What this entity is
Canonical name: National Microbiome Data Collaborative (NMDC). 1
Known alias: NMDC. 1
Stable external identifier: None was reported in this audit. 1
The National Microbiome Data Collaborative is a DOE-BER authority associated with a heterogeneous data ecosystem that includes canonical NMDC resources, derivatives, external re-hosts, and a namesake collision with NEON. 1
Related resources include nmdc-metadata, nmdc-results, nmdc.ncbi_biosamples, nmdc mags, nmdc-arkin, and kbase.nmdc_neon.
Key facts from the context audit
The audit resolved 20 NMDC-named database entries to 7 real, maintained resources spanning three tenants and six provenance classes. 1
The seven maintained resources include genuine NMDC resources, an NCBI BioSample re-host, a Pfam re-host, an Arkin Lab derivative, an NMDC-derived KBase resource, and a namesake resource representing the National Ecological Observatory Network rather than NMDC. 1
The nmdc tenant is not exclusively NMDC: nmdc.ncbi_biosamples contains an NCBI BioSample harvest with 51,711,888 biosamples and 756,112,544 attribute rows, while nmdc.ref_data contains 27,481 Pfam terms. 1
The canonical NMDC biosample universe contains 16,640 samples in nmdc.metadata.biosample_set, compared with 51,711,888 biosamples in the co-hosted NCBI mirror, creating an approximately 3,000× scale trap for resource selection. 1
The freshest NMDC-related resource identified by the audit is nmdc mags, with 62,346 metagenome-assembled genomes (MAGs), although it is located in the kbase tenant rather than the nmdc tenant. 1
Iceberg snapshot ages span approximately four months across NMDC-labeled resources: the latest commits were 2026-07-02 for kbase.nmdc_mags and kbase.nmdc_neon, 2026-05-27 for kbase.nmdc_arkin, 2026-05-20 for nmdc.metadata, nmdc.results, and nmdc.ref_data, and 2026-03-09 for nmdc.ncbi_biosamples. 1
The report recommends exposing max(committed_at) in discovery tooling because catalog tables have no comments, databases have empty properties, and no changelog exposes resource currency. 1
The NMDC data model is LinkML-based and defines the *_set schema used in nmdc.metadata. 1
The resource ecosystem has heterogeneous authority: NMDC is the authority for NMDC resources, NEON is the authority for kbase.nmdc_neon, NCBI BioSample is the authority for nmdc.ncbi_biosamples, and Pfam/InterPro is the authority for nmdc.ref_data. 1
The audit found that kbase.nmdc_neon represents the National Ecological Observatory Network, an NSF program distinct from NMDC and its DOE-BER context, so treating the namesake as NMDC would create an agency-attribution error. 1
The Arkin derivative adds embeddings and traits that do not exist upstream, while the NCBI mirror adds an attribute-harmonization layer to 51,711,888 raw NCBI samples. 1
The NMDC ecosystem also includes nmdc.results.annotation_kegg_orthology, which contains 1.83B rows; row counts for NMDC tables returned instantly through Iceberg metadata using SELECT COUNT(*). 1
Metadata introspection and data reads have different access surfaces: DESCRIBE DATABASE EXTENDED kbase.nmdc_* raised ForbiddenException for a kesciencero/microbialdiscoveryforge principal even when COUNT(*) on the same tables succeeded. 1
get_databases() returns both dotted Iceberg aliases, such as nmdc.metadata, and underscore Hive aliases, such as nmdc_metadata, for every tenant database, so consumers must de-duplicate to the dotted form before iteration. 1
The PHB ecology analysis refines this resource picture by using NMDC metagenomes as a cross-validation layer rather than treating NMDC as a single homogeneous dataset: 3,014/3,492 NMDC taxon columns (86.3%) mapped to GTDB genera with known PHB status across 6,365 samples, with a median 87.2% of taxonomic abundance matched to pangenome genera. 2 The analysis matched 693 genera between pangenomes and NMDC metagenomes; genera with at least 50% phaC prevalence had significantly higher NMDC abundance than lower-prevalence genera (Mann–Whitney p = 8.41 x 10^-22). 2
The prophage ecology study supports and refines this cross-validation picture by using taxonomy-based prophage-burden inference across 6,365 NMDC metagenomic samples, achieving 87.2% median matching coverage and identifying 57 significant module–abiotic correlations at FDR < 0.05. 3 Concordance between pangenome enrichment and NMDC correlations was reported for head morphogenesis, tail, and anti-defense modules, while packaging, lysis, integration, and lysogenic regulation were significant in NMDC data without pangenome enrichment beyond phylogenetic expectation. 3 This is an indirect bridge that assumes genus-level conservation of prophage content and had not been independently validated for prophage genes. 3
Provenance and discovery implications
The nmdc label is systematically overloaded rather than being a reliable dataset boundary, because the audit observed four predicted confusion modes across tenant placement, provenance, scale, and namesake identity. 1
This supports cross-tenant-data-bridging: NMDC-related resources are split between the nmdc and kbase tenants, while prefix-based inventory can fail to connect kbase.nmdc_* resources to NMDC. 1
This supports provenance-aware-resource-discovery: provenance, authority, scale, and snapshot currency need to be surfaced together rather than inferred from a database name. 1 The PHB cross-validation supports this requirement: its mapping depended on an explicit two-tier bridge from NMDC taxon columns to GTDB genera, rather than on the NMDC label alone. 2 The prophage analysis further supports it: NMDC was used as a derived metagenomic validation layer whose taxonomy matching and genus-level conservation assumption must be exposed alongside its correlations. 3
The audit inferred provenance classes from schema, table properties, tenant metadata, and prior project usage because no ingestion manifest was exposed in the catalog. 1
The interpretation that label overload causes sub-optimal resource selection remains a hypothesis rather than a directly measured user-behavior finding, because the audit did not directly observe users choosing the wrong resource. 1
The PHB study’s NMDC correlations with environmental variables were statistically significant but modest, with all reported absolute Spearman correlations below 0.12; because NMDC measurements were point-in-time values rather than direct measures of temporal variability, they provide cross-validation but do not by themselves establish the feast/famine interpretation. 2
The prophage study adds a distinct environmental-use case: its strongest NMDC correlations were packaging with pH (Spearman rho=0.519), all modules with pH (rho=0.474), all modules with temperature (rho=0.399), all modules with depth (rho=0.361), and all modules with total nitrogen (rho=0.333). 3 The positive pH association is explicitly a hypothesis about alkaline conditions or pH-linked ecology, not a causal conclusion, because the burden inference was indirect. 3
Related source
- NMDC Context Audit — Summary of the NMDC context audit, including resource provenance, tenant placement, scale, currency, access surfaces, and proposed remediation. 1
- Polyhydroxybutyrate Granule Formation Pathways — Distribution Across Clades and Environmental Selection — PHB pathway ecology analysis using NMDC metagenomic cross-validation and GTDB pangenome mappings. 2
- Prophage Gene Modules and Terminase-Defined Lineages Across Bacterial Phylogeny and Environmental Gradients — Prophage module ecology, environmental associations, TerL lineages, and NMDC metagenomic cross-validation. 3