Center for Evolutionary Hologenomics

What Center for Evolutionary Hologenomics does

The Center for Evolutionary Hologenomics (CEH) is a non-profit academic research center established in 2021 at the University of Copenhagen's Faculty of Health and Medical Sciences, within the GLOBE Institute. It was founded as a Danish National Research Foundation Center of Excellence, directed by Professor Tom Gilbert, who introduced the hologenomic approach: the joint analysis of host genomes and microbial metagenomes, together with their combined functions, rather than studying each in isolation. CEH develops and applies multi-omics methods spanning genomics, metagenomics, metatranscriptomics, metabolomics, and epigenomics, supplemented by CRISPR and gut-on-a-chip experimental platforms, to investigate how host-microbiome interactions shape ecological and evolutionary processes across animals, plants, and food production systems.

The center's research is organized around multiple major externally funded projects, including the EU Horizon 2020 HoloFood project (focused on aquaculture and poultry production), FindingPheno (experimental de-extinction), 3D'omics (spatial multi-omics), the Earth Hologenome Initiative, and BarleyMicroBreed (barley genome assembly across 50 varieties with 12 partners across 10 countries). Core technical infrastructure includes genome-resolved metagenomics for reconstructing prokaryotic genomes, intestinal organoids derived from wild animals, and a series of educational offerings: the Host-Microbiota Multi-Omics course, a Computational Phage Genomics PhD course, and the Ancient DNA PhD Summer Course. CEH also operates an active science communication program including the Evolutionary Hologenomics Podcast (since 2021), the Microbial Connections Podcast (2025), YouTube content, school outreach, Science Cafés, and Nerd Nite Copenhagen sponsorship.

CEH is funded primarily through research grants: the Danish National Research Foundation as the core funder, supplemented by EU Horizon 2020 grants via multi-institution consortia. The center does not sell products or services; its commercial revenue is effectively zero and its operating budget consists entirely of grant inflows. Its customer base in a functional sense comprises academic collaborators, PhD/MSc/BSc students, the broader scientific community (via open-access publications in Nature Reviews Genetics, iScience, Cell Press, ISME Communications), and the Danish and international public via outreach programming. It is organizationally a child entity of the publicly owned University of Copenhagen and has no subsidiaries or M&A activity.

Name

Center for Evolutionary Hologenomics

Legal name

Center for Evolutionary Hologenomics - University of Copenhagen

Website

https://ceh.ku.dk

Company type

Private

Founded year

2021

Operating status

Operating

Headcount range

1–10 employees

Short description

The Center for Evolutionary Hologenomics is a non-profit University of Copenhagen research center that develops multi-omics and computational methods to jointly study host genomes and microbial metagenomes, serving academic researchers, students, and the public through funded research and education.

Ownership category

akta.pro rank

Product category

Academic Research Services

NAICS

Research and Development in Biotechnology (except Nanobiotechnology) (541714)

SIC

Services-Commercial Physical & Biological Research (8731)

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), Microbiome Analytics, Sequencing & Bioinformatics Platforms (HLAAAFAI), Public Health Genomics & Sequencing (WGS/Metagenomics) Networks (HLAJAIAK)

Keywords

• Hologenomics research
• Multi-omics integration
• Host-microbiome analysis
• Evolutionary biology research
• Academic research center

Headquarters

HQ city

Copenhagen

HQ country

Denmark

HQ region

Europe

Offices1 record

Markets served

GTM type

B2B

Offering type

Services

Cost components

Personnel, Technology or R&D, Operations, Infrastructure, Marketing or Sales

Revenue model

1. Research Grants and Funding: Funded by the Danish National Research Foundation for basic research at the Faculty of Health and Medical Sciences, University of Copenhagen. Also receives EU Horizon 2020 funding for projects like HoloFood, FindingPheno, and 3D'omics.

Go-to-market motion1 record

Distribution channels1 record

Marketing channels11 records

Core offering

The Center for Evolutionary Hologenomics is an academic research center that conducts fundamental research applying a hologenomic approach to jointly analyze host genomes and microbial metagenomes. It develops state-of-the-art 'omics and computational techniques to study host-microbiome interactions, offers graduate and PhD-level educational courses, and engages in science communication through podcasts, public events, and school outreach programs.

Differentiator

Problem solved

Functional benefit

Products and services

• Hologenomics Research
• Host-Microbiota Multi-Omics Course
• Computational Phage Genomics Course
• Ancient DNA PhD Summer Course
• Evolutionary Hologenomics Podcast
• Microbial Connections Podcast Series

Quantifiable outcome

• Published landmark papers in Nature Reviews Genetics and iScience on hologenomics

Named customers2 records

Segments4 records

Ideal customer profiles3 records

Technology focussed No

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Feature5 records

Partnerships

Eleven partnerships are on record, tiered core, major and minor.

• European Bioinformatics Institute (EMBL-EBI)coreStrategic or Co-development Partner · 1 September 2022Partner in HoloFood project and co-organizer of training course in Organisation and Utilisation of Hologenomic Datasets. Provides expertise in omic data repositories including MGnify, European Nucleotide Archive, MetaboLights, and BioSamples.
• HoloFood ConsortiumcoreStrategic or Co-development PartnerEU Horizon 2020 funded project (grant agreement No 817729) focused on applying hologenomics to food production. Partners include UCPH, EMBL-EBI, NTNU, AU, EHU/UPV, and others from 10 different countries.
• Copenhagen Plant Science CentremajorStrategic or Co-development PartnerCollaboration on plant hologenomics research with Assistant Professor Chris Barnes leading the Plant Hologenome group. Aims to promote collaborations between plant scientists across University of Copenhagen departments.
• Copenhagen ZoomajorStrategic or Co-development PartnerCollaboration on cotton-top tamarin conservation research through Linett Rasmussen's PhD project combining historic-modern DNA analysis for species conservation efforts.
• FindingPheno ProjectcoreStrategic or Co-development PartnerEU Research and Innovation Actions project awarded to Associate Professor Shyam Gopalakrishnan and colleagues. Project runs from September 2022 to February 2025.
• Earth Hologenome InitiativecoreStrategic or Co-development PartnerInternational initiative led by CEH researchers including postdoc Aoife Leonard, focused on mapping hologenomes across life on Earth.
• BarleyMicroBreed ProjectmajorStrategic or Co-development PartnerEuropean Commission funded project with 12 partners from 10 countries. CEH team led by Christopher Barnes will assemble genomes of 50 barley varieties.
• 3D'omics ProjectcoreStrategic or Co-development PartnerEU Horizon 2020 project led by Associate Professor Antton Alberdi focusing on spatial and integrated multi-omics approaches. Includes training course development.
• Rob Dunn (North Carolina State University)majorStrategic or Co-development PartnerProfessor at North Carolina State University and GLOBE Institute, author of books on fermentation and food. Collaborates on public engagement events including BLOOM x IDA symposium.
• Wild Animal Microbiome Evolution (WAME)majorStrategic or Co-development PartnerSpecial Topic Network funded by European Society for Evolutionary Biology. CEH participates in virtual symposium series on longitudinal microbiome dynamics.
• Medicinsk MuseionminorStrategic or Co-development PartnerCollaboration on Sensing Holobiont - art, food and science event exploring the holobiont concept through sensory experiences.

Scale indicators3 records

Recent moves6 records

Expansion highlights6 records

Emerging players

• Second Genome: Second Genome applies microbiome analytics and multi-omics to drug discovery and therapeutics. Comparable in multi-omics methodology but oriented toward commercial translation, offering a reference point for CEH's potential commercialization paths.
• CosmosID: CosmosID provides commercial microbiome bioinformatics and metagenomics analysis services. It operates in an adjacent commercial layer to CEH's academic multi-omics capability and serves similar research customers.
• Phase Genomics: Phase Genomics is a technology partner that presented research at CEH (Hi-C for phage-microbe interactions). It provides commercial proximity ligation and metagenomics tools that complement CEH's holobiont research workflows.

Broad incumbents

• Wellcome Sanger Institute: Sanger is a large-scale genomic and metagenomic research center producing reference datasets and computational tools for microbiome science. Comparable to CEH in pursuing foundational genomics-to-microbiome research but with vastly larger headcount and funding.
• Broad Institute (Microbiome Program): Broad's microbiome and microbial sciences programs run large-scale multi-omics, metagenomics, and computational biology in a similar academic/non-profit model. Comparable in research mission (integrative host-microbiome 'omics) and modality, with much larger scale.
• Joint Genome Institute (JGI): JGI is a public user facility specializing in large-scale genome sequencing and metagenomics, including genome-resolved metagenomics closely aligned with CEH's analytical methods. It serves a global research community analogous to CEH's base.

Direct peers

• European Bioinformatics Institute (EMBL-EBI): EMBL-EBI is CEH's core partner on HoloFood and co-organizer of the hologenomic datasets training course. Both operate at the intersection of omics data generation, bioinformatics services, and public data infrastructure (MGnify, ENA, MetaboLights, BioSamples) for the microbiome/genomics research community.
• Max Planck Institute for Evolutionary Biology: Max Planck's Plön institute conducts foundational research in evolutionary biology, host-microbe interactions, and phylogenomics. Comparable academic research center pursuing overlapping questions on host-microbiome coevolution.
• SDSC/UC San Diego Center for Microbiome Innovation: UC San Diego's Center for Microbiome Innovation is a large academic hub running multi-omics, microbiome, and host-microbe interaction research. Comparable in mission (cross-disciplinary microbiome center) and modality (multi-omics integration), but US-based and larger.

Others

• DNAnexus: DNAnexus is a cloud platform for genomic and biomedical data, providing infrastructure similar to what CEH leverages via EMBL-EBI. Comparable as enabling data infrastructure for multi-omics research, though not a research competitor.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat4 records

Key risks6 records

Key highlights6 records

Customer concentration

• Xx.com/evohologen
• YouTubeyoutube.com/playlist?list=PLcxy6kYBP46gSzbxIr9eVeiLyPbh4SIGN
• LinkedInlinkedin.com/company/center-for-evolutionary-hologenomics

Revenue estimate

Valuation estimate

Number of profiles

Profiles10 records

Funding overview

Funding rounds

Investors

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M&A

Investments

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