The period extending from 2025 to 2035 is likely to be marked by strong growth in the metagenomics market, driven by advances in next-generation sequencing (NGS), increasing interest in microbiome applications, and expanding spheres of application in clinical diagnostics, environmental biology, and agriculture.
Metagenomics is the direct study of the genetic material from a microbial community in its natural environment, allowing for the study of unculturable microbes and giving insight into complex ecosystems.
The market is further supported by increasing R&D investment in infectious disease surveillance, antimicrobial resistance (AMR) profiling, and personalized nutrition. The growing availability of bioinformatics tools, reduced sequencing costs, and integration with AI and machine learning are enhancing the accessibility and scalability of metagenomic workflows.
The metagenomics market is projected to grow at a CAGR of 6.7%, increasing from USD 231.1 million in 2025 to approximately USD 442.07 million by 2035.
Key Market Metrics
| Metric | Value |
|---|---|
| Market Size in 2025 | USD 231.1 Million |
| Projected Market Size in 2035 | USD 442.07 Million |
| CAGR (2025 to 2035) | 6.7% |
The North American region occupies the largest proportion of the metagenomics markets on a regional level, particularly due to having major research infrastructures and genomic infrastructures, as well as applications in human microbiome project work, disease diagnoses, and drug discovery.
Many leading academic centers and biotechnology companies in the United States have forged ahead in the field of metagenomic sequencing bioinformatics. According to the WHO, the emerging scope of metagenomics in North America is related to antimicrobial resistance and public health surveillance.
The market in Europe depends much on public funding for microbiome research, precision medicine projects, and environmental programs. Countries such as Germany, the UK, and the Netherlands have started the integration of metagenomics into agriculture, wastewater monitoring, and food safety. WHO reports that European investments into microbial ecosystem analysis and zoonotic disease monitoring using metagenomic tools are accelerated by the focus on "One Health" strategies.
Those with the fastest growth are Asia-Pacific, with such growth being driven by the areas of interest in microbiome health interventions in connection with genomics research-and increasingly accepted in sequencing technologies for agriculture and public health.
This region is mainly represented by China, Japan, South Korea, and India. United Nations reports have predicted investments in genomics and bioinformatics by the Asia-Pacific region would overwhelm the global average until 2035; thus, it is anticipated that the area would be a focal point in clinical and environmental metagenomics.
Data interpretation complexity, standardization gaps, and high infrastructure costs
The inherent complexity of metagenomics data and the requisite advanced computational tools and trained personnel have remained the bigger challenges. The entire range, from sampling to methodology, sequencing protocol, and data interpretation framework, is yet to be standardized across laboratories and contexts of research.
Installation of high-throughput sequencing and computing resources is still devastatingly unaffordable, even for the low and middle-income settings. The World Health Organization calls for the equitable development of global health equity standards for genomic surveillance metagenomics tools.
Personalized microbiome-based medicine, AMR monitoring, and environmental diagnostics
There are emerging opportunities in the personalized health segments such as microbiome-based diagnostics, products development, and therapeutic response prediction. In clinical microbiology, metagenomic sequencing is almost single-handedly revolutionizing the diagnostics for those rare and polymicrobial infections that can simply not be cultured.
The environmental potential areas like soil health monitoring, water quality assessment, and remediation are rapidly on the rise. WHO indicates that providing metagenomics data into the functioning surveillance system of public health and environment could significantly boost the preparedness of the whole world against pandemics and threats related to climate change.
From 2020 to 2024, the COVID-19 pandemic contributed to the acceleration of genomic research and to the showcasing of the metagenomic potential in pathogen, wastewater, and AMR surveillance. Governmental and philanthropic investments in sequencing infrastructure have mushroomed around the world.
The market between 2025 and 2035 is expected to make the shift toward real-time metagenomic analysis, cloud data integration, and AI-enabled diagnosis. Portable sequencers, microbiome-aware clinical decision support systems, and synthetic biology that may emanate from metagenomic insights are going to characterize the next phase of innovation.
Market Shifts: A Comparative Analysis 2020 to 2024 vs. 2025 to 2035
| Market Shift | 2020 to 2024 Trends |
|---|---|
| Regulatory Landscape | Pilot integration into AMR and outbreak surveillance |
| Consumer Trends | Focus on microbiome kits and gut health awareness |
| Industry Adoption | Academic research and pilot clinical use |
| Supply Chain and Sourcing | Centralized NGS service providers |
| Market Competition | Dominated by sequencing equipment and reagent manufacturers |
| Market Growth Drivers | Human microbiome projects, COVID-19, and NGS adoption |
| Sustainability and Impact | High resource use in sequencing workflows |
| Smart Technology Integration | Batch sequencing and manual annotation |
| Sensorial Innovation | N/A |
| Market Shift | 2025 to 2035 Projections |
|---|---|
| Regulatory Landscape | Global standardization of metagenomic diagnostics and data sharing |
| Consumer Trends | Rise in precision microbiome therapies and data-backed health decisions |
| Industry Adoption | Expansion into diagnostics, nutrition, agriculture, and wastewater management |
| Supply Chain and Sourcing | Growth of local sequencing hubs and decentralized bioinformatics platforms |
| Market Competition | Entry of AI-driven diagnostics, cloud analytics, and microbiome biotech firms |
| Market Growth Drivers | One Health surveillance, global food security, and synthetic biology |
| Sustainability and Impact | Eco-efficient lab operations and green bioinformatics infrastructure |
| Smart Technology Integration | Real-time microbiome mapping, AI-based taxonomy, and predictive metagenomics |
| Sensorial Innovation | Field-deployable, sensor-enabled sampling kits for environmental microbiomes |
The metagenomics market in the USA shows an unwavering growth attributable to the advancement in next-generation sequencing (NGS), microbiome study, and infectious disease surveillance. Institutions and biotechnologies are employing metagenomics for applications in drug discovery, environmental monitoring, and precision medicine.
As per OECD, there are federal efforts in support of microbiome and pathology innovation under NIH Human Microbiome Program and grants from DARPA and BARDA. The growing application of metagenomics in agriculture and food safety in terms of microbial diversity assessment can further stimulate growth in this area.
| Country | CAGR (2025 to 2035) |
|---|---|
| United States | 7.0% |
Much of the advancement of the metagenomics market in the UK takes place on the back of microbial genomic research, AMR (antimicrobial resistance) surveillance, and personalized health, strongly supported by academia and the government.
As per OECD, the United Kingdom is the global leader in genomic medicine, and organizations such as Wellcome Sanger Institute use metagenomics to study gut flora, environmental biodiversity, and zoonotic transmission. NHS-supported genomic projects and public health microbiology programs also expand demand for metagenomic sequencing in clinical and environmental settings.
| Country | CAGR (2025 to 2035) |
|---|---|
| United Kingdom | 6.5% |
The EU market for metagenomics is gaining traction through investments in food safety, environmental microbiome research, and translational medicine. Germany, France, and the Netherlands are applying metagenomics to monitor wastewater, soil biodiversity, and chronic disease studies.
According to UN data, programs such as Horizon Europe and One Health fund applications of metagenomics in agriculture, human health, and antimicrobial stewardship. EU laboratories are also adopting portable NGS platforms and cloud analysis tools to improve response to microbial surveillance and outbreak.
| Country | CAGR (2025 to 2035) |
|---|---|
| European Union | 6.7% |
Like any other country, Japan's metagenomics market is maturing steadily, thanks to the applications enhanced by probiotic development, gastrointestinal health, and even fermentation studies. However, the focus of the country towards healthy aging and traditional studies on their diet has motivated the public to be inspired by the gut microbiota profiling and functional genomics.
According to the OECD, investments of the Japanese government and universities are at work with microbial biotechnology platforms, thereby widening the scope of metagenomic studies in basic and clinical research. The food industry is also the largest user of metagenomic tools and applications in the metagenomics arena by ensuring food safety and quality.
| Country | CAGR (2025 to 2035) |
|---|---|
| Japan | 6.4% |
The South Korea metagenomics market has been expanded at a fast pace with applications increasingly being applied towards health, agriculture, and bioenvironmental research. National investments towards developing genomic medicine and bioinformatics platforms integrated with AI, as per OECD data, are speeding up the country's lead in precision health.
Research institutes in Korea use metagenomic sequencing to study a number of dimensions including surveillance of hospital-acquired infections, antibiotic resistance genes, and the environmental microbial ecosystem. These are joint public-private partnerships between university and biotech startups for developing innovative microbiome-based diagnostics and therapeutics.
| Country | CAGR (2025 to 2035) |
|---|---|
| South Korea | 6.9% |
The metagenomics market has been experiencing steady growth as the researchers and clinicians have now started utilizing various advanced genomic tools to investigate complex microbial communities. Library preparation kits are renowned for preparing DNA samples for sequencing, giving high-quality data output.
Within the product type and end-use application categories, library preparation kits and pharmaceutical and biotechnology companies dominate the global market share with their efficiency, reproducibility, and application in state-of-the-art research and development activities.
These two segments, in particular, support microbial analysis fully, assist in the search of new drugs, and promote development in personalized medicine.With an increased focus on microbial profiling in varied sectors, library preparation kits for pharmaceutical and biotechnology companies remain in the forefront of driving innovations and solving complex biological problems.
Library preparation kits dominate product use due to standardized protocols, high-throughput capabilities, and compatibility with diverse sequencing platforms
| Product Type | Market Share (2025) |
|---|---|
| Library Preparation Kits | 68.5% |
Library preparation kits lead the metagenomics market from a standpoint on the basis of a streamlined workflow that converts raw DNA samples into sequencing-ready libraries. They assure standardized protocols for consistency and completion and play a huge role in minimizing sample preparation time while also minimizing errors. As a result, these kits have become an indispensable tool in high-throughput sequencing by now.
The dominance of library preparation kits can be attributed to their outstanding diversity of sample types, compatibility with multiple sequencing or sequencing technologies, and ability to perform with high-quality data all important for the direct and independent interpretation of microbial analysis. Their wide adoption serves as sufficient testament to their importance for metagenomic studies of efficiency and reliability.
Pharmaceutical & biotechnology companies dominate end user adoption due to intensive R&D activities, focus on novel therapeutics, and integration of metagenomic insights into drug development pipelines
| End User | Market Share (2025) |
|---|---|
| Pharmaceutical & Biotechnology Companies | 66.2% |
Pharmaceutical and biotechnology companies are the largest end-user segments for the metagenomics market, driven by their efforts in new drug and therapy development, and enhancement and advancement of diagnostic tools. The incorporation of metagenomics has aided in speeding up discovering and optimizing biologically active compounds in research and development efforts.
Such preferences are further supported by the much investment by these companies in cutting-edge technology, necessitating holistic microbial insights to cater to extensive researches. The demand for innovative solutions to healthcare needs has kept pharmaceutical and biotechnology companies among the cutting-edge users of metagenomics for the benefit of medical science.
Rapid expansion in the metagenomics market is driven by the increasing efficiency of research and clinical scientists in high-throughput sequencing for understanding complex microbial communities-humans gut soils oceans and industrial bioreactors. Metagenomics accomplishes the unculturable analysis of microbial DNA, revealing new species, antimicrobial resistance genes, and metabolic pathways due to the use of these high-throughput tools.
Demand is thus attributed to the expanding applications of precision medicine, environmental monitoring, agricultural microbiome management, and diagnostics for infectious diseases. Advances in next-generation sequencing (NGS), bioinformatics pipelines, and sample preparation workflows will result in greater accessibility of metagenomic tools in prospects of global markets. WHO estimates that metagenomic surveillance is a very important area for influencing early detection for emerging pathogens as well as antibiotic resistance in public health systems.
Market Share Analysis by Key Players & Metagenomics Solution Providers
| Company Name | Estimated Market Share (%) |
|---|---|
| Illumina, Inc. | 14-17% |
| Thermo Fisher Scientific | 11-14% |
| Qiagen N.V. | 9-12% |
| Oxford Nanopore Technologies | 7-10% |
| BGI Genomics Co., Ltd. | 6-9% |
| Other Providers | 38-45% |
| Company Name | Key Offerings/Activities |
|---|---|
| Illumina, Inc. | In 2024, introduced enhanced NovaSeq kits optimized for low-biomass environmental samples in 2025, launched microbiome-specific sequencing panels with preconfigured bioinformatics. |
| Thermo Fisher Scientific | In 2024, expanded Ion Torrent workflows for clinical pathogen metagenomics in 2025, developed One Health metagenomics bundles for zoonotic disease monitoring. |
| Qiagen N.V. | In 2024, released QIAseq 16S/ITS kits for targeted amplicon-based profiling in 2025, added integrated microbiome data portals for translational research applications. |
| Oxford Nanopore Technologies | In 2024, launched long-read adaptive sampling tools for real-time microbial genome assembly in 2025, enabled rapid AMR gene detection in hospital wastewater surveillance. |
| BGI Genomics Co., Ltd. | In 2024, introduced cost-optimized metagenomic sequencing services for agri-biotech and soil microbiome research in 2025, deployed multi-sample pathogen detection pipelines in Southeast Asia. |
Key Market Insights
Illumina, Inc. (14-17%)
Illumina leads in NGS systems and library prep tools for both shotgun and amplicon-based metagenomic studies. Its solutions support human microbiome analysis, environmental biodiversity research, and infectious disease diagnostics at global scale.According to WHO, widespread genomic surveillance using metagenomics supports antimicrobial resistance tracking and outbreak preparedness.
Thermo Fisher Scientific (11-14%)
Thermo Fisher offers integrated sample-to-answer solutions for metagenomic sequencing using Ion Torrent technology. Its applications span foodborne pathogen surveillance, zoonotic disease tracking, and microbial diversity studies.According to UN, expanding microbial diagnostics through metagenomics helps address global food safety, One Health, and biosurveillance initiatives.
Qiagen N.V. (9-12%)
Qiagen provides sample prep, DNA stabilization, and 16S/ITS sequencing tools for microbiome and metagenome profiling. It also supports downstream analytics through QIAGEN CLC Genomics Workbench and microbiome portals.According to OECD, effective bioinformatics integration is essential for interpreting complex metagenomic datasets in health and environmental contexts.
Oxford Nanopore Technologies (7-10%)
Oxford Nanopore enables long-read sequencing of entire microbial genomes directly from environmental or clinical samples. Its real-time sequencing workflows allow in-field detection of novel pathogens and resistance markers.According to WHO, real-time metagenomics supports faster outbreak containment and on-site microbial risk assessment.
BGI Genomics Co., Ltd. (6-9%)
BGI offers scalable metagenomic services with competitive pricing for academic, agricultural, and public health use. It operates internationally with partnerships in food safety, aquaculture, and environmental remediation.According to World Bank Report, low-cost metagenomic platforms increase access to genomic surveillance tools in emerging markets.
Other Key Players (38-45% Combined)
Numerous companies and institutions contribute to this evolving field with specialized kits, software, and services. These include:
The overall market size for the metagenomics market was approximately USD 231.1 million in 2025.
The metagenomics market is expected to reach approximately USD 442.07 million by 2035.
The demand for metagenomics is rising due to its ability to study every type of microorganism, regardless of whether it can be cultured or not.
The top 5 countries driving the development of the metagenomics market are the United States, China, Germany, Japan, and the United Kingdom.
Library preparation kits and pharmaceutical & biotechnology company adoption are expected to command significant shares over the assessment period.
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Metagenomics Market
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