Metagenomics Market Size & Outlook, 2025-2033

Metagenomics Market Overview

The global metagenomics market size was valued at USD 2.34 billion in 2024 and is projected to grow from USD 2.62 billion in 2025 to reach USD 6.52 billion by 2033, growing at a CAGR of 12.05% during the forecast period (2025–2033).

Key Market Indicators

• North America dominated the metagenomics industry and accounted for a 39.13% share in 2024.
• Based on product, the kits & reagents segment held the largest share of 59.22% of the metagenomics industry in 2024, owing to their essential role in sample preparation, DNA extraction, and library construction.
• Based on workflow, the sequencing segment is witnessing steady growth, driven by the widespread use of high-throughput sequencing platforms such as Illumina and Oxford Nanopore.
• Based on application, the environmental metagenomics segment dominated the metagenomics industry in 2024 due to its critical role in studying microbial diversity in ecosystems such as soil, oceans, and wastewater.

Market Size & Forecast

• 2024 Market Size: USD 2.34 Billion
• 2033 Projected Market Size: USD 6.52 Billion
• CAGR (2025-2033): 12.05%
• North America: Largest market in 2024
• Asia Pacific: Fastest growing market

A major driver of the global metagenomics market is its expanding application across non-clinical sectors such as agriculture, environmental science, and industrial biotechnology. In agriculture, metagenomic techniques help analyze soil microbiota to enhance crop yield, improve disease resistance, and reduce chemical usage. Environmental applications include monitoring microbial pollution, studying ecosystem dynamics, and supporting climate change research. 

Additionally, in the industrial sector, metagenomics aids in discovering novel enzymes for use in biofuels, bioplastics, and bioremediation. The growing demand for microbiome-based products in the food, cosmetic, and nutraceutical industries further accelerates market growth. Furthermore, technological advances in sequencing platforms, like nanopore and long-read technologies, are improving accuracy, reducing costs, and enabling real-time analysis. These innovations are making metagenomics more accessible across diverse industries, thereby broadening its market base and fueling long-term growth prospects globally.

Market Trends

Integration with Bioinformatics and Ai Tools

The integration of bioinformatics and artificial intelligence (AI) is significantly advancing the market. These technologies streamline the analysis of complex genomic data, enabling faster identification of microbial communities, gene functions, and metabolic pathways. AI algorithms help process large-scale sequencing data with greater accuracy and speed, improving outcomes in diagnostics, drug discovery, and environmental microbiology. 

• For instance, Metagenomi, Inc. recently published a Nature Communications paper in March 2025, describing a compact CRISPR-associated transposase (CAST) system for large-gene integration in human cells. This breakthrough was facilitated by their AI-powered metagenomics platform, which enabled the discovery of previously unknown programmable genome editing tools through microbial sequence mining. 

Such AI-bioinformatics integration is expected to drive innovation, reduce research timelines, and unlock new applications across clinical, agricultural, and industrial domains.

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Market Driver

Growing Prevalence of Infectious and Chronic Diseases

The rising global burden of chronic and infectious diseases is a key driver of growth in the metagenomics market. Metagenomic approaches enable comprehensive microbial profiling, offering critical insights into disease mechanisms, diagnosis, and treatment pathways. These techniques are particularly valuable in understanding gut microbiota's role in chronic illnesses and identifying pathogenic microorganisms in infectious diseases. 

• According to the World Health Organization (WHO), chronic diseases, including cardiovascular diseases, cancer, diabetes, and chronic respiratory conditions, accounted for 74% of all global deaths in 2021. Furthermore, in its 2023 report, the WHO highlighted that tuberculosis (TB) likely continued to be the world’s deadliest infectious disease, responsible for approximately 1.25 million deaths and over 10 million new cases globally. 

As the demand for accurate, rapid, and non-culture-based diagnostic techniques rises, metagenomics emerges as a valuable solution across clinical and public health domains. 

Market Restraint

High Cost and Complexity of Metagenomic Workflows

One of the key restraints in the global market is the high cost and complexity of metagenomic workflows. Although sequencing technologies have become more affordable over time, the overall process, including sample collection, DNA extraction, library preparation, sequencing, and extensive bioinformatics analysis, remains expensive and technically demanding. 

Additionally, metagenomic data requires powerful computational infrastructure and skilled personnel to manage, interpret, and store large volumes of data. These challenges pose a significant barrier for smaller laboratories, research institutions, and organizations in low- and middle-income countries. Moreover, the lack of standardized protocols across laboratories further complicates reproducibility and scalability, slowing down broader clinical and commercial adoption of metagenomic technologies.

Market Opportunity

Public-Private Partnerships and Funding

The global metagenomics market is witnessing significant growth opportunities through increased public-private collaborations and targeted funding initiatives. These partnerships are crucial in accelerating research, improving clinical applications, and building advanced infrastructure for metagenomic sequencing and analysis. Governments, research institutions, and private players are aligning their interests to enhance real-time pathogen detection and microbiome understanding. These collaborations also facilitate the integration of next-generation sequencing with AI-powered data analytics to support diagnostics, surveillance, and treatment.

• For instance, in December 2024, the UK Health Security Agency (UKHSA) launched the mSCAPE (Metagenomics Surveillance Collaboration and Analysis Programme) with NHS, Genomics England, and Oxford Nanopore to enhance real-time pathogen surveillance. Supported by a £50 million Novo Holdings investment, it aims to deliver clinical detection within six hours across 30 NHS sites, targeting respiratory pathogens and antimicrobial resistance using long-read metagenomic sequencing.

Such initiatives are expected to catalyze innovation and global market expansion.

Regional Insights

North America is witnessing robust growth in the market due to its strong biotechnology infrastructure, increased research funding, and advanced sequencing technologies. The rising prevalence of chronic illnesses and increasing integration of microbiome-based diagnostics into clinical practice are driving market demand. Academic collaborations, along with public-private partnerships, are supporting large-scale microbiome studies. Additionally, the widespread use of next-generation sequencing in drug development and infectious disease surveillance is further enhancing adoption across research institutes and clinical laboratories, reinforcing the region’s leadership in innovation-driven metagenomic applications.

U.s. Metagenomics Market Trends

• The U.S. market is driven by robust investments in microbiome research, precision medicine, and genomic diagnostics. Institutions like the NIH support large-scale initiatives such as the Human Microbiome Project. Leading biotech companies, including Illumina and Thermo Fisher Scientific, offer cutting-edge sequencing platforms. Moreover, clinical trials integrating metagenomic data for personalized therapies in oncology and gastrointestinal disorders are expanding market potential.
• Canada’s market is growing with support from government-backed research initiatives and academic partnerships. Projects like Integrated Microbiome Platforms for Advancing Canadian Food and Health (ImPACT) highlight national efforts in microbiome science. Canadian universities, including the University of British Columbia, are leveraging metagenomics for environmental monitoring and public health surveillance, particularly in tracking antimicrobial resistance and waterborne pathogens, thus enhancing market relevance and adoption.

Asia-Pacific Metagenomics Market Trends

Asia Pacific is emerging as a dynamic growth region in the market, driven by rising public health concerns, increasing research funding, and expanding biotechnology sectors. Rapid urbanization and industrialization have created a demand for environmental microbiome analysis. Additionally, growing interest in traditional medicine and dietary habits is leading to studies on region-specific microbiota. Improved access to genomic technologies, coupled with the development of local bioinformatics capacities, is enhancing metagenomic applications across healthcare, agriculture, and water quality monitoring. Government support and academic initiatives are further accelerating market expansion.

• China's market is witnessing rapid growth due to strong government support in microbiome research and biotechnology. Initiatives like the China National GeneBank and collaborations with BGI Genomics enhance large-scale sequencing capabilities. The market benefits from expanding applications in public health, agriculture, and environmental monitoring. For instance, Chinese researchers use metagenomics to track antibiotic resistance genes in water bodies, driving investment in microbial ecosystem management.
• India's market is expanding with rising interest in microbiome-based health solutions and agricultural innovation. The Department of Biotechnology supports projects like the Indian Microbiome Initiative, fostering indigenous R&D. Indian startups and research institutes are applying metagenomics in precision medicine and soil microbiota analysis. For example, metagenomic studies are being used to understand gut microbiota variations in Indian populations to develop tailored probiotic therapies and nutrition plans.

Europe Metagenomics Market Trends

Europe is experiencing steady expansion in the global market, supported by significant investment in microbiome research and sustainable environmental monitoring projects. Regulatory emphasis on food safety, environmental conservation, and antibiotic resistance surveillance is accelerating demand for metagenomic tools. Academic institutions and biotech firms are collaborating to explore the role of microbiomes in personalized medicine and agriculture. Furthermore, well-established genomic databases and ethical data-sharing practices are fostering trust and cross-border research collaborations, enabling the region to develop advanced diagnostics and ecological studies powered by metagenomic insights.

• Germany's market is witnessing robust growth due to strong investments in microbiome research and advanced sequencing infrastructure. Institutions like the Max Planck Institute are driving innovations in environmental and clinical metagenomics. The government’s support for precision medicine and sustainable agriculture further fuels adoption. Additionally, Germany’s biotech hubs, including Berlin and Munich, attract global players focused on microbiome-based diagnostics and therapeutic developments.
• The UK’s market is expanding rapidly, driven by initiatives such as the UK Biobank and NHS Genomic Medicine Service. Research institutions like the Wellcome Sanger Institute are pioneering human microbiome and pathogen surveillance studies. Metagenomics is being integrated into public health monitoring, agriculture, and wastewater surveillance. Supportive policies and collaborations with pharmaceutical firms are positioning the UK as a key player in translational metagenomics research and applications.

Market Segmentation

Product Insights

Kits & reagents hold the largest share in the global market due to their essential role in sample preparation, DNA extraction, and library construction. These consumables are used across all stages of metagenomic workflows, ensuring repeat purchases and consistent demand. Additionally, the increasing availability of specialized kits for specific sample types, such as soil, water, and gut microbiomes, further boosts segment dominance. Their critical application in both research and clinical settings continues to drive robust market growth.

Technology Insights

Shotgun metagenomic sequencing dominates the technology segment as it enables comprehensive analysis of all microbial genomes within a sample, offering greater taxonomic and functional resolution compared to 16S rRNA sequencing. Its ability to detect rare or novel microorganisms, antibiotic resistance genes, and functional pathways makes it highly valuable in clinical diagnostics, environmental studies, and drug development. As sequencing costs decline and bioinformatics tools improve, the adoption of shotgun metagenomics continues to accelerate across various applications.

Workflow Insights

The sequencing segment leads the market, primarily driven by the widespread use of high-throughput sequencing platforms such as Illumina and Oxford Nanopore. It represents the core step in metagenomic studies, enabling rapid and accurate identification of complex microbial communities. Technological advancements, reduced sequencing costs, and increasing demand for precision diagnostics and microbiome profiling have further solidified sequencing as the central and most resource-intensive stage in the workflow.

Application Insights

Environmental metagenomics emerges as a dominant application area due to its critical role in studying microbial diversity in ecosystems such as soil, oceans, and wastewater. It aids in monitoring pollution, detecting pathogens, and assessing climate change impacts on microbial ecology. Governments and academic institutions increasingly fund environmental microbiome research, driving adoption. The growing need to understand and manage global ecological challenges through microbial insight significantly boosts the demand for these solutions. 

Distribution Channel Insights

The direct/B2B sales segment plays a vital role in the market, catering to large-scale food and beverage manufacturers. These direct transactions allow for better pricing, bulk procurement, and long-term supply agreements. Leading producers in this industry maintain strong relationships with multinational food companies, ensuring consistent demand. This channel ensures product customization, technical support, and timely delivery, making it the preferred mode of distribution for major players across the bakery, infant formula, dairy processing, and nutrition industries.

Company Market Share

Companies in the global metagenomics market are focusing on expanding their product portfolios by developing advanced sequencing platforms, user-friendly bioinformatics tools, and cloud-based data analytics. Strategic collaborations with research institutes and healthcare providers are boosting innovation. Investments in R&D and acquisitions of niche biotech firms are enabling entry into emerging applications such as microbiome-based therapeutics, agriculture, and environmental studies, thereby strengthening their market presence and competitive positioning globally.

Illumina, Inc: Illumina, Inc. is a leading player in the global metagenomics industry, renowned for its advanced next-generation sequencing (NGS) platforms. Headquartered in San Diego, California, Illumina provides high-throughput sequencing technologies and reagents that are pivotal for metagenomic research and microbiome analysis. The company supports applications across human health, agriculture, and environmental studies. Through constant innovation, partnerships, and product launches, such as the NovaSeq and MiSeq systems, Illumina continues to drive accessibility and precision in metagenomics and microbial genomics worldwide.

• In October 2024, Illumina announced compact, affordable MiSeq i100 instruments (starting around $49,000 and $109,000), optimized for smaller labs. These systems deliver faster run times (~4 hours), room-temperature reagents, and promise broader access to sequencing capabilities, starting shipping globally in 2025.

List of key players in Metagenomics Market

1. Illumina, Inc.
2. Thermo Fisher Scientific Inc.
3. QIAGEN N.V.
4. Agilent Technologies, Inc.
5. PerkinElmer, Inc.
6. Oxford Nanopore Technologies plc
7. BGI Group
8. Eurofins Scientific
9. F. Hoffmann-La Roche Ltd
10. Bio-Rad Laboratories, Inc.

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Recent Developments

• June 2025- Phase Genomics, Inc., launched ProxiMeta Starter and Elite Bundles, bringing Hi‑C metagenomics within reach for diverse research users. The Starter Bundle is ideal for early-career researchers (up to two samples) with support and guaranteed library prep success. The Elite Bundle caters to experienced labs, offering deep sequencing and in-house Hi‑C assembly for up to eight samples.
• April 2025- Metabolon introduced a comprehensive microbiome solution that merges metagenomic sequencing, a new metabolite panel, and advanced multi‑omics bioinformatics tools. The platform enables deeper insights into microbial species and their functional metabolic outputs via machine‑learning integration of shotgun and 16S sequencing data.