What Metagen does

Metagen Inc. (株式会社メタジェン) is a Japanese biotechnology company founded in March 2015 as a spin-off from Keio University's Institute for Advanced Biosciences and Tokyo Institute of Technology, headquartered in Tsuruoka, Yamagata Prefecture, with additional R&D and business offices in Tokyo. The company develops and commercializes gut environment analysis technologies, anchored by its proprietary Metabologenomics® methodology — a registered-trademark approach that combines metabolomics and metagenomics to comprehensively evaluate gut bacterial function and metabolic profiles. Its flagship evaluation service MGNavi® classifies individual gut environments into discrete types to enable personalized dietary and healthcare recommendations, and a wholly-owned subsidiary, Metagen Therapeutics Corporation, pursues drug discovery related to the gut environment.

The company monetizes primarily through B2B professional services: an R&D Support Platform that takes partner companies from study design through result interpretation; a Product Development Support Business that helps corporate clients commercialize gut-health products; a Science PR Business that translates microbiome science into consumer messaging; and a Gut Environment Type Business Consulting service jointly delivered with Integrate Inc. Secondary B2C revenue comes via co-developed consumer products distributed through partner channels, notably Body Granola with Calbee (launched April 2024) and Inner Garden with Meiji (launched December 2024), along with subscription sales through partner e-commerce. Pricing is project-based and not publicly disclosed.

At the center of Metagen's go-to-market is the Gut Design Project (GDP), a co-creation community that has expanded to 38+ member companies across Japan's food, beverage, personal care, dairy, ingredients, distribution, and analytical instrumentation sectors — including Calbee, Meiji, Morinaga Milk Industry, Ajinomoto, Ito En, Kirin Holdings, Shiseido, Glico, Danone Japan, ITOCHU, and Agilent Technologies. GDP operates simultaneously as a sales channel, a joint product development platform, and a market-creation mechanism for the Gut Design® concept, supported by owned media (onakademy on note.com), annual awareness campaigns (Gut Design Months), closed B2B salons, and consumer webinars. The company employs 11-50 staff and is led by founder-CEO Fukuda Masatsugu (福田真嗣), a prominent gut microbiome researcher whose lab continues to publish in 2026.

Name

Metagen

Legal name

株式会社メタジェン

Website

https://metagen.co.jp

Company type

Private

Founded year

2015

Operating status

Operating

Headcount range

11–50 employees

Short description

Metagen is a Japanese gut-environment biotechnology company that applies proprietary Metabologenomics® analysis to provide gut type classification, R&D support, and personalized product co-development services to food, beverage, and healthcare corporations, including a 38+ member co-creation community anchored by Calbee, Meiji, and Kirin Holdings.

Ownership category

akta.pro rank

Product category

Microbiome Research and Personalized Healthcare Services

NAICS

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

SIC

In Vitro & In Vivo Diagnostic Substances (2835)

akta.pro primary industry

Microbiome & Metagenomics Services (HLAGANAH)

akta.pro secondary industry

Metabolomics & Lipidomics Services (HLAGANAG)

Keywords

• Gut microbiome research
• Microbiome analytics services
• Personalized nutrition platforms
• Metabolomics and metagenomics
• Co-creation biotech consulting

Headquarters

HQ city

Tsuruoka

HQ country

Japan

HQ region

Asia

Offices3 records

Markets served

GTM type

B2B

Offering type

Services

Cost components

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

Revenue model

1. Research and Development Support Services (研究開発支援プラットフォーム): Full-spectrum research support from study design consultation, execution, data analysis, interpretation, and business planning through their R&D support platform. Services span from academic research themes to product development support.
2. Product Development Support Services (商品開発支援事業): Support for developing products and services tailored to individual gut environments based on the Gut Design® concept, including logic design and business co-creation.
3. Science PR Services (サイエンスPR事業): Science communication and PR support services to help companies effectively communicate gut health science to consumers and stakeholders.
4. Business Consulting (腸内環境タイプ別ビジネスコンサルティング): In collaboration with Integrate Inc., provides gut environment type-based business consulting covering product development, business strategy, and marketing strategy implementation.
5. B2C Products (Co-development): Revenue from co-developed products with partner companies such as Body Granola with Calbee and Inner Garden with Meiji, through subscription and product sales.

Go-to-market motion3 records

Distribution channels4 records

Marketing channels6 records

Core offering

Metagen provides gut environment research and personalized healthcare services built on its proprietary Metabologenomics® analysis methodology. Its core offerings include MGNavi® gut environment evaluation, MG Diet Support, Gut Environment Type Business Consulting, and a comprehensive R&D Support Platform that helps partner companies design studies, analyze gut microbiota data, and develop personalized products. Through the Gut Design Project co-creation community, Metagen collaborates with 38+ member companies to commercialize science-based personalized food, beverage, and personal care products.

Product overview

Metagen is a gut environment research and technology company that operates a comprehensive product and service ecosystem centered on its proprietary Metabologenomics® methodology and the Gut Design® concept. The core offerings include MGNavi® (gut environment evaluation service), MG Diet Support (diet support service), and gut environment type business consulting. The company also provides a research support platform encompassing R&D consulting, product development support, and science PR services. Through the Gut Design Project co-creation community, Metagen collaborates with over 30 partner companies to develop personalized gut health products and services. Educational offerings include the Bactero-Igo board game, while onakademy serves as an owned media platform for disseminating gut health knowledge.

Differentiator

Problem solved

Functional benefit

Brands

• メタボロゲノミクス® (Metabologenomics): Comprehensive gut environment evaluation methodology using metabolomics and metagenomics analysis
• 腸内デザイン® (Gut Design)
• onakademy
• MG Members
• MGNavi®

Products and services

• MGNavi® (MGNavi®) Gut environment evaluation service that analyzes individual gut flora and metabolic substances to classify gut environment types, used as a foundation for personalized recommendations and consulting engagements.
• MG Diet Support Diet support service based on gut environment analysis that helps users understand their gut type and choose appropriate dietary approaches aligned to their gut environment classification.
• Gut Environment Type Business Consulting Consulting service developed jointly with Integrate Inc. that offers end-to-end support from product development considering individual gut environment types through business strategy and marketing strategy planning and implementation for client companies.
• R&D Support Platform Comprehensive platform supporting partner companies' research themes from test planning and execution to result analysis and output, leveraging Metagen's Metabologenomics® methodology across academic research and product development support.
• Research Value-Added Exploration Business Business service providing support for exploring research themes and adding value to research activities for partner companies, from study design consultation through execution and commercialization.
• Product Development Support Business Business service supporting the development of new products and services based on gut environment science, including product logic design and business co-creation for client companies in food, beverage, and personal care sectors.
• Science PR Business Business service providing science-based public relations support to help companies effectively communicate gut health science to consumers and stakeholders.
• Gut Design Project (GDP) Corporate co-creation community project that shares the Gut Design® concept and promotes market creation through collaborative R&D, product development, and awareness activities with 38+ member companies across food, beverage, and healthcare industries in Japan and ASEAN.
• Body Granola Personalized granola subscription service co-developed with Calbee and based on gut flora testing results, sold through Calbee's e-commerce platform to health-conscious consumers.
• Inner Garden Personalized gut-type skincare and personal care products launched by Meiji using Metagen's gut environment classification to match ingredients to individual gut types.

Quantifiable outcome

• Gut Design Project expanded to 38+ member companies and launched ASEAN chapter with 6 initial members by February 2026
• +1 more outcomes

Named customers6 records

Segments3 records

Ideal customer profiles2 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Feature4 records

Partnerships

Nine partnerships are on record, tiered core, major and flagship.

• Kirin Holdings (麒麟ホールディングス)coreStrategic or Co-development Partner · 1 March 2026Kirin Holdings entered joint research collaboration with Cowellnex and Metagen to develop gut microbiota tests and personalized food recommendation algorithms for Japanese individuals, expanding Kirin's science-based health and nutrition portfolio.
• Cowellnex Co., Ltd. (コウェルネックス)coreStrategic or Co-development Partner · 27 February 2026Joint venture between Kirin Holdings and Kyowa Kirin. Metagen and Cowellnex began joint research in February 2026 to develop new gut microbiota test items and personalized food recommendation algorithms based on high-precision gut microbiota data from Japanese individuals, accumulated over approximately 3 years through Cowellnex's MicroBio Me service using shotgun metagenomic analysis.
• Gut Design Project ASEAN Initial Members (6 companies)majorStrategic or Co-development Partner · 12 February 2026Expansion of Gut Design Project to ASEAN region starting with 6 initial companies from Japan and Singapore, marking the formal launch of gut design initiatives in Southeast Asia under the Gut Design Project ASEAN framework.
• Meiji (株式会社明治)flagshipStrategic or Co-development Partner · 1 December 2024Co-developed Inner Garden, personalized gut-type skincare/personal care products launched December 2024. Products are formulated based on matching ingredients to individual gut environment types identified through Metagen's proprietary classification technology.
• Calbee (カルビー)flagshipStrategic or Co-development Partner · 1 April 2024Metagen and Calbee co-developed Body Granola, a personalized granola subscription service based on gut flora testing results. This represents one of the first personalized food products in Japan based on gut environment classification, launched as part of the 'personalized food program' concept.
• Cykinso (サイキンソー)majorStrategic or Co-development Partner · 1 November 2023Capital and business partnership announced November 2023. Despite being competitors in some areas, the two companies announced collaboration to co-create the future of gut health, with the goal of enabling 8 billion people worldwide to benefit from personal gut environment information.
• Integrate Inc. (株式会社インテグレート)coreStrategic or Co-development Partner · 6 October 2022Strategic partnership for 'Gut Environment Type Business Consulting' service combining Metagen's gut environment classification technology with Integrate's marketing strategy expertise to support personalized product development and marketing strategy implementation for client companies.
• Keio University Institute for Advanced Biosciences (慶應義塾大学先端生命科学研究所)coreTechnology or IntegrationMetagen is a spin-off from Keio University's research institute located in Tsuruoka. The company was founded based on research developed at this institute and maintains close ties for continued research collaboration.
• Tokyo Institute of Technology (東京工業大学)coreTechnology or IntegrationMetagen was founded based on technology developed at Tokyo Institute of Technology. The company collaborated with TIT to develop the gut bacteria board game 'Bacteroigo' and maintains academic partnerships for research.

Scale indicators5 records

Recent moves6 records

Expansion highlights6 records

Direct peers

• Cykinso: Japan's leading direct-to-consumer gut flora testing service. Closely comparable to Metagen in gut-microbiome testing methodology and Japanese consumer market; also a capital and business partner since November 2023.
• Cowellnex: Joint venture between Kirin Holdings and Kyowa Kirin providing Japanese gut-microbiome testing via MicroBio Me. Operates in the same personalized gut-health space as Metagen and is now a joint research partner (February 2026).

Broad incumbents

• DayTwo: Global personalized nutrition platform using gut-microbiome analysis to recommend foods for blood-sugar control. A broader incumbent in microbiome-driven personalization with comparable scientific model and consumer proposition.
• Viome: US-based gut-microbiome testing and personalized nutrition company. Larger scale incumbent with comparable metatranscriptomic + personalized nutrition model; broader geographic reach than Metagen.
• Vedanta Biosciences: Clinical-stage microbiome therapeutics company developing defined bacterial consortia for immune-mediated diseases. Comparable R&D platform and drug-discovery direction to Metagen's therapeutics subsidiary.
• Seres Therapeutics: Public microbiome therapeutics company with an approved gut-microbiome-based therapy (VOWST). Established incumbent that defines the competitive landscape for Metagen Therapeutics' drug-discovery ambitions.
• Yakult Honsha: Japanese probiotic dairy giant with deep gut-microbiome science heritage and the Lactobacillus casei strain brand. Established incumbent whose consumer brand and R&D resources represent both a potential GDP-style partner and a competitive threat.

Emerging players

• Second Genome: Microbiome-focused drug discovery company using bacterial-derived molecules for inflammatory diseases. Comparable scale and therapeutic direction to Metagen Therapeutics but with broader pipeline scope.
• Finch Therapeutics (now Federated Therapeutics): Microbiome therapeutics company developing Full-Spectrum Microbiota and targeted bacterial cocktails. Direct therapeutic-platform competitor to Metagen Therapeutics.
• Eligo Bioscience: Paris-based synthetic-biology company developing engineered phage-based microbiome therapeutics. Adjacent technology approach to gut-microbiome drug discovery pursued by Metagen Therapeutics.

Market position

Strengths4 records

Weaknesses4 records

Competitive moat5 records

Key risks5 records

Key highlights6 records

Customer concentration

• Xx.com/browngems
• Facebookfacebook.com/metabologenomics
• LinkedInjp.linkedin.com/company/metabologenomics

Revenue estimate

Valuation estimate

Number of profiles

Profiles5 records

Subsidiaries1 record

Funding overview

Funding rounds

Investors

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Metagen