National Microbiome Data Collaborative

Scientific Data Infrastructuremicrobiomedata.org

The National Microbiome Data Collaborative is a U.S. Department of Energy-funded scientific data infrastructure initiative, operated by Lawrence Berkeley and Pacific Northwest National Laboratories, that provides free, FAIR-compliant multi-omics microbiome data sharing tools (Data Portal, Submission Portal, API) to academic researchers, DOE User Facility users, and federal agency researchers worldwide.

Company typePrivate
Founded2020
HeadquartersBerkeley, United States
Headcount1–10
GTM typeB2B
OfferingSoftware

What National Microbiome Data Collaborative does

The National Microbiome Data Collaborative (NMDC) is a U.S. Department of Energy-funded scientific data infrastructure initiative that enables FAIR-compliant (Findable, Accessible, Interoperable, Reusable) sharing of multi-omics microbiome data. Operated under Lawrence Berkeley National Laboratory (LBNL) with Pacific Northwest National Laboratory (PNNL) as a partner institution, the NMDC is funded through the DOE Office of Science's Genomic Science Program under BER contracts DE-AC02-05CH11231 and DE-AC05-76RL01830. The program's core product suite comprises three integrated components: the Data Portal (a graphical web interface for discovering and downloading standardized multi-omics data), the Submission Portal (a LinkML and DataHarmonizer-driven web interface for contributing study and biosample metadata with real-time validation), and the Runtime API (RESTful programmatic access at api.microbiomedata.org). Supporting products include standardized bioinformatics workflows for metagenomes, metatranscriptomes, metaproteomes, and metabolomics data processing on HPC systems, plus the Field Notes mobile app for field metadata capture (now discontinued for active development as of January 2026).

The NMDC serves academic microbiome researchers, DOE User Facility users (JGI and EMSL), federal agency researchers (USGS, FDA, NIST, NOAA), and early-career researchers, with all resources provided free of charge under a government-funded, non-commercial model. The technology stack is built on linked data and the Linked Data Modeling Language (LinkML) schema framework, with ontology mappings to community standards (MIxS, EnvO, GOLD, PROV, PSI, MSI) and integrations with the ORCID identity system for authenticated access. Distribution is global and self-serve, with adoption driven by community-led engagement through the Champions Program (100+ advocates across institutions) and cohort-based Ambassador Programs (2021–2025), peer-reviewed publications, conference participation, and a quarterly newsletter. Recent restructuring signals — discontinuation of NMDC EDGE, suspension of Field Notes development, and paused acceptance for the Champions Program — indicate a 2026 contraction in program scope, though core infrastructure remains operational.

National Microbiome Data Collaborative firmographics

Firmographics

Name: National Microbiome Data Collaborative
Legal name: Lawrence Berkeley National Laboratory
Website: https://microbiomedata.org
Company type: Private
Founded year: 2020
Operating status: Operating
Headcount range: 1–10 employees
Short description: The National Microbiome Data Collaborative is a U.S. Department of Energy-funded scientific data infrastructure initiative, operated by Lawrence Berkeley and Pacific Northwest National Laboratories, that provides free, FAIR-compliant multi-omics microbiome data sharing tools (Data Portal, Submission Portal, API) to academic researchers, DOE User Facility users, and federal agency researchers worldwide.
Ownership category
akta.pro rank

National Microbiome Data Collaborative industry classification

Industry

Product category: Scientific Data Infrastructure
NAICS: Research and Development in Biotechnology (except Nanobiotechnology) (541714), Scientific Research and Development Services (5417), Computer Systems Design and Related Services (54151)
SIC: Services-Commercial Physical & Biological Research (8731), Services-Prepackaged Software (7372), Services-Computer Processing & Data Preparation (7374)
akta.pro primary industry: Bioinformatics & Multi-omics Analysis Software (HLAGAJAD)
akta.pro secondary industries: Bioinformatics, Multi-Omics Data Analysis & Interpretation Services (HLAGANAI), Microbiome & Metagenomics Services (HLAGANAH)

Keywords

Microbiome data infrastructure
Multi-omics data management
FAIR data sharing
Bioinformatics workflows
Scientific data repositories

Where National Microbiome Data Collaborative is headquartered

Location

Headquarters

HQ city: Berkeley
HQ country: United States
HQ region: North America

Offices2 records

Markets served

National Microbiome Data Collaborative business model

Business model

GTM type: B2B
Offering type: Software
Cost components: Personnel, Technology or R&D, Infrastructure, Operations

Revenue model

Government Funding: The NMDC is funded by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL) and DE-AC05-76RL01830 (PNNL). All NMDC products and services are provided free of charge to the research community as a government-funded scientific resource.

Pricing tiers

Model	Billing	Price
Freemium	Monthly	Free Access

Go-to-market motion3 records

Distribution channels7 records

Marketing channels9 records

National Microbiome Data Collaborative product offering

Product offering

Core offering

The NMDC provides a free, community-driven distributed data infrastructure for microbiome science, comprising a Data Portal for discovering standardized multi-omics data, a Submission Portal with template-driven metadata validation, and a Runtime API for programmatic access. Standardized bioinformatics workflows process metagenomes, metatranscriptomes, metaproteomes, and metabolomics data into FAIR-compliant, reproducible data products for the global research community.

Product overview

The National Microbiome Data Collaborative (NMDC) is a distributed data infrastructure initiative comprising three core integrated products: the Data Portal (https://data.microbiomedata.org/) for data discovery and access, the Submission Portal (https://data.microbiomedata.org/submission/home) for metadata contribution, and the API (https://api.microbiomedata.org/docs) for programmatic access. The ecosystem also includes the Field Notes mobile app for field data collection and standardized bioinformatics workflows for multi-omics data processing. NMDC supports microbiome research by connecting data, people, and ideas through community-driven resources that adhere to FAIR (Findable, Accessible, Interoperable, Reusable) principles. The organization also operated community engagement programs (Ambassador and Champions programs) to promote data stewardship and metadata standards adoption, though these are no longer actively maintained.

Differentiator

Problem solved

Functional benefit

Brands

NMDC: Abbreviated name for the National Microbiome Data Collaborative
NMDC EDGE
NMDC Field Notes

Products and services

NMDC Data Portal

Quantifiable outcome

Ambassadors are required to host at least 1 workshop per year, reaching their immediate research communities
+2 more outcomes

Companies that use National Microbiome Data Collaborative

Customer profile

Named customers3 records

Segments4 records

Ideal customer profiles3 records

National Microbiome Data Collaborative technology and API

Technology

Technology focussed Yes

API detail

Has API: Yes
API docs
API detail

Core technology

AI maturity

App detail

Integration6 records

AI capability3 records

Feature6 records

National Microbiome Data Collaborative partnerships and signals

Strategic signal

Partnerships

14 partnerships are on record, tiered core and minor.

Joint Genome Institute (JGI)coreStrategic or Co-development PartnerDOE User Facility and key partner for genome and metagenome sequencing. The NMDC collaborates with JGI to support integration of multi-omics data generated at JGI, particularly through the FICUS Program. Submission Portal is designed to be compliant with JGI sample submission requirements.
Environmental Molecular Sciences Laboratory (EMSL)coreStrategic or Co-development PartnerDOE User Facility for molecular sciences research. NMDC supports data integration from EMSL's proteomics and metabolomics capabilities. Submission Portal accommodates EMSL sample submission requirements and EMSL Data Policies including embargo information.
Genomic Standards Consortium (GSC)coreStrategic or Co-development PartnerOpen-membership organization developing standards for sequence data. NMDC leverages GSC's MIxS standard and environmental extensions for biosample metadata. NMDC team participates in GSC's Compliance and Interoperability Group (CIG) to improve metadata elements.
DataHarmonizer (Centre for Infectious Disease Genomics and One Health, Simon Fraser University)coreTechnology or IntegrationOngoing open-source collaboration where NMDC leverages DataHarmonizer template-driven spreadsheet application for harmonizing, validating, and transforming sequence contextual data. DataHarmonizer supports real-time validation in the Submission Portal.
FAIR Microbiome Implementation Network (IN)coreStrategic or Co-development PartnerInternational initiative under GO FAIR to advance FAIR principles in microbiome research. NMDC developed this IN to connect with the international microbiome standards community and align efforts with GO FAIR community.
FAIRsharingminorStrategic or Co-development PartnerNMDC is registered with FAIRsharing, which provides journals with a curated source of recommended repositories. This registration supports data policy compliance and increases visibility of NMDC as a trusted repository.
Environment Ontology (EnvO)coreStrategic or Co-development PartnerCommunity-led ontology representing environmental entities such as biomes, environmental features, and environmental materials. NMDC collaborates with EnvO to ensure consistent environmental classification in biosample metadata.
Genomes OnLine Database (GOLD)coreStrategic or Co-development PartnerDOE JGI-hosted repository of genome, metagenome, and metatranscriptome projects with associated metadata. NMDC supports GOLD's five-level ecosystem classification system and collaborates to curate and update shared study and metadata information.
GO FAIRminorStrategic or Co-development PartnerInternational organization advancing FAIR data practices. NMDC participates through the FAIR Microbiome IN to synergize efforts with the broader GO FAIR community.
Lawrence Berkeley National LaboratorycoreStrategic or Co-development PartnerPrimary operating institution for NMDC under DOE BER contract. Hosts NMDC team members and provides HPC infrastructure for bioinformatics workflows. Copyright holder for NMDC brand and resources.
Pacific Northwest National LaboratorycoreStrategic or Co-development PartnerPartner institution for NMDC under DOE BER contract. Contributes scientific expertise to NMDC program activities including workflow development and community engagement.
Proteomics Standards Initiative (PSI)minorStrategic or Co-development PartnerStandards body developing controlled vocabularies and standards for proteomics data. NMDC supports PSI standards for metaproteomics data types in the Submission Portal.
Metabolomics Standards Initiative (MSI)minorStrategic or Co-development PartnerStandards body for metabolomics data. NMDC supports MSI standards for mass spectrometry data types including ionization mode, mass resolution, and scan rate in metadata capture.
STREAMS (Standards for Technical Reporting in Environmental and host-Associated Microbiome Studies)minorStrategic or Co-development PartnerNMDC is working with the broader research community to develop STREAMS guidelines based on the STORMS checklist. These guidelines will provide standardized checklists for environmental and host-associated microbiome researchers.

Scale indicators4 records

Recent moves6 records

Expansion highlights7 records

National Microbiome Data Collaborative competitors and assessment

Company assessment

Emerging players

MetaboLights: EMBL-EBI's database for metabolomics experiments and associated metadata. Comparable as a public metabolomics repository aligned with MSI standards — directly relevant to one of NMDC's supported omics layers.
GNPS (Global Natural Products Social Molecular Networking): UC San Diego community-driven mass spectrometry knowledge platform widely used for metabolomics and natural products analysis. Comparable to NMDC as a community-driven platform for microbiome-related molecular data, with overlapping metabolomics use cases.
PRIDE: EMBL-EBI's proteomics data repository, particularly relevant for metaproteomics — one of the omics types NMDC supports. Comparable as a standards-driven public proteomics data infrastructure with PSI integration.

Broad incumbents

European Nucleotide Archive (ENA): EMBL-EBI's primary nucleotide sequence repository hosting raw sequencing reads and assemblies. Comparable to NMDC as a foundational public multi-omics data archive, but with a broader mandate across all of genomics, not just microbiomes.
NCBI Sequence Read Archive (SRA): NIH/NCBI's primary repository for raw sequencing data, including metagenomic studies. Comparable as the dominant public archive for microbiome sequencing reads, though it lacks NMDC's standardized multi-omics processing layer.

Direct peers

MGnify: EMBL-EBI's microbiome analysis platform that provides standardized assembly, taxonomic, and functional analysis of microbiome sequencing data. Closely comparable to NMDC as a community-facing microbiome data resource, though NMDC extends further into metaproteomics and metabolomics.
CyVerse: NSF-funded cyberinfrastructure for life sciences providing data management, computing, and training for life science research. Comparable to NMDC as a public-sector life science data infrastructure, though broader in scope beyond microbiome science.
Joint Genome Institute GOLD / IMG: DOE JGI's repository of genome, metagenome, and metatranscriptome sequencing projects with associated metadata. Directly comparable as a DOE-funded microbiome/genome data resource, and an explicit integration partner of NMDC.
DOE Systems Biology Knowledgebase (KBase): DOE-funded computational platform for systems biology that integrates data, tools, and workflows for microbial and plant research. Comparable to NMDC as a DOE-backed bioinformatics infrastructure serving the same scientific community.
Qiita: Open-source microbiome study management and analysis platform from UC San Diego. Directly comparable to NMDC as a community-driven microbiome data and analysis resource for academic researchers.

Market position

Strengths4 records

Weaknesses4 records

Competitive moat5 records

Key risks5 records

Key highlights6 records

Customer concentration

National Microbiome Data Collaborative financial estimates

Financial estimate

Revenue estimate

Valuation estimate

National Microbiome Data Collaborative leadership team

Management profile

Number of profiles

National Microbiome Data Collaborative funding detail

Funding detail

Funding overview

Funding rounds

Investors

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National Microbiome Data Collaborative M&A and investment

M&A and investment

M&A

Investments

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Frequently asked questions about National Microbiome Data Collaborative

What does National Microbiome Data Collaborative do?

Is National Microbiome Data Collaborative a public or private company?

National Microbiome Data Collaborative is a private company. It is classified as state government owned and is currently operating.

When was National Microbiome Data Collaborative founded?

National Microbiome Data Collaborative was founded in 2020. It employs 1 to 10 people.

Where is National Microbiome Data Collaborative based?

National Microbiome Data Collaborative is headquartered in Berkeley, United States, in the North America region.

How does National Microbiome Data Collaborative make money?

One revenue line is on record: government Funding.

Who are National Microbiome Data Collaborative's main competitors?

Emerging players on record are MetaboLights, GNPS (Global Natural Products Social Molecular Networking) and PRIDE. Broad incumbents are European Nucleotide Archive (ENA) and NCBI Sequence Read Archive (SRA). Direct peers are MGnify, CyVerse, Joint Genome Institute GOLD / IMG, DOE Systems Biology Knowledgebase (KBase) and Qiita.

Does National Microbiome Data Collaborative have an API?

Yes. Programmatic access to standardized microbiome metadata and data through the NMDC Runtime API. The API enables developers to programmatically query and retrieve microbiome data from the Data Portal. Developer documentation is at api.microbiomedata.org/docs.

What industry is National Microbiome Data Collaborative in?

National Microbiome Data Collaborative's product category is Scientific Data Infrastructure. Its primary akta.pro industry code is HLAGAJAD, Bioinformatics & Multi-omics Analysis Software, with a secondary code of HLAGANAI, Bioinformatics, Multi-Omics Data Analysis & Interpretation Services. Its NAICS code is 541714 and its SIC code is 8731.