Metabologenomics

What Metabologenomics does

Metabologenomics (株式会社メタジェン, branded Metagen) is a Japanese gut-microbiome science company founded on March 18, 2015 and headquartered in the Tsuruoka Metropolitan Campus, Yamagata Prefecture, with a Tokyo R&D center and Tokyo office. The company was spun out of research conducted at the Keio University Institute for Advanced Biosciences and is led by CEO Shinji Fukuda (福田真嗣), a visiting professor at the same institute. Metagen's core technology is Metabologenomics®, a proprietary integrated analytical methodology that combines metagenome analysis (identification of gut bacterial species and functional genes) with metabolome analysis (measurement of metabolic substances produced by those bacteria) to produce a comprehensive evaluation of individual gut environments. This is paired with 'Gut Typing' stratification technology, which classifies individuals into gut types and matches them to effective ingredients and products.

The company operates four interlocking revenue streams. (1) Research Value-Added Exploration Services (研究付加価値探索事業) provide end-to-end study design, execution, analysis, and business proposal support to enterprise R&D teams. (2) Product Development Support Services (商品開発支援事業) cover gut-type-specific product logic design, ingredient selection, and go-to-market support. (3) Science PR Services (サイエンスPR事業) help partners communicate gut health science credibly to consumers through content, media, and science-based marketing. (4) Consumer and partner-branded services include MGNavi® gut environment evaluation and the MG Diet Support subscription, which is the consumer manifestation of the company's stratified healthcare thesis. Pricing is not publicly disclosed, but disclosed employee salary bands (¥3.27M–¥4.49M annual) suggest project-based B2B fee structures.

Metagen's go-to-market is anchored by the Gut Design Co-creation Project (GDP), an enterprise consortium that grew from 3 founding members in 2016 to 32+ companies by April 2024, spanning food (Calbee, Meiji, Morinaga Milk, Ezaki Glico, Ajinomoto, Ito En, Mizkan, Hakubaku, Nisshin Seifun), ingredients and materials (Daicel, Fuso Chemical, Welneo Sugar, Hokto, Kaneryo Kaiso), pharmaceuticals and cosmetics (Shiseido, Teijin, Saishunkan), and distribution (Itochu, Oisix ra Daichi). Co-developed consumer products include Body Granola with Calbee (April 2024) and Inner Garden with Meiji (December 2024). The company also runs the onakademy content platform on note.com, hosts GDP salons and webinars, and in February 2026 extended the GDP model to ASEAN via Gut Design Project ASEAN with 6 initial partners from Japan and Singapore.

Name

Metabologenomics

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

Metabologenomics is a Japanese gut-microbiome science company that provides research, product development, and science-PR support to food, pharmaceutical, and cosmetics enterprises through its proprietary Metabologenomics® analytics platform and 32+ member Gut Design Co-creation Project ecosystem.

Ownership category

akta.pro rank

Product category

Microbiome Research and Consulting 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 industries

Microbiome & Metagenomics Services (HLAGANAH), Metabolomics & Lipidomics Services (HLAGANAG), Probiotics & Digestive Health Supplements (CRADAGAF)

Keywords

• Gut microbiome research
• Microbiome analytics services
• Personalized gut health
• Metagenomics consulting
• Science PR services

Headquarters

HQ city

Yamagata

HQ country

Japan

HQ region

Asia

Offices3 records

Markets served

GTM type

B2B

Offering type

Services

Cost components

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

Revenue model

1. Research Value-Added Exploration Services (研究付加価値探索事業): End-to-end research support from study design consultation, execution, data analysis and interpretation, through to business proposal — serving enterprise clients seeking to incorporate gut health science into their R&D programs.
2. Product Development Support Services (商品開発支援事業): Gut type-specific product development consulting, from ingredient selection and logic design for science-backed products to business and PR co-support for commercializing new offerings.
3. Science PR Services (サイエンスPR事業): Science communication and PR services that help partner companies convey gut health science accurately to consumers and stakeholders, including content development and media relations.
4. Gut Environment Testing & Consumer Services (e.g., MG Diet Support): Consumer-facing or partner-branded gut health testing and personalized diet support services. Includes MGNavi® gut environment evaluation services. Revenue is generated per test or subscription.
5. Gut Environment Type-Specific Business Consulting: Consulting engagements co-delivered with株式会社インテグレート for businesses developing gut type-based products/services, including business strategy and marketing strategy. B2B consulting fees.

Pricing tiers

Go-to-market motion3 records

Distribution channels5 records

Marketing channels8 records

Core offering

Metabologenomics provides B2B gut-microbiome research, product-development consulting, and science-PR services to enterprise partners in the food, beverage, pharmaceutical, and cosmetics industries. Its offerings are anchored by a proprietary Research and Development Support Platform built on the Metabologenomics® analytical methodology, with supporting streams including Research Value Creation (study design and execution), Product Development Support, Science PR, and Gut Environment Type Business Consulting (co-delivered with Integrate Inc.). The company also runs the Gut Design Co-creation Project (GDP) consortium of 32+ member companies, enabling co-development of personalized products such as Body Granola (with Calbee) and Inner Garden (with Meiji).

Product overview

Metabologenomics operates as a gut environment research and technology company offering a integrated portfolio of services centered on its proprietary Metabolomics® technology. The core offering includes a Research and Development Support Platform that provides end-to-end research consulting, a gut environment-based diet support service (MG Diet Support), and gut-type specific business consulting. The company also collaborates on consumer products including Body Granola with Calbee and Inner Garden with Meiji. The Gut Design Project (GDP) is an enterprise collaboration platform where member companies co-develop products and services based on the 'Gut Design®' concept. Additional services include Research Value Creation, Product Development Support, and Science PR services, all focused on gut microbiome science and personalized healthcare.

Differentiator

Problem solved

Functional benefit

Products and services

• Research and Development Support Platform (研究開発支援プラットフォーム) End-to-end B2B platform supporting enterprise clients across all stages of gut environment research — from research theme consultation and test planning through execution, results analysis, and output delivery. Powered by the proprietary Metabologenomics® analytical methodology.
• Research Value Creation (研究付加価値探索事業) Service providing added-value exploration in gut environment research for enterprise partners — covering research consultation, execution, and analysis to deliver actionable scientific findings.
• Product Development Support (商品開発支援事業) Service supporting enterprise product development leveraging gut environment research — from science-based product logic design and ingredient selection through to business support and PR assistance for commercial launch.
• Science PR (サイエンスPR事業) PR support service that leverages rigorous science to help partner companies communicate gut environment research and products effectively to consumers and stakeholders.
• Gut Environment Type Business Consulting (腸内環境タイプ別ビジネスコンサルティング) B2B consulting service co-delivered with Integrate Inc. that supports enterprise clients in product development, business strategy, and marketing strategy tailored to individual gut environment types — combining Metagen's gut typing science with Integrate's wellness marketing expertise.
• MG Diet Support (MGダイエットサポート) Gut environment-based stratified healthcare diet support service that helps users understand their gut environment ('see'), know the right approach for their gut type ('know'), and act on personalized dietary recommendations ('act'). Combines gut flora testing with personalized dietary guidance.
• Body Granola Personalized granola product co-developed with Calbee and Cykinso, customized based on individual gut flora testing results. Sold through subscription as the first product under the company's stratified healthcare initiative.
• Inner Garden Gut-type specific personalized care product co-developed with Meiji Co., Ltd. / Meiji Food Materia, featuring gut-type matched ingredient formulations tailored to different consumer gut types.
• Bacteroigo Board Game (バクテロイゴ) Educational board game in which players become gut bacteria competing in territory battles within the intestine, designed to help users — particularly children — understand gut bacteria in an enjoyable way. Co-developed with Tokyo Institute of Technology and Leave a Nest and published December 2015.
• Gut Design Co-creation Project / GDP (腸内デザイン共創プロジェクト) Enterprise collaboration platform sharing the 'Gut Design®' concept across 32+ member companies from food, beverage, pharmaceutical, cosmetics, and ingredient sectors. Members co-develop products, share research platforms, and run joint awareness campaigns (Gut Design Months, Short-Chain Fatty Acid Day) to build the gut design market collectively.

Quantifiable outcome

• Body Granola co-developed with Calbee — first personalized food product in Japan based on gut flora examination, launched 2024
• +2 more outcomes

Named customers12 records

Segments4 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

AI capability1 record

Feature6 records

Partnerships

46 partnerships are on record, tiered regional expansion partners, capital and strategic partner, long-term strategic partner, co-delivery partner, core gdp member, core gdp member — flagship co-development and founding academic partner.

• Gut Design Project ASEAN Partners (6 companies from Japan and Singapore)regional expansion partnersStrategic or Co-development Partner · 12 February 2026In February 2026, the GDP was expanded to the ASEAN region under 'Gut Design Project ASEAN,' with initial 6 companies from Japan and Singapore. This marks Metagen's first international expansion, aiming to establish the gut design market in Southeast Asia.
• 株式会社サイキンソー (Cykinso, Inc.)capital and strategic partnerStrategic or Co-development Partner · 1 November 2023Metagen entered a capital and business partnership with Cykinso (another gut health company) in November 2023, despite being traditionally considered competitors. Both companies agreed to 'co-creation over competition,' with the shared vision of enabling 8 billion people globally to use their gut health information for wellness. Featured in GDP Salon Vol.15 discussion.
• 株式会社リバネス (Leave a Nest Co., Ltd.)long-term strategic partnerStrategic or Co-development Partner · 1 January 2023Science platform company that has been involved with Metagen since its founding in 2015. Co-developed the 'Bacteroigo' board game (2015), co-organized the Hyper Interdisciplinary Forum (2026), and participated in 3-company top roundtable discussions. Metagen's development has been 'accompanied' by Leave a Nest since pre-founding stages.
• 株式会社インテグレート (Integrate Inc.)co-delivery partnerStrategic or Co-development Partner · 6 October 2022Marketing strategy firm co-delivering the 'Gut Environment Type-Specific Business Consulting' service with Metagen. Metagen provides gut science and typing technology; Integrate provides wellness marketing strategy and consumer perception expertise. Joint service launched October 2022.
• 株式会社あじかん (Ajikan Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP partner collaborating on research and product development related to gut health ingredients. Contributed to GDP online seminars on dietary fiber and gut bacteria, including presentations on 'gut bacteria + burdock (dietary fiber)' as keys to successful gut health.
• 味の素株式会社 (Ajinomoto Co., Inc.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP member company participating in the gut health co-creation ecosystem. Ajinomoto's ingredient and seasoning expertise complements Metagen's gut science platform for developing functional food products.
• アジレント・テクノロジー株式会社 (Agilent Technologies Japan)core gdp memberTechnology or Integration · 1 January 2020Analytical instrumentation company providing LC/LC-MS equipment support and lab tours for GDP member events. Collaborated on hosting the Gut Design Salon Vol.8 at Agilent's headquarters.
• 江崎グリコ株式会社 (Ezaki Glico Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP partner; developed 'BifiX Yogurt α' using proprietary Bifidobacterium GCL2505 strain and inulin. Active participant in Short-Chain Fatty Acid Day (March 4) awareness campaign and GDP seminars.
• カルビー株式会社 (Calbee, Inc.)core gdp member — flagship co-developmentStrategic or Co-development Partner · 1 January 2020Co-developed 'Body Granola,' Japan's first personalized granola customized based on individual gut flora examination results, launched 2024. A flagship GDP co-development case widely featured in GDP events and media. Also collaborating on cereal gut health research.
• 株式会社明治 / 株式会社明治フードマテリア (Meiji Co., Ltd. / Meiji Food Materia)core gdp member — flagship co-developmentStrategic or Co-development Partner · 1 January 2020Co-developed 'Inner Garden,' a gut type-specific personalized care product launched December 2024. Metagen provided research support and scientific supervision. Featured prominently in GDP events and the PIVOT video content series.
• 森永乳業株式会社 (Morinaga Milk Industry Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP partner with 50+ years of Bifidobacterium research. Conducted the Kobe Demonstration Study on symbiotic yogurt and gut environment changes. Participated in 3-company top roundtable discussions with Metagen and Leave a Nest.
• 森下仁丹株式会社 (Morishita Jintan Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP partner developing seamless large intestine delivery capsules containing short-chain fatty acids. Collaborated on GDP seminars presenting research on 'tannic acid fatty acids' reaching the large intestine.
• 株式会社資生堂 (Shiseido Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP member since 2022, participating in gut health research and product development within the cosmetics and beauty company's broader wellness strategy.
• 帝人株式会社 (Teijin Limited)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP partner researching prebiotic ingredients (inulin, Super Barley) for scientific evidence. Also researched inulin's role in suppressing COVID-19 severity through gut environment modulation, presented at GDP salons.
• 野村乳業株式会社 (Nomura Nyugyo Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP partner since 2022; developed plant-derived lactic acid bacteria products and participated in GDP webinars on gut health and fermented foods.
• 株式会社ダイセル (Daicel Corporation)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP partner developing gut metabolic material ingredients. Presented research on new functional ingredients at GDP salons. Active in the Short-Chain Fatty Acid Day coalition.
• ホクト株式会社 (Hokto Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP partner researching continuous mushroom intake's effects on short-chain fatty acid production and immune function enhancement. Presented at GDP salons and Short-Chain Fatty Acid Day events.
• 伊藤忠商事株式会社 (Itochu Corporation)core gdp memberChannel Partner/ Reseller/ Distributor · 1 January 2020Trading company GDP member bringing distribution and market access expertise to the gut health ecosystem, particularly for international market development.
• オイシックス・ラ・大地株式会社 (Oisix ra Daichi Inc.)core gdp memberChannel Partner/ Reseller/ Distributor · 1 January 2020Organic food delivery service participating in GDP; contributed to online seminars on 'delicious meals that gut bacteria love' and the gut design food delivery ecosystem.
• ウェルネオシュガー株式会社 (Welneo Sugar Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Sugar and sweetener company participating in GDP's gut health ecosystem, contributing to the food science and functional ingredient network.
• カクイ株式会社 (Kakui Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP member company contributing to the cross-industry gut health ecosystem.
• カネリョウ海藻株式会社 (Kaneryo Kaiso Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Seaweed company GDP member since 2023, bringing unique functional ingredient perspective from the marine food sector.
• 扶桑化学工業株式会社 (Fuso Chemical Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Specialty chemicals company in GDP; presented research on gluconic acid's role in enhancing Bifidobacterium and short-chain fatty acid production at GDP salons.
• 株式会社Mizkan (Mizkan Holdings)core gdp memberStrategic or Co-development Partner · 1 January 2020Seasoning and food company GDP member since 2024; participated in GDP webinars on fermentation dietary fiber and gut health education.
• 池田糖化工業株式会社 (Ikeda Carbohydrate Industry Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Carbohydrate manufacturing company GDP member since 2024, contributing functional ingredient and carbohydrate science expertise.
• 再春館製薬所株式会社 (Saishunkan Pharmaceutical Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Pharmaceutical company GDP member bringing healthcare and pharmaceutical industry perspective to the gut health ecosystem.
• 日本食品化工株式会社 (Nippon Food Chemical Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Food ingredients company GDP member since 2022; participated in sessions at the Hyper Interdisciplinary Forum 2026 on gut health and food science.
• 株式会社サンフレッセ (Sanflass Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Food service company GDP member since 2023, representing the food service/distribution sector in the gut health ecosystem.
• CPCC株式会社 (CPCC Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020GDP member contributing to the cross-industry gut health ecosystem.
• 株式会社spaceblastcore gdp memberStrategic or Co-development Partner · 1 January 2020GDP member bringing technology/innovation perspective to the gut health ecosystem.
• 株式会社digzymecore gdp memberTechnology or Integration · 1 January 2020Biotech company GDP member providing enzyme/biotech technology capabilities relevant to gut microbiome analysis and fermentation.
• 株式会社バイオインパクト (Bioimpact Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Bio company GDP member contributing to the gut health ingredient and research ecosystem.
• 株式会社vacancore gdp memberStrategic or Co-development Partner · 1 January 2020Technology/services company GDP member contributing diverse capabilities to the gut health ecosystem.
• 日はくばく株式会社 (Hakubaku Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Food company GDP member contributing grain and whole grain ingredient expertise to the gut health ecosystem.
• 原田食品株式会社 (Harada Food Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Food manufacturing company GDP member since 2023, representing the mid-tier food production sector.
• Rhelixa Inc.core gdp memberTechnology or Integration · 1 January 2020Biotechnology company GDP member providing microbiome analysis and bioinformatics capabilities to the ecosystem.
• ダノンジャパン株式会社 (Danone Japan Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Global dairy and water company GDP member, bringing international perspective and global gut health research to the ecosystem.
• 株式会社伊藤園 (Ito En Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Beverage company GDP member since 2021; presented at the Hyper Interdisciplinary Forum 2026 on gut health beverages and ingredients.
• 日清製粉グループ本社 (Nisshin Seifun Group Inc.)core gdp memberStrategic or Co-development Partner · 1 January 2020Flour and grain processing conglomerate GDP member since 2024, contributing functional grain ingredient and food science expertise.
• 株式会社オンチップ・バイオテクノロジーズ (On-chip Biotechnologies Co., Ltd.)core gdp memberTechnology or Integration · 1 January 2020Biotech company providing microfluidic and cell analysis technologies relevant to gut microbiome research.
• 池内興業合同会社 (Ikeuchi Kosha Godo Kaisha)core gdp memberStrategic or Co-development Partner · 1 January 2020Manufacturing company GDP member since 2023, representing diverse industrial capabilities in the ecosystem.
• Aqua Clala Co., Ltd. (アクアクララ株式会社)core gdp memberStrategic or Co-development Partner · 1 January 2020Water delivery service company GDP member since 2024, bringing hydration and functional beverage perspective.
• 住友理工株式会社 (Sumiseki Materials Co., Ltd.)core gdp memberStrategic or Co-development Partner · 1 January 2020Sealant and industrial materials company GDP member since 2024, representing non-food industry participation in gut health.
• 株式会社バカン (VACAN Inc.)core gdp memberStrategic or Co-development Partner · 1 January 2020Technology company GDP member since 2024, bringing digital/innovation capabilities to the gut health ecosystem.
• 東京工業大学 (Tokyo Institute of Technology)founding academic partnerStrategic or Co-development Partner · 15 December 2015University partner where the 'Bacteroigo' board game concept was originally devised by a Tokyo Tech student. Metagen was founded based on technology developed at Keio University, with Tokyo Tech contributing to the broader gut science ecosystem.
• 慶應義塾大学先端生命科学研究所 (Keio University Institute for Advanced Biosciences)founding academic partnerStrategic or Co-development Partner · 1 January 2015Metagen was founded based on research conducted at Keio University's Institute for Advanced Biosciences in Tsuruoka, Yamagata. CEO Fukuda serves as a Visiting Professor at the institute. The Tsuruoka research campus houses Metagen alongside other biotech startups, creating an innovation ecosystem.

Scale indicators3 records

Recent moves7 records

Expansion highlights6 records

Emerging players

• Eagle Genomics: UK-based bioinformatics platform applying AI to microbiome and multi-omic data for enterprise R&D. Comparable as an enabling platform for microbiome-driven product development, though positioned more as enterprise SaaS than as an integrated science-to-product service like Metagen's.
• CosmosID: US-based microbiome analytics platform providing NGS-based microbial identification and bioinformatics services. Comparable to Metagen's analytical backbone (Metabologenomics®) as a sequencing/informatics platform, though serving primarily pharmaceutical and academic clients rather than consumer-facing brands.

Broad incumbents

• Danone: Global dairy and plant-based nutrition company with active gut health research (via Danone Japan membership in Metagen's GDP). Comparable as a customer/partner and as a competing incumbent with internal capabilities in probiotic and personalized nutrition — particularly in Japan and APAC.
• Morinaga Milk Industry: Japanese dairy manufacturer with 50+ years of Bifidobacterium research and major GDP partner. Comparable because it combines internal microbiome science capability with consumer probiotic/synbiotic product portfolios — making it both a customer and a potential competitive incumbent in personalized gut health.
• Yakult Honsha: Global probiotic dairy beverage leader with deep lactobacillus microbiome research. While not directly competing with Metagen's analytics platform, Yakult's brand and scientific presence in the Japanese gut health market sets the competitive backdrop for personalized nutrition claims and influencer consumer mindshare.

Direct peers

• Zoe: UK/US personalized nutrition company combining gut microbiome testing with blood glucose and blood fat responses to deliver personalized dietary recommendations. Comparable to Metagen in gut-type stratification and science-backed personalization, but focused on direct-to-consumer subscription model.
• Cykinso: Japan-based gut microbiome testing and personalized health company. Cykinso is Metagen's closest domestic competitor in consumer-facing gut flora analysis; the two entered a capital and business alliance in November 2023 despite being competitors, sharing a vision of enabling global access to gut health information.
• DayTwo: Israel-originated personalized gut health and nutrition company using microbiome analysis to provide individualized dietary recommendations for blood sugar control. Directly comparable business model to Metagen's gut-type stratification approach, though now operating primarily via B2B2C through health plans and providers.
• Viome Life Sciences: US-based personalized nutrition company that uses gut microbiome and other omics testing to recommend individualized supplements and foods. Comparable to Metagen in combining metagenomic/metabolomic analysis with consumer product recommendations, though operating at larger scale and via DTC channels.

Others

• Integrate Inc. Japanese marketing strategy firm co-delivering Metagen's Gut Environment Type-Specific Business Consulting since October 2022. Comparable as a strategic partner rather than competitor, but materially relevant because Integrate bridges Metagen's gut science with consumer marketing capability for enterprise clients.

Market position

Strengths5 records

Weaknesses4 records

Competitive moat6 records

Key risks5 records

Key highlights6 records

Customer concentration

• Xtwitter.com/browngems
• Facebookfacebook.com/metabologenomics?locale=ja_JP
• LinkedInlinkedin.com/company/metabologenomics

Revenue estimate

Valuation estimate

Number of profiles

Profiles6 records

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 Metabologenomics