_abundance`	number	Relative abundance of the dominant taxon (0-1)
`phylum_abundances`	object	Map of phylum name to relative abundance

The profile is a per-sample community summary, not a full per-taxon abundance table — pass its sample_id and abundance data through to microbiome_diversity or microbiome_differential for further analysis.

Microbiome Diversity output

Field	Type	Description
`sample_id`	string	Sample identifier
`shannon`	number	Shannon diversity index
`simpson`	number	Simpson diversity index (0-1)
`chao1`	number	Chao1 richness estimator
`observed_species`	number	Number of observed species
`beta_distances`	object	Bray-Curtis distance to each other sample, keyed by `sample_id`

The alpha metrics (Shannon, Simpson, Chao1, observed species) are always returned per sample; beta_distances is populated when metrics includes "beta" or "both". There is no ordination (PCoA/NMDS) output and no PERMANOVA test — those aren't part of this tool's result.

Alpha diversity interpretation

Metric	Low Value	High Value
Shannon (H')	< 2.0 (low diversity)	> 4.0 (high diversity)
Simpson (1-D)	< 0.7 (dominated by few species)	> 0.9 (even community)
Observed species	Context-dependent	Context-dependent
Chao1	Close to observed (few unseen species)	>> observed (many unseen rare species)

Beta distance interpretation

Bray-Curtis distance	Interpretation
0.0	Identical communities
0.0 - 0.3	Similar communities
0.3 - 0.6	Moderately different
0.6 - 1.0	Very different communities

Microbiome Differential output

Field	Type	Description
`group1_label`	string	Label for group 1
`group2_label`	string	Label for group 2
`n_group1`	number	Number of samples in group 1
`n_group2`	number	Number of samples in group 2
`significant_taxa`	array	Taxa with adjusted p-value < 0.05
`total_tested`	number	Total taxa tested

Significant taxa fields

Field	Type	Description
`taxon_name`	string	Taxon name
`taxon_rank`	string	Taxonomic rank
`log2_fold_change`	number	Log2 fold change between groups
`p_value`	number	Raw p-value
`adjusted_p_value`	number	FDR-adjusted p-value
`mean_abundance_group1`	number	Mean abundance in group 1
`mean_abundance_group2`	number	Mean abundance in group 2

significant_taxa is pre-filtered to adjusted p-value < 0.05 — there's no separate significant boolean or prevalence field in the result.

Fold change interpretation

Log2 Fold Change	Raw Fold Change	Interpretation
> 3.0	> 8x	Very strong enrichment
2.0 to 3.0	4x to 8x	Strong enrichment
1.0 to 2.0	2x to 4x	Moderate enrichment
-1.0 to 1.0	0.5x to 2x	Not biologically significant
-2.0 to -1.0	0.25x to 0.5x	Moderate depletion
< -2.0	< 0.25x	Strong depletion

Interpreting Metagenomics outputs