Center for Microbiome Innovation

What Center for Microbiome Innovation does

The Center for Microbiome Innovation (CMI) is a university research center administered by UC San Diego's Jacobs School of Engineering that coordinates interdisciplinary microbiome research across more than 130 affiliated faculty members. Founded to accelerate microbiome science through structured industry-academia collaboration, the center functions as an organized platform connecting corporate partners with UC San Diego's microbiome research capabilities in clinical medicine, bioengineering, computer science, biological sciences, and data sciences. Leadership comprises Faculty Director Rob Knight (Professor of Pediatrics, Bioengineering, Computer Science & Engineering, and Data Science; National Academy of Engineering member elected 2024) and Executive Director Andrew Bartko (Professor of Practice in Bioengineering). The center pursues five stated objectives: leveraging UC San Diego's interdisciplinary expertise, developing methods for manipulating microbiomes for human and environmental health, generating large-scale public multi-omic data, building the talent and technology workforce for the microbiome field, and creating integrated academia-industry learning opportunities.

CMI's core technology stack spans metagenomics, metabolomics, metatranscriptomics, and high-performance computing environments supporting AI and machine learning methodologies. Key proprietary and co-developed capabilities include The Microsetta Initiative (a global citizen science platform for human microbiome mapping incorporating dietary questionnaires and strain-level metagenomic sequencing), Compositional Tensor Factorization (CTF, published in Nature Biotechnology as a context-aware dimensionality reduction method for microbial community dynamics), advanced host filtration workflows using T2T-CHM13v2.0 complete human reference genomes to eliminate false sex biases in metagenomic data, SourceTracking for environmental microbial source contribution analysis, and a transformer-based AI model published in Nature Communications that estimates human age from microbiome composition with 28% greater accuracy than prior methods. Machine learning models also achieve over 90% accuracy in detecting liver disease from gut bacterial signatures and strong country-of-origin prediction from gut bacteria alone. The center maintains research collaborations with IBM Research on the AI for Healthy Living (AIHL) initiative focused on knowledge base construction for human microbiome-disease associations.

The center operates a partnership-driven revenue model in which industry partners gain access to sampling services, multi-omics technologies, computational infrastructure, and faculty expertise in exchange for individually negotiated partnership fees that are not publicly disclosed. Named industry partners span consumer health (Haleon), food and nutrition (Danone Nutricia Research, Nestlé, Sanitarium Health Food Company, Metagenics), pharmaceuticals (Pfizer, Hologic), beauty and cosmetics (L'Oréal, Evonik Industries), life sciences technology (Complete Genomics, eCyte, Millipore Sigma), and technology (IBM Research, Panasas). Additional funding flows from federal grants (a $7.3M U.S. Department of Energy award in 2020 for bioenergy crop research is the most prominent disclosed grant) and institutional support from UC San Diego. CMI also functions as a training platform for graduate students and postdoctoral researchers working in interdisciplinary teams, embedding workforce development into its service offering.

Name

Center for Microbiome Innovation

Legal name

University of California San Diego Center for Microbiome Innovation

Website

https://cmi.ucsd.edu

Company type

Private

Founded year

2015

Operating status

Operating

Headcount range

51–100 employees

Short description

The Center for Microbiome Innovation (CMI) is a UC San Diego research center coordinating interdisciplinary microbiome research across 130+ affiliated faculty. It operates as an industry-academia partnership platform connecting corporate partners with expertise in metagenomics, metabolomics, computational biology, and AI to advance human and environmental health.

Ownership category

akta.pro rank

Product category

Microbiome Research Services

NAICS

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

SIC

Services-Commercial Physical & Biological Research (8731)

akta.pro primary industry

Microbiome Analytics, Sequencing & Bioinformatics Platforms (HLAAAFAI)

akta.pro secondary industry

Microbiome & Metagenomics Services (HLAGANAH)

Keywords

• Microbiome research services
• Multi-omics analysis
• Industry-academic partnerships
• Computational biology tools
• Citizen science platforms

Headquarters

HQ city

La Jolla

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Services

Cost components

Personnel, Technology or R&D, Operations, Infrastructure

Revenue model

1. Industry Partnership Programs: CMI generates revenue through structured industry partnership programs where companies pay to collaborate with UC San Diego microbiome researchers. Partners gain access to world-class expertise, sampling services, -omics technologies, and data analysis capabilities.

Go-to-market motion2 records

Distribution channels3 records

Marketing channels6 records

Core offering

CMI operates as an academic-industry partnership center that delivers coordinated microbiome research services to corporate partners, including microbiome sampling, multi-omics technologies (metagenomics, metabolomics, metatranscriptomics), high-performance computing, AI/ML-based data analysis, and access to UC San Diego's 130+ faculty researchers. The center facilitates joint research programs, citizen science platforms like The Microsetta Initiative, and computational tools for partners in pharmaceuticals, consumer health, food and nutrition, cosmetics, and life sciences.

Product overview

The Center for Microbiome Innovation (CMI) is a research center at UC San Diego that provides a coordinated platform of microbiome research services rather than a single commercial product. Core offerings include The Microsetta Initiative (a citizen science research platform), Microbiome Sample Processing Services (laboratory and computational facilities for -omics analysis), and various research initiatives like AI for Healthy Living (AIHL) and The Human Diets and Microbiome Initiative (THDMI). CMI also develops computational tools including SourceTracking and Compositional Tensor Factorization (CTF) for microbiome analysis. The center facilitates industry partnerships to accelerate microbiome discovery through joint research programs and access to specialized scientific and technological capabilities.

Differentiator

Problem solved

Functional benefit

Brands

• The Human Diets & Microbiome Initiative (THDMI): A research initiative focused on mapping the human microbiota across different countries and understanding diet's impact on the human gut microbiome.
• The Microsetta Initiative
• Artificial Intelligence for Healthy Living (AIHL)

Quantifiable outcome

• 28% greater accuracy in predicting human age from microbial communities using transformer technology
• +2 more outcomes

Named customers10 records

Segments2 records

Ideal customer profiles2 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

AI capability8 records

Feature5 records

Partnerships

14 partnerships are on record, tiered strategic, core and standard.

• eCytestrategicTechnology or Integration · 24 March 2026Partnership with eCyte, Inc., a leader in single-cell metabolic phenotyping, to empower CMI researchers with novel tools for profiling microbiome metabolic function at single-cell resolution.
• HaleoncoreStrategic or Co-development Partner · 22 April 2025Partnership with global consumer health company Haleon to accelerate development of innovative microbiome-based solutions for human health and well-being. Unites CMI's world-class microbiome expertise with Haleon's state-of-the-art science and clinical capabilities and global portfolio of brands across OTC medicines to vitamins, minerals and supplements (VMS). Focus areas include healthy aging, cardiovascular health, cognitive health, women's health and general well-being.
• Complete GenomicscoreTechnology or Integration · 9 January 2025Partnership with genomics sequencing solutions provider Complete Genomics to accelerate CMI's innovative projects through next generation sequencing technologies and spatial genomics workflows. Complete Genomics provides DNBSEQ sequencing platforms (G800 and T7) and STOmics portfolio. CMI and Complete Genomics planning monthly workshops on UC San Diego campus.
• L'OréalcoreStrategic or Co-development Partner · 22 September 2020Partnership with world's leading beauty company L'Oréal (founded 1909, 110+ years of scientific innovation heritage) as CMI's first cosmetic industry partner. Leverages L'Oréal's 15 years of microbiome research and provides access to latest studies and advanced technologies for skin microbiome research influencing future skincare products.
• NestlécoreStrategic or Co-development Partner · 25 November 2019Partnership to increase understanding of microbiome's impact on human health and accelerate development of innovative nutritional solutions promoting health and wellbeing. Builds on CMI's world-class microbiome expertise complementing Nestlé's nutrition research capabilities.
• IBM ResearchcoreStrategic or Co-development Partner · 2 October 2019AI for Healthy Living (AIHL) collaboration focused on constructing knowledge bases for human microbiome-disease associations. IBM and UC San Diego exploring challenges in staying up-to-date with latest discoveries in human microbiome research where thousands of articles are published each year.
• Evonik IndustriescoreStrategic or Co-development Partner · 28 August 2019Three-year partnership to explore skin microbiome model systems for cosmetic raw materials. Evonik's scientists will use CMI research to enhance Care Biotics technology platform for developing commercial microbiotic products. Target is improvement of existing cosmetic raw materials and potential discovery of new ones for promoting healthier skin microbiome.
• Danone Nutricia ResearchcoreStrategic or Co-development Partner · 31 January 2019Partnership to advance understanding of the connection between diet and human gut through The Human Diets & Microbiome Initiative (THDMI). Goals include collecting human microbiota samples across different countries for mapping with more global population representation and higher sequencing resolution, and improving collection of dietary habits to increase knowledge of microbiome's impact on human health.
• PfizerstandardStrategic or Co-development PartnerIndustry partner for microbiome research collaborations.
• HologicstandardStrategic or Co-development PartnerIndustry partner for microbiome research collaborations.
• MetagenicsstandardStrategic or Co-development PartnerIndustry partner for microbiome research collaborations.
• Millipore SigmastandardTechnology or IntegrationIndustry partner for microbiome research collaborations.
• Sanitarium Health Food CompanystandardStrategic or Co-development PartnerIndustry partner for microbiome research collaborations.
• PanasasstandardTechnology or IntegrationIndustry partner providing HPC storage solutions. CMI added two petabytes of Panasas HPC storage for COVID-19 research and genomic data sequencing.

Scale indicators4 records

Recent moves6 records

Expansion highlights5 records

Broad incumbents

• Seres Therapeutics: Clinical-stage commercial microbiome therapeutics company developing defined bacterial consortia — overlaps with CMI on microbiome-based therapeutic translation and is a likely destination for CMI-derived translational research.
• Broad Institute: Large-scale academic biomedical research institute (MIT/Harvard) with significant microbiome and metagenomics programs, computational biology platforms, and industry partnerships — overlaps with CMI on multi-omic data generation and analytical tooling.

Emerging players

• CosmosID: Commercial provider of microbiome sequencing services and bioinformatics tools for industry and academic clients — directly competes with CMI's sample-processing and bioinformatics offering on speed, cost, and turnkey delivery.
• Vedanta Biosciences: Clinical-stage company engineering defined bacterial consortia for immune-mediated diseases — adjacent emerging player in microbiome therapeutics that competes for industry R&D partnerships in the same space.
• Second Genome: Microbiome-focused drug-discovery company combining multi-omic profiling with computational biology — comparable in its use of AI/ML on microbiome data and ability to attract industry collaborations.

Direct peers

• MIT Center for Microbiome Informatics and Therapeutics (CMIT): MIT-based interdisciplinary research center focused on microbiome science, computational methods, and therapeutic translation — the closest academic peer to CMI in mission, structure, and industry-partnership model.
• Baylor College of Medicine — Alkek Center for Metagenomics and Microbiome Research: Academic center providing microbiome sample processing, sequencing, and bioinformatics services to academic and industry clients — directly comparable in service portfolio to CMI's Microbiome Sample Processing Services.
• Mayo Clinic Microbiome and Microbiota Program: Clinical-academic microbiome program within Mayo Clinic conducting multi-omic research and translational work across human disease — comparable in disease-focused microbiome science and partnership engagement.
• Stanford Microbiome Group: Interdisciplinary Stanford group conducting human microbiome research and computational method development — overlaps with CMI on AI/ML applied to microbiome data and translational programs.
• University of Pennsylvania — Center for Microbiome Research: Penn-led academic microbiome center performing multi-omic analysis, hosting citizen-science cohorts, and partnering with industry — operates an analogous research-platform-plus-industry-partnership model.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat4 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/CMIdigest
• Facebookfacebook.com/CMIdigest
• LinkedInlinkedin.com/company/cmi-ucsandiego

Revenue estimate

Valuation estimate

Number of profiles

Profiles4 records

Funding overview

Funding rounds

Investors

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M&A

Investments

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Frequently asked questions about Center for Microbiome Innovation