Microbiome Sequencing Services Market to Reach USD 12.6 Billion by 2031 Amidst Surging Demand from Pharma, Food, and Personalized Medicine Sectors

Chicago, 29th May 2025 — Clearview Market Insights (CVMI) forecasts that the global microbiome sequencing services market will grow from USD 3.4 billion in 2024 to USD 12.6 billion by 2031, registering a compound annual growth rate (CAGR) of 20.5 percent. This explosive growth is supported by rapid adoption across pharmaceutical development, nutraceutical innovation, precision agriculture, environmental monitoring, and emerging consumer health products.

We are witnessing a shift from exploratory microbiome research to actionable diagnostics and commercial-scale applications," said Dr. Ravi Deshmukh, Senior Genomics Analyst at CVMI. "Microbiome sequencing services now directly impact clinical trials, regulatory submissions, soil health programs, and personalized nutrition platforms.

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Key Figures

Metric	2024	2031	CAGR (2024–31)
Market Value (USD Billion)	3.4	12.6	20.5 %
Human Health Applications	42 %	44 %	—
16S rRNA Share	38 %	30 %	—
Shotgun Metagenomics	34 %	40 %	—
Long-Read Sequencing	5 %	12 %	—
Top 5 Vendors’ Share	67 %	61 %	—

Growth Drivers

• Precision Medicine & Drug Discovery – Biopharma players leverage microbiome profiling for immunotherapy response prediction, gut-brain axis targeting, and next-generation antibiotic development.
• Functional Foods & Personalized Nutrition – Wellness brands now routinely test gut microbiota to optimize prebiotic and probiotic formulations, moving toward consumer-specific dietary supplements.
• Agricultural Productivity – Soil microbiome sequencing helps optimize yield, control disease, and reduce chemical inputs through biologically driven farming.
• Environmental Surveillance – National monitoring programs use metagenomics to track water, soil, and urban microbiomes affected by climate stress and pollution.
• Cosmeceuticals and Dermatology – Skin microbiome studies enable evidence-based formulation of skincare, anti-aging, and dermo-probiotic products.

Company Highlights

Company	2024 Market Share	Strategic Focus
Illumina	28 %	Microbiome-specific library prep kits and end-to-end sequencing bundles
Zymo Research	12 %	Extraction and prep kits; turnkey sequencing workflows
CosmosID	10 %	Curated metagenomics and AI-driven pathogen detection tools
Eurofins Genomics	9 %	Sample logistics and regulatory-compliant sequencing for food, pharma, and environment
Novogene	8 %	High-throughput agricultural and multi-omics pipelines

Regional Insights

• North America – Home to NIH Microbiome projects, pharma partnerships, and the booming consumer microbiome testing industry. Holds 42% market share.
• Europe – Strong public funding, microbiome start-ups, and cross-border research collaborations. Key centers include Germany, France, and the Netherlands.
• Asia-Pacific – Fastest growing at 24.2% CAGR, led by China and India’s national microbiome initiatives and growing soil/agriculture applications.
• Latin America – High microbiome use in precision agriculture and livestock optimization. Brazil leads with national soil health data infrastructure.
• Middle East & Africa – Nascent markets with increasing interest in climate-resilient agriculture and water-quality metagenomics.

2024–25 Milestones

Quarter	Event	Outcome
Q1 2024	Illumina released NovaSeq Microbiome Plus kit	Reduced error rates in low-biomass samples by 20%
Q2 2024	CosmosID launched AMR-enhanced metagenomic pipeline	Clinical labs cut annotation time by 35%
Q3 2024	Zymo introduced portable extraction kits	Field researchers in India and Brazil scaled soil microbiome sampling
Q4 2024	Novogene doubled throughput with HiSeq-X integration	Shortened turnaround to 48 hours for high-volume agricultural studies
Q1 2025	GutBiomeX debuted AI-powered FMT donor matching	Clinical trials initiated in Canada and Germany

Technology Trends

• Long-Read Sequencing Growth – Accuracy and completeness of rare and novel microbial genomes improve functional annotation and clinical insights.
• AI-Augmented Annotation – Taxonomic classification time cut by over 40%; enables automation and real-time interpretation.
• Multi-Omics Integration – Combination of metagenomics with metabolomics and proteomics enhances understanding of microbiota-host interactions.
• Blockchain-Backed Microbiome Data – Improves consent traceability, access rights, and commercial use licensing for personal and clinical datasets.
• In-Field Sequencing Kits – Used in agriculture and conservation; allow real-time microbial monitoring for yield prediction and ecosystem health.

Strategic Roadmap to 2031

• 2025 – Personalized gut microbiome reports integrated into consumer apps and dietary recommendations.
• 2026 – AI-generated microbiome taxonomies become standard in food and pharma validation.
• 2027 – Sequencing cost per sample falls below USD 10, accelerating mass adoption.
• 2028 – Multi-omics diagnostics receive first FDA and EMA approval.
• 2029 – Global harmonization on DTC testing guidelines in microbiome field.
• 2030 – Regenerative farming policies mandate soil microbiome certification.
• 2031 – Human microbiome data included in electronic health records in leading OECD nations.

 

 

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