Microbiome Sequencing Services Market - By Technology: 16S rRNA Sequencing, Shotgun Metagenomics, Whole Genome Sequencing, Others; By Application: Human Microbiome Research, Agricultural Microbiology, Environmental Microbiology, Industrial Microbiology; By End-User: Research Institutes, Biotechnology Companies, Pharmaceutical Companies, Academic Institutions; By Region: North America, Europe, Asia-Pacific, Latin America, Middle East & Africa.
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
4 | Market Challenges
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:
By Application:
By End User:
7 | Regional Analysis
8 | Technology and Innovation
9 | Regulatory Environment
10 | Recent Developments (Q4 2023 – Q2 2025)
11 | Strategic Outlook
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.
Global Microbiome Sequencing Services Market Report
Need help?
Chat with our team in a minute.