BitBiome
BitBiome is a Tokyo-based microbial genomics company combining proprietary single-cell sequencing, a 2.5B+ sequence database, and AI-driven enzyme engineering to serve industrial biotech customers in food, chemicals, personal care, animal health, and bio-recycling.
- Company typePrivate
- Founded2018
- HeadquartersTokyo, Japan
- Headcount51–100
- GTM typeB2B
- OfferingServices
What BitBiome does
BitBiome is a Tokyo-headquartered biotechnology company, founded in 2018, that operates a vertically integrated platform for microbial genomics and AI-driven enzyme engineering. The platform has three core components: bit-MAP, a proprietary single-cell microbial genome sequencing technology; bit-GEM, a proprietary microbial genome database containing more than 2.5 billion sequences of which approximately 50% are novel; and bit-QED, an AI/ML-based enzyme design platform that combines structural modeling, large language models, and in silico directed evolution. BitBiome also maintains a US presence in Palo Alto, California, supporting commercial and partnership activity in North America.
The company sells into industrial biotechnology customers across food and ingredients (Ajinomoto, Sanwa Starch), specialty chemicals (Tokyo Ohka Kogyo), personal care (Kao), textiles and bio-recycling (Bell Polyester under NEDO funding), animal health (Kyoritsu Seiyaku), distribution (Tojo Vikas for India), and life sciences tools (Twist Bioscience for enzyme kit distribution), plus an unnamed flavors and fragrances market leader. Revenue is generated through a mix of custom sequencing service contracts, joint development agreements with milestone or licensing components, grant-funded research programs (NEDO and AMED), and an emerging standardized enzyme/reagent kit channel via Twist Bioscience. Total capital raised across equity and non-dilutive funding exceeds $45M as of a 2026 oversubscribed seed extension, with strategic participation from IQT, IT-Farm, Valuence Ventures, and Darwin Ventures. The company was named to the Forbes Asia 100 To Watch list in 2025.
The business model is best characterized as a hybrid services-plus-platform model: short- to medium-term cash flow comes from sequencing services and JDAs, non-dilutive grant income supports longer-horizon platform R&D, and the strategic optionality of bit-QED and bit-GEM is positioned to generate higher-margin licensing or royalty income over time as customer programs mature.
BitBiome firmographics
Firmographics- Name
- BitBiome
- Legal name
- bitBiome, Inc.
- Website
- https://bitbiome.bio
- Company type
- Private
- Founded year
- 2018
- Operating status
- Operating
- Headcount range
- 51–100 employees
- Short description
- BitBiome is a Tokyo-based microbial genomics company combining proprietary single-cell sequencing, a 2.5B+ sequence database, and AI-driven enzyme engineering to serve industrial biotech customers in food, chemicals, personal care, animal health, and bio-recycling.
- Ownership category
- akta.pro rank
BitBiome industry classification
Industry- Product category
- Microbial Genomics & Enzyme Engineering Services
- NAICS
- Research and Development in Biotechnology (except Nanobiotechnology) (541714)
- SIC
- Laboratory Analytical Instruments (3826)
- akta.pro primary industry
- Bioinformatics & Multi-omics Analysis Software (HLAGAJAD)
- akta.pro secondary industry
- Microbiome & Metagenomics Services (HLAGANAH)
Keywords
Where BitBiome is headquartered
LocationHeadquarters
- HQ city
- Tokyo
- HQ country
- Japan
- HQ region
- Asia
Offices2 records
Markets served
BitBiome business model
Business model- GTM type
- B2B
- Offering type
- Services
- Cost components
- Personnel, Technology or R&D, Operations, Marketing or Sales, Infrastructure
Revenue model
- Enzyme Discovery, Engineering, and Strain Development Services: Custom B2B fee-for-service revenue from database mining, assaying, directed evolution, and strain engineering using bit-QED. Engagement is typically project-based with flexible scope (single-step to end-to-end workflow including wet lab validation and production).
- Sequencing Services (bit-MAP®): Fee-based single-cell microbial sequencing services delivered via a Collect → Ship → Receive Report workflow with full bioinformatics report (taxonomies, novelty, completeness, contamination). Includes human, animal, and environmental samples.
- Enzyme Kit Product Sales (via Twist Bioscience): bitBiome's enzyme screening kit (48 validated transaminases across 18 substrates with freeze-dried enzymes, yielding 1,800 variants after six rounds of refinement) is commercialized through Twist Bioscience's storefront. Revenue likely flows via distribution agreement.
- Joint Development, Manufacturing & Supply Partnerships: Revenue from joint development and manufacturing collaborations where bitBiome develops bio-based production processes and serves as manufacturing/supply partner upon commercialization (e.g., food-grade flavor & fragrance ingredient collaboration with double-digit metric ton annual demand; PET bio-recycling with Bell Polyester Products).
- Public/Grant (Non-Dilutive) Funding: bitBiome receives non-dilutive funding from Japanese government programs (NEDO Biomanufacturing Revolution Promotion Program; AMED P-PROMOTE Next-Generation Cancer Medical Acceleration Research Project with Nagoya University; JST PRESTO), which supplements its commercial revenue streams.
Go-to-market motion1 record
Distribution channels5 records
Marketing channels9 records
BitBiome product offering
Product offeringCore offering
BitBiome provides a microbial biomanufacturing platform combining proprietary single-cell microbial genome sequencing (bit-MAP®), a proprietary microbial sequence database (bit-GEM, 2.5B+ sequences), and an AI-driven enzyme and strain engineering platform (bit-QED) that uses bioinformatics, cheminformatics, machine learning, and large language models for in silico enzyme design and directed evolution. The platform is delivered to enterprise customers as fee-for-service sequencing, custom enzyme discovery and engineering, and joint development/manufacturing partnerships spanning pharmaceuticals, food & agriculture, materials & plastics, flavors & fragrances, and life science tools.
Product overview
bitBiome operates a unified microbial biomanufacturing platform built around three tightly integrated core modules: bit-MAP® (the patented single-cell microbial sequencing engine that powers data generation), bit-GEM (the proprietary microbial genome catalog of 2.5+ billion sequences grown from bit-MAP outputs), and bit-QED (the AI-driven enzyme discovery, engineering, and strain development platform that mines and engineers sequences from bit-GEM). These three modules together form the foundation of the offering, which is delivered to customers through complementary products and services: Sequencing Services (single-cell sequencing-as-a-service with bioinformatics reporting) and a commercial Enzyme Kit (a Twist Bioscience-distributed transaminase screening kit for ownable enzyme development). The platform also supports internal R&D pipeline development across Food & Agriculture, Materials & Textiles, Plastics, Drug Discovery, Drug Biomanufacturing, Synbio, and Gene Editing applications, and is positioned as a one-stop-shop from microbial discovery through commercial-scale biomanufacturing.
Differentiator
Problem solved
Functional benefit
Brands
- bit-MAP®: bitBiome's patented single-cell sequencing technology for microbes using microfluidics to capture and sequence individual bacterial genomes within isolated capsules; 100x more efficient than shotgun metagenomics.
- bit-GEM
- bit-QED
Products and services
- bit-MAP® Patented single-cell microbial sequencing technology that uses microfluidics to capture and sequence individual bacterial genomes inside isolated capsules, eliminating the need for culturing. Reported as 100x more efficient than shotgun metagenomics and capable of recovering microbial dark matter from low-biomass and high-diversity samples. Foundation of BitBiome's platform.
- bit-GEM Proprietary microbial genome database of 2.5 billion sequences (and growing by ~1 billion per year) built on bit-MAP single-cell sequencing of microbes from natural samples, including unculturable and extremophile sources. Approximately 60% of samples are environmental and ~50% taxonomically novel compared with public databases.
- bit-QED AI-driven enzyme discovery, engineering, and strain development platform that combines sequence and structure-based mining of bit-GEM with machine learning, large language models, 3D structural modeling, and automated wet-lab high-throughput screening. Reduces a 2-3 year process to months or weeks and is positioned as a one-stop-shop for biomanufacturing.
- Sequencing Services Single-cell microbial sequencing-as-a-service: customers collect human/animal/environmental samples and ship them to bitBiome, which delivers a full bioinformatics report including taxonomies. Includes a miniaturized multi-drop metagenomics workflow providing 10x the data while retaining single-cell resolution.
- Enzyme Kit (Transaminase Screening Kit) Kick-start enzyme development kit leveraging 48 validated unique transaminases tested against 18 different substrates, delivered as freeze-dried enzymes. Six rounds of bitBiome's bioinformatics and refinement yield 1,800 new variants for testing. Commercialized in partnership with Twist Bioscience.
Quantifiable outcome
- 100x more efficient gene analysis than shotgun metagenomics
- +8 more outcomes
Companies that use BitBiome
Customer profileNamed customers11 records
Segments7 records
Ideal customer profiles6 records
BitBiome technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- No
- API docs
- API detail
Core technology
AI maturity
App detail
AI capability8 records
Feature6 records
BitBiome partnerships and signals
Strategic signalPartnerships
21 partnerships are on record, tiered major, flagship and minor.
- Kyoritsu Seiyaku CorporationmajorStrategic collaboration to jointly develop products utilizing bitBiome's bio-manufacturing technologies for animal health and nutrition. Kyoritsu Seiyaku contributes decades of veterinary experience for pets and livestock; commercialize jointly in global market.
- Unnamed major market leader in flavors & fragrancesmajorJoint development and manufacturing collaboration to create a bio-synthetic production process for a high-value food-grade ingredient used in flavors and fragrances. Initial demand projected at double-digit metric tons per year.
- Kao CorporationflagshipJoint implementation of NEDO-commissioned 'Research and Development of Technologies to Promote Biomanufacturing' project to establish a saccharification enzyme supply platform that enables use of unused biomass resources. bitBiome handles enzyme discovery work.
- Tojo Vikas International Pvt. Ltd.majorStrategic joint development and commercialization collaboration for sustainable flavor and fragrance biomanufacturing. Combines bitBiome's proprietary microbial database and bio-manufacturing platform with Tojo Vikas' market knowledge and ingredient commercialization expertise.
- Bell Polyester Products Co., Ltd.majorSelected together for NEDO 'Bio-recycling of Waste Plastic Resources' project — bitBiome develops proprietary enzymes using bit-QED, Bell Polyester Products produces bio-recycled co-polymerized PET resin via Bio BellPET line.
- Sanwa Starch Co., Ltd.majorEnzyme development contract under NEDO Biomanufacturing project 'Development and Social Implementation of Functional Sugar Materials from Untapped Domestic Biomass.' bitBiome uses bit-QED to discover and supply saccharification enzymes.
- Nagoya University (Tokai National Higher Education and Research System)majorCollaboration under AMED P-PROMOTE Next-Generation Cancer Medical Acceleration Research Project to develop combination therapy of Fusobacterium-specific endolysin and immune checkpoint inhibitors for ovarian cancer.
- Tokyo Ohka Kogyo Co., Ltd. (TOK)flagshipJoint development agreement to develop bio-processes using bitBiome's enzyme discovery and engineering platform to replace petroleum-derived raw materials in TOK products, supporting TOK Vision 2030 decarbonization goals.
- Ajinomoto Co., Inc.flagshipJoint research agreement: bitBiome conducts a comprehensive search and screens new enzymes from bit-GEM, and Ajinomoto evaluates and verifies the usefulness of the enzymes for its healthcare, food & wellness, ICT, and green initiatives.
- Twist BioscienceflagshipStrategic partnership bringing together bitBiome's bit-GEM database and Twist's DNA synthesis platform for enzyme development (particularly for synthesis of active pharmaceutical ingredients); expands reach of purpose-built enzymes to US and European labs; Twist also distributes bitBiome's enzyme screening kit.
- The University of Texas at Austin (Dr. Alper's laboratory)majorJoint research agreement: bitBiome uses its microbial single-cell genome analysis to search for novel bacterial species and enzymes capable of degrading plastics and other non-biodegradable components by evaluating composting site samples (raw and enriched in PHB/PLA bioplastics).
- Université de MontréalminorListed as a partner/collaborator on bitBiome's Applications page (logo).
- MeijiminorListed as a partner/collaborator on bitBiome's Applications page (logo).
- Japan Science and Technology Agency (JST)majorListed as a partner/collaborator on bitBiome's Applications page (logo); Founder CSO Hosokawa is a JST PRESTO researcher (2015) and 2019 JST PRESTO Innovation Award recipient.
- Kaken (JSPS KAKENHI)minorListed as a partner/collaborator on bitBiome's Applications page (logo).
- NEDO (New Energy and Industrial Technology Development Organization)flagshipListed as a partner/collaborator on bitBiome's Applications page (logo). NEDO commissions multiple projects bitBiome participates in (Biomanufacturing Revolution Promotion Program with Kao, Sanwa Starch, Bell Polyester Products).
- Universal Materials Incubator (UMI)minorListed as a partner/collaborator on bitBiome's Applications page (logo).
- Waseda UniversityflagshipListed as a partner/collaborator on bitBiome's Applications page (logo). bitBiome originated from research at Waseda University by Founder CSO Masahito Hosokawa; HQ is co-located at Waseda University Research Innovation Center.
- FujifilmminorListed as a partner/collaborator on bitBiome's Applications page (logo).
- NCCJminorListed as a partner/collaborator on bitBiome's Applications page (logo).
- AMED (Japan Agency for Medical Research and Development)majorAdoption of bitBiome's endolysin therapeutic project under AMED's P-PROMOTE Next-Generation Cancer Medical Acceleration Research Program (June 2025), in collaboration with Nagoya University.
Scale indicators13 records
Recent moves6 records
Expansion highlights7 records
BitBiome competitors and assessment
Company assessmentDirect peers
- Codexis: Codexis is a public enzyme engineering company specializing in biocatalysis for pharmaceutical and fine chemical manufacturing. It is the most directly comparable peer to BitBiome's bit-QED platform — both target novel enzyme discovery and directed evolution for industrial customers, and BitBiome has hired multiple former Codexis executives (CBO, Head of BD, advisors).
- Carbios: Carbios is a French biotech that uses engineered enzymes to depolymerize PET plastic into monomers for closed-loop recycling. It is a direct peer in the PETase enzyme development and bio-recycling vertical where BitBiome partners with Bell Polyester Products under NEDO funding.
- Antheia: Antheia is a synthetic biology company engineering yeast strains to produce plant-based alkaloid APIs and fine chemicals at commercial scale. It is highly comparable to BitBiome's joint development manufacturing model in flavors & fragrances and pharma ingredients, and shares an advisor (John Nicols, Antheia Board Chair).
Emerging players
- Protein Evolution: Protein Evolution is an AI-and-biotechnology company focused on enzymatic recycling of textiles and mixed plastics. It is a direct emerging peer in the enzymatic plastic/textile recycling vertical where BitBiome partners with Bell Polyester Products.
- Samsara Eco: Samsara Eco is an Australian biotech using engineered enzymes for infinite plastic recycling. It competes with BitBiome's bit-QED PETase development work and shares the same enterprise sustainability customer thesis around textile and packaging brands.
- Generate Biomedicines: Generate Biomedicines is a generative AI biology company designing novel proteins across therapeutics and industrial applications. It is comparable to BitBiome's bit-QED platform as a next-generation AI protein design player, but focused primarily on therapeutics whereas BitBiome targets industrial enzymes.
- Cradle Bio: Cradle uses generative AI to design novel proteins and enzymes for biotech customers. It is comparable to BitBiome's bit-QED AI-driven enzyme engineering platform, though Cradle focuses on generative protein design while bitBiome combines AI with proprietary single-cell sequencing data.
- Bota Bio: Bota Bio is an AI-driven biomanufacturing platform that designs and engineers microbes for sustainable production of ingredients across flavors & fragrances, personal care, and nutrition. It overlaps with BitBiome's enzyme discovery + strain engineering offering, particularly in flavor & fragrance biomanufacturing where both companies are pursuing enterprise deals.
Broad incumbents
- Ginkgo Bioworks: Ginkgo Bioworks is a large, established synthetic biology platform serving pharma, food, and industrial customers via its cell engineering platform and Codon/Foundry services. It competes broadly with BitBiome in enzyme and strain engineering, but at a much larger scale and with a horizontal platform rather than BitBiome's vertically integrated sequencing-to-manufacturing approach.
- LanzaTech: LanzaTech is a commercial-scale gas fermentation biomanufacturing company producing sustainable fuels and chemicals from waste gases. It is comparable to BitBiome in commercial biomanufacturing ambition and customer base (industrial / specialty chemical / fuel majors), but uses carbon capture gas fermentation rather than enzyme-driven bioconversion.
Market position
Strengths5 records
Weaknesses5 records
Competitive moat5 records
Key risks6 records
Key highlights7 records
Customer concentration
BitBiome social profiles
Digital presenceBitBiome compliance and trust
Trust signalCompliance1 record
BitBiome financial estimates
Financial estimateRevenue estimate
Valuation estimate
BitBiome leadership team
Management profileNumber of profiles
Profiles7 records
BitBiome subsidiaries and ownership
Company hierarchySubsidiaries1 record
BitBiome funding detail
Funding detailFunding overview
Funding rounds10 records
Investors18 records
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
BitBiome M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about BitBiome
What does BitBiome do?
BitBiome provides a microbial biomanufacturing platform combining proprietary single-cell microbial genome sequencing (bit-MAP®), a proprietary microbial sequence database (bit-GEM, 2.5B+ sequences), and an AI-driven enzyme and strain engineering platform (bit-QED) that uses bioinformatics, cheminformatics, machine learning, and large language models for in silico enzyme design and directed evolution. The platform is delivered to enterprise customers as fee-for-service sequencing, custom enzyme discovery and engineering, and joint development/manufacturing partnerships spanning pharmaceuticals, food & agriculture, materials & plastics, flavors & fragrances, and life science tools.
Is BitBiome a public or private company?
BitBiome is a private company. It is classified as venture growth investor backed and is currently operating.
When was BitBiome founded?
BitBiome was founded in 2018. It employs 51 to 100 people.
Where is BitBiome based?
BitBiome is headquartered in Tokyo, Japan, in the Asia region.
How does BitBiome make money?
Five revenue lines are on record. Enzyme Discovery, Engineering, and Strain Development Services are the primary driver. The others are sequencing Services (bit-MAP®), enzyme Kit Product Sales (via Twist Bioscience), joint Development, Manufacturing & Supply Partnerships and public/Grant (Non-Dilutive) Funding.
Who are BitBiome's main competitors?
Direct peers on record are Codexis, Carbios and Antheia. Emerging players are Protein Evolution, Samsara Eco, Generate Biomedicines, Cradle Bio and Bota Bio. Broad incumbents are Ginkgo Bioworks and LanzaTech.
Does BitBiome have an API?
No public API is recorded for BitBiome.
What industry is BitBiome in?
BitBiome's product category is Microbial Genomics & Enzyme Engineering Services. Its primary akta.pro industry code is HLAGAJAD, Bioinformatics & Multi-omics Analysis Software, with a secondary code of HLAGANAH, Microbiome & Metagenomics Services. Its NAICS code is 541714 and its SIC code is 3826.