Report Code : CVMI2603252601580 | Published Date : March 30, 2025
1 | Market Overview
The microbiome sequencing services market has evolved from a research-driven niche into a foundational component of precision medicine, agriculture, cosmetics, and food safety. The capacity to decode the complex microbial ecosystems inhabiting the human gut, soil, skin, water, and beyond has unveiled new insights into health, productivity, and disease pathways. Utilizing next-generation sequencing (NGS), metagenomics, and bioinformatics, microbiome sequencing services now offer actionable intelligence for pharmaceutical companies, nutrition brands, academic institutions, and environmental agencies. Growing awareness of the human microbiota's role in immunity, metabolism, and disease susceptibility has further propelled global demand.
2 | Market Size and Forecast
Year |
Market Value (USD Billion) |
Notes |
2019 |
1.2 |
Historical baseline using contract lab revenues and academic sequencing budgets |
2024 |
3.4 |
Five-year CAGR 23.1% |
2031 |
12.6 |
Seven-year CAGR 20.5% (2024–2031) |
The market is set to expand rapidly due to multi-sector adoption, falling sequencing costs, and bioinformatics platform maturity. Scenario modeling indicates that expanded national microbiome initiatives or reimbursement frameworks for gut microbiome diagnostics could push the market beyond USD 14 billion by 2031.
3 | Primary Market Drivers
- Healthcare transformation: Microbiome-based diagnostics and therapies are reshaping precision medicine, with applications in inflammatory bowel disease, obesity, oncology, and neurodegenerative disorders.
- Pharmaceutical R&D: Drug development pipelines increasingly use microbiome sequencing to assess host-microbiota interactions, especially for immunotherapies and antibiotic resistance studies.
- Nutraceutical and functional food demand: Companies use microbiome sequencing to validate probiotic strains, guide prebiotic formulations, and deliver personalized nutrition.
- Agricultural productivity: Soil microbiome analysis informs crop rotation, fertilizer decisions, and regenerative farming models.
- Cosmetic innovation: Skin microbiome mapping enables the development of targeted dermo-cosmetic products with measurable impact on skin flora.
4 | Market Challenges
- High data complexity and interpretation costs can delay clinical translation or product claims.
- Regulatory uncertainty around direct-to-consumer microbiome testing hinders scalability.
- Bioinformatics infrastructure varies widely across regions, impacting real-time data processing.
- Limited reference databases for niche ecosystems (e.g., rhizosphere, marine environments) affect accuracy.
- Data privacy and ethical concerns around human microbiome ownership and data monetization.
5 | Competitive Landscape
Company |
Estimated 2024 Share |
Competitive Strengths |
Recent Strategic Moves |
Illumina |
28% |
Sequencing platforms + end-to-end workflow services |
Launched microbiome-specific NovaSeq kits for service providers |
Zymo Research |
12% |
DNA extraction + library prep tailored for microbiome |
Expanded contract services in Europe, launched 16S and shotgun panels |
CosmosID |
10% |
Curated metagenomics library, pathogen ID strength |
Opened bioinformatics hub in Singapore to serve APAC |
Eurofins Genomics |
9% |
Large-scale sample logistics and QA infrastructure |
Acquired national microbiome lab in Brazil |
Novogene |
8% |
High-throughput sequencing + agricultural focus |
Partnered with agri-biotech firms on soil microbiome monitoring |
Others |
33% |
Regional CROs, university-based labs, AI-bioinformatics startups |
Commercial pilots in oral, urogenital, and aquaculture microbiomes |
6 | Detailed Market Segmentation
By Sequencing Type:
- 16S rRNA Sequencing – 38%
- Shotgun Metagenomic Sequencing – XX%
- Whole-Genome Sequencing – XX%
- Other Targeted Approaches – XX%
By Application:
- Human Health and Diagnostics – XX%
- Food and Beverage – XX%
- Agriculture and Soil – 15%
- Environmental Monitoring – XX%
- Animal Health and Veterinary – XX%
- Cosmetics and Personal Care – XX%
By End User:
- Academic and Research Institutions – 36%
- Pharmaceutical and Biotech Companies – XX%
- Contract Research Organizations (CROs) – XX%
- Food & Agri-tech Firms – XX%
- Government and Environmental Agencies – XX%
7 | Regional Analysis
- North America – Largest share (42%); NIH Human Microbiome Project legacy, pharma R&D, and personalized wellness boom.
- Europe – Strong clinical adoption in the UK, Germany, France; EU Horizon projects and gut-brain axis research hubs.
- Asia-Pacific – Fastest growth at 24.2% CAGR; Chinese and Indian national microbiome programs, rising agriculture and aquaculture use.
- Latin America – Agricultural and livestock applications lead adoption; Brazil’s soil health initiative key growth vector.
- Middle East & Africa – Early-stage, with UAE and South African universities investing in microbiome for climate-resilient farming.
8 | Technology and Innovation
- Long-read sequencing (e.g., Oxford Nanopore, PacBio) enables higher resolution of rare microbial taxa.
- AI-powered taxonomic classifiers reduce turnaround and annotation labor by 40%.
- Multi-omics platforms integrate microbiome with metabolomics, transcriptomics, and proteomics.
- Synthetic biology tools validate functional roles of novel microbes in vitro.
- Blockchain-secured microbiome data platforms improve privacy and monetization models.
9 | Regulatory Environment
- FDA guidance emerging for microbiome therapeutics and live biotherapeutic product (LBP) pathways.
- EMA and EFSA frameworks evaluating probiotic claims and microbiome sequencing in food safety.
- Japan and South Korea classifying gut diagnostics as class II medical devices.
- GDPR implications on personal microbiome data under EU health data interoperability laws.
10 | Recent Developments (Q4 2023 – Q2 2025)
- Illumina released NovaSeq Microbiome Plus library prep kit optimized for low-biomass samples.
- CosmosID expanded pathogen databases for clinical infection control programs.
- Zymo launched a field-deployable extraction kit for remote soil sampling.
- Novogene reported 2x throughput gains via new HiSeq X platform integration.
- GutBiomeX startup in Canada commercialized FMT donor-matching service using full-genome sequencing.
11 | Strategic Outlook
- Service providers should expand bioinformatics and interpretation dashboards for non-academic users.
- CROs should build domain-specific databases (e.g., oral, skin, rumen) to attract product developers.
- Pharma and food manufacturers must establish reproducibility pipelines with multi-year microbiome tracking.
- Policymakers need to fast-track diagnostic and regulatory pathways for microbiome-based interventions.
- Investors should target AI-integrated platforms with proprietary metadata and therapeutic pipelines.
12 | Methodology
Clearview Market Insights compiled revenue estimates from sequencing platform suppliers, CRO databases, and project grant filings. Interviews were conducted with 115 stakeholders across five continents, including microbiologists, clinical researchers, and nutraceutical firms. The forecast model combined ARIMA and Monte Carlo simulations adjusted for sequencing price decline curves and public-health policy variables.
Reasons To Buy

Scope

-
Key Player
- Charles River Laboratories
- Eurofins Scientific
- BGI Genomics Co., Ltd.CosmosID
- Microba
- QIAGEN N.V.
- Microbiome Insights Inc.
- BaseClear B.V.
- CD Genomics
- Zymo Research Corporation
- OraSure Technologies
- MR DNA (Molecular Research LP)
- Clinical-Microbiomics A/S
- Novogene Co., Ltd.
- Macrogen, Inc.
Global Microbiome Sequencing Services Market Report
Global Microbiome Sequencing Services Market Report
- 1. Global Microbiome Sequencing Services Market Research Report
- 1.1 Study Objectives
- 1.2 Global Microbiome Sequencing Services Market - Overview
- 1.3 Reason to Read This Report
- 1.4 Methodology and Forecast Analysis
- 2.1 Global Microbiome Sequencing Services Market Research Report – Detailed Scope and Definitions
- 2.1.1 By Technology
- 2.1.2 By Application
- 2.1.3 By End-User
- 2.1.4 By Region
- 3.1. Drivers - Macro-Economic Based, Supply Side, and Demand Side Drivers
- 3.2. Restraints – By Technology, By Application, By End-User, By Country
- 3.3. Opportunities – By Technology, By Application, By End-User, By Country
- 3.4. Trends – By Technology, By Application, By End-User, By Country
- 3.5. PEST Analysis
- 3.6. Porters Five Rule Analysis
- 3.7. Company’s Share Analysis (CSA) by Region or By Country
- 3.8. Global Microbiome Sequencing Services Market Research Report – DROTs Impact Analysis
- 4.1. Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 4.2. Annual Market Trend Assessment – Year-on-Year (YoY) Growth Analysis (%)
- 4.3. Incremental Market Value/Volume Opportunity between 2019 - 2023 and 2024 - 2031
- 4.4. Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 5.1 16S rRNA Sequencing
- 5.1.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 5.1.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 5.1.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 5.1.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 5.2 Shotgun Metagenomics
- 5.2.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 5.2.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 5.2.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 5.2.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 5.3 Whole Genome Sequencing
- 5.3.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 5.3.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 5.3.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 5.3.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 5.4 Others
- 5.4.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 5.4.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 5.4.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 5.4.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 6.1 Human Microbiome Research
- 6.1.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 6.1.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 6.1.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 6.1.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 6.2 Agricultural Microbiology
- 6.2.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 6.2.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 6.2.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 6.2.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 6.3 Environmental Microbiology
- 6.3.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 6.3.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 6.3.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 6.3.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 6.4 Industrial Microbiology
- 6.4.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 6.4.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 6.4.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 6.4.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 7.1 Research Institutes
- 7.1.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 7.1.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 7.1.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 7.1.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 7.2 Biotechnology Companies
- 7.2.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 7.2.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 7.2.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 7.2.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 7.3 Pharmaceutical Companies
- 7.3.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 7.3.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 7.3.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 7.3.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 7.4 Academic Institutions
- 7.4.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 7.4.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 7.4.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 7.4.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 8.1 North America
- 8.1.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 8.1.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 8.1.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 8.1.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 8.2 Europe
- 8.2.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 8.2.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 8.2.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 8.2.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 8.3 Asia-Pacific
- 8.3.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 8.3.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 8.3.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 8.3.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 8.4 Latin America
- 8.4.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 8.4.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 8.4.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 8.4.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 8.5 Middle East & Africa
- 8.5.1 Market Performance Review & Future Outlook: Assessing 2019 - 2023 and Predicting 2024 - 2031 Trends (USD Millions)
- 8.5.2 Annual Market Trend Assessment – Yearly Growth Observation (Y-O-Y)(%)
- 8.5.3 Incremental Market Value/Volume Opportunity between 2019 - 2023 and From 2024 to 2031
- 8.5.4 Market Shares Analysis in Years - 2019, 2023, 2024 and 2031
- 8.6 Global Microbiome Sequencing Services Market - Opportunity Analysis Index, By Technology, By Application, By End-User, and Region, 2024 - 2031
- 9.1 By Technology Analysis 2019 - 2023 and Forecast, 2024 - 2031 by Market Assessment (USD Mn), Yearly Growth Rate (%), and Market Presence (%)
- 9.1.1 16S rRNA Sequencing
- 9.1.2 Shotgun Metagenomics
- 9.1.3 Whole Genome Sequencing
- 9.1.4 Others
- 9.2.1 Human Microbiome Research
- 9.2.2 Agricultural Microbiology
- 9.2.3 Environmental Microbiology
- 9.2.4 Industrial Microbiology
- 9.3.1 Research Institutes
- 9.3.2 Biotechnology Companies
- 9.3.3 Pharmaceutical Companies
- 9.3.4 Academic Institutions
- 9.4.1 United States
- 9.4.2 Canada
9.6 Regional Trends Analysis
9.7 North America Global Microbiome Sequencing Services Market Research Report - Company Profiles- 9.7.1 Company 1 (United States)
- 9.7.2 Company 2 (Canada)
- 9.7.3 Company 3 (Canada)
- 10.1 By Technology Analysis 2019 - 2023 and Forecast, 2024 - 2031 by Market Assessment (USD Mn), Yearly Growth Rate (%), and Market Presence (%)
- 10.1.1 16S rRNA Sequencing
- 10.1.2 Shotgun Metagenomics
- 10.1.3 Whole Genome Sequencing
- 10.1.4 Others
- 10.2.1 Human Microbiome Research
- 10.2.2 Agricultural Microbiology
- 10.2.3 Environmental Microbiology
- 10.2.4 Industrial Microbiology
- 10.3.1 Research Institutes
- 10.3.2 Biotechnology Companies
- 10.3.3 Pharmaceutical Companies
- 10.3.4 Academic Institutions
- 10.4.1 Germany
- 10.4.2 United Kingdom
- 10.4.3 France
- 10.4.4 Spain
- 10.4.5 Italy
- 10.4.6 Russia
- 10.4.7 Netherlands
- 10.4.8 Poland
- 10.4.9 Rest of Europe
10.6 Regional Trends Analysis
10.7 Europe Global Microbiome Sequencing Services Market Research Report - Company Profiles- 10.7.1 Company 1 (Germany)
- 10.7.2 Company 2 (United Kingdom)
- 10.7.3 Company 3 (United Kingdom)
- 11.1 By Technology Analysis 2019 - 2023 and Forecast, 2024 - 2031 by Market Assessment (USD Mn), Yearly Growth Rate (%), and Market Presence (%)
- 11.1.1 16S rRNA Sequencing
- 11.1.2 Shotgun Metagenomics
- 11.1.3 Whole Genome Sequencing
- 11.1.4 Others
- 11.2.1 Human Microbiome Research
- 11.2.2 Agricultural Microbiology
- 11.2.3 Environmental Microbiology
- 11.2.4 Industrial Microbiology
- 11.3.1 Research Institutes
- 11.3.2 Biotechnology Companies
- 11.3.3 Pharmaceutical Companies
- 11.3.4 Academic Institutions
- 11.4.1 China
- 11.4.2 Japan
- 11.4.3 India
- 11.4.4 South Korea
- 11.4.5 Australia & NZ
- 11.4.6 ASEAN
- 11.4.7 Rest of Asia-Pacific
11.6 Regional Trends Analysis
11.7 Asia-Pacific Global Microbiome Sequencing Services Market Research Report - Company Profiles- 11.7.1 Company 1 (China)
- 11.7.2 Company 2 (Japan)
- 11.7.3 Company 3 (Japan)
- 12.1 By Technology Analysis 2019 - 2023 and Forecast, 2024 - 2031 by Market Assessment (USD Mn), Yearly Growth Rate (%), and Market Presence (%)
- 12.1.1 16S rRNA Sequencing
- 12.1.2 Shotgun Metagenomics
- 12.1.3 Whole Genome Sequencing
- 12.1.4 Others
- 12.2.1 Human Microbiome Research
- 12.2.2 Agricultural Microbiology
- 12.2.3 Environmental Microbiology
- 12.2.4 Industrial Microbiology
- 12.3.1 Research Institutes
- 12.3.2 Biotechnology Companies
- 12.3.3 Pharmaceutical Companies
- 12.3.4 Academic Institutions
- 12.4.1 Brazil
- 12.4.2 Mexico
- 12.4.3 Argentina
- 12.4.4 Peru
- 12.4.5 Colombia
- 12.4.6 Rest of Latin America
12.6 Regional Trends Analysis
12.7 Latin America Global Microbiome Sequencing Services Market Research Report - Company Profiles- 12.7.1 Company 1 (Brazil)
- 12.7.2 Company 2 (Mexico)
- 12.7.3 Company 3 (Mexico)
- 13.1 By Technology Analysis 2019 - 2023 and Forecast, 2024 - 2031 by Market Assessment (USD Mn), Yearly Growth Rate (%), and Market Presence (%)
- 13.1.1 16S rRNA Sequencing
- 13.1.2 Shotgun Metagenomics
- 13.1.3 Whole Genome Sequencing
- 13.1.4 Others
- 13.2.1 Human Microbiome Research
- 13.2.2 Agricultural Microbiology
- 13.2.3 Environmental Microbiology
- 13.2.4 Industrial Microbiology
- 13.3.1 Research Institutes
- 13.3.2 Biotechnology Companies
- 13.3.3 Pharmaceutical Companies
- 13.3.4 Academic Institutions
- 13.4.1 Saudi Arabia
- 13.4.2 UAE
- 13.4.3 South Africa
- 13.4.4 Egypt
- 13.4.5 Israel
- 13.4.6 Rest of Middle East and Africa
13.6 Regional Trends Analysis
13.7 Middle East & Africa Global Microbiome Sequencing Services Market Research Report - Company Profiles- 13.7.1 Company 1 (Saudi Arabia)
- 13.7.2 Company 2 (UAE)
- 13.7.3 Company 3 (UAE)
- 14.1 Strategic Dashboard of Top Market Players
14.2 Company Profiles (Introduction, Financial Assessments, Portfolio of Offerings, Milestones and Achievements, Strategic Initiative, and SWOT Analysis)- 14.2.1 Illumina
- 14.2.2 QIAGEN
- 14.2.3 Oxford Nanopore Technologies
- 14.2.4 BGI Genomics
- 14.2.5 Zymo Research
- 14.2.6 Eurofins Scientific
16. Principal Presumptions and Acronyms