Metagenomics Sequencing Market - Global Industry Size, Share, Trends, Opportunity, and Forecast, Segmented By Product and Service (Reagents & consumables, Instruments, Services), By Technology (Shotgun metagenomic sequencing, 16S rRNA sequencing, Whole genome sequencing & de novo assembly, Meta transcriptomics), By Application (Drug discovery, Ecological & environmental metagenomics, Clinical diagnostics, Biofuel, Industrial applications), By Region and Competition, 2021-2031F

Forecast Period	2027-2031
Market Size (2025)	USD 3.17 Billion
CAGR (2026-2031)	14.73%
Fastest Growing Segment	Drug discovery
Largest Market	North America
Market Size (2031)	USD 7.23 Billion

Market Overview

The Global Metagenomics Sequencing Market will grow from USD 3.17 Billion in 2025 to USD 7.23 Billion by 2031 at a 14.73% CAGR. Metagenomics sequencing is defined as the culture-independent analysis of genetic material recovered directly from environmental or clinical samples, enabling the comprehensive profiling of microbial communities without laboratory cultivation. The market is fundamentally driven by the escalating global burden of infectious diseases and the critical necessity for antimicrobial resistance surveillance, which require rapid and unbiased pathogen identification capabilities. Furthermore, the continuous reduction in high-throughput sequencing costs is expanding the technology's accessibility, supporting its integration into clinical diagnostics, agricultural biotechnology, and environmental monitoring.

However, a significant challenge impeding market expansion is the complexity of managing and interpreting the massive volume of genomic data generated. The lack of standardized bioinformatics pipelines and high-quality data infrastructure often creates a bottleneck for effective workflow implementation. According to the Pistoia Alliance, in its 2024 Lab of the Future Global Survey, 52% of life science professionals cited low-quality and poorly curated datasets as the primary barrier to the adoption of advanced analytical technologies. This bioinformatics hurdle remains a critical constraint on the scalable deployment of metagenomic solutions.

Key Market Drivers

Rapid Technological Advancements in Next-Generation Sequencing (NGS) Platforms are fundamentally reshaping the Global Metagenomics Sequencing Market by enhancing data resolution and reducing turnaround times. Innovations in long-read sequencing and high-throughput capabilities now allow for precise microbial identification without culture, driving adoption across clinical and industrial applications. This technical momentum is evident in the financial performance of key innovators. According to Oxford Nanopore Technologies, July 2025, in the 'Trading Update', the company reported first-half revenue of approximately £105 million, representing 25% growth driven by strong uptake in applied markets. This trajectory highlights the increasing reliance on advanced sequencing tools. Reinforcing this market scale, according to Illumina, in 2025, the company generated $1.08 billion in third-quarter revenue, underscoring the vast commercial ecosystem that supports metagenomic analysis workflows.

Concurrently, a Surge in Government Funding and Public-Private Genomic Initiatives is accelerating the deployment of metagenomic solutions for pathogen surveillance and environmental monitoring. Governments worldwide are prioritizing genomic infrastructure to prepare for future biological threats, thereby creating a sustained demand for sequencing technologies. These investments are pivotal in subsidizing high operational costs and fostering large-scale research collaborations. According to the European Commission, May 2025, in the 'Horizon Europe work programme 2025', the body allocated €7.3 billion to research and innovation, with significant funding directed toward health and bioeconomy sectors that utilize metagenomic methodologies. Such capital infusion not only mitigates development risks but also incentivizes the integration of metagenomics into national public health strategies and agricultural management systems.

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Key Market Challenges

The substantial complexity associated with bioinformatics and data management stands as a critical barrier impeding the Global Metagenomics Sequencing Market. As sequencing platforms generate exponentially growing volumes of complex genomic data, the computational infrastructure required to efficiently process, store, and interpret this information often lags behind. The absence of standardized protocols leads to fragmented workflows, making it difficult for organizations to integrate metagenomic findings into routine decision-making processes or compare results across different studies.

This technical bottleneck directly hampers market growth by creating significant operational inefficiencies and increasing the resource burden on end-users. The inability to seamlessly manage these vast datasets prevents the translation of raw sequencing outputs into actionable intelligence, thereby discouraging adoption among potential users who lack specialized computational expertise. According to the Pistoia Alliance, in 2025, 57% of life science professionals identified data silos as the top persistent challenge impeding the effective utilization of laboratory data. Consequently, these bioinformatics constraints limit the technology’s scalability and restrict its penetration into cost-sensitive clinical and industrial sectors.

Key Market Trends

The Integration of Artificial Intelligence for Enhanced Data Interpretation is rapidly emerging as a primary trend, fundamentally addressing the bottleneck of bioinformatics complexity that restricts scalable sequencing adoption. Market players are increasingly embedding machine learning algorithms directly into genomic workflows to decipher the "dark matter" of microbial data, enabling high-speed pathogen detection and functional prediction that manual curation cannot achieve. This shift from simple data generation to intelligent, actionable insight is proving to be a significant revenue driver for companies at the forefront of this convergence. According to Tempus AI, February 2025, in the 'Fourth Quarter and Full Year 2024 Results', the company reported full-year genomics revenue of $451.7 million, representing a 24.4% year-over-year increase, a growth trajectory attributed directly to the expanded adoption of its AI-enabled precision medicine and data structuring solutions.

Simultaneously, the market is witnessing a decisive Shift Towards Multi-Omics Approaches for Functional Microbiome Analysis, moving beyond the static cataloging of DNA sequences to understanding active microbial gene expression and protein synthesis. This trend is driven by the need to correlate genomic data with phenotypic outcomes, integrating metatranscriptomics and metaproteomics to provide a holistic view of microbial community dynamics in both clinical and environmental settings. Major industry leaders are aggressively consolidating these capabilities to offer end-to-end multi-modal platforms. According to Thermo Fisher Scientific, January 2025, in the 'Fourth Quarter and Full Year 2024 Results', the company reported fourth-quarter revenue of $11.40 billion, a performance bolstered by its strategic expansion into the proteomics sector, including the integration of Olink’s solutions to support advanced multi-omics research workflows.

Segmental Insights

The Drug discovery segment represents the fastest-growing vertical within the Global Metagenomics Sequencing Market, primarily due to the rising demand for microbiome-derived therapeutics. Pharmaceutical entities are leveraging metagenomics to identify novel bioactive molecules and genetic markers that were previously inaccessible through traditional culturing methods. This capability significantly expedites the validation of new drug targets for treating infectious and chronic diseases. Furthermore, the integration of genomic data into precision medicine workflows supports the creation of tailored treatments, thereby solidifying the pivotal role of metagenomics in modern pharmaceutical research and development strategies.

Regional Insights

North America maintains a leading position in the global metagenomics sequencing market due to substantial investments in biotechnology research and development. The region benefits significantly from established healthcare infrastructure and consistent funding from federal agencies, including the National Institutes of Health, which actively supports genomic study initiatives. Furthermore, the concentration of key industry players within the United States facilitates the commercialization of sequencing technologies for clinical applications. This dominance is reinforced by favorable regulatory frameworks that encourage the integration of metagenomics into precision medicine and diagnostic procedures across academic and pharmaceutical sectors.

Recent Developments

• In April 2025, Metabolon, Inc. launched a comprehensive microbiome research solution that integrated high-quality metagenomics sequencing with a new microbiome metabolite panel. This innovative toolkit was developed to combine metagenomic data, which identifies microbial species and their genetic potential, with metabolomic data that reveals the functional contributions of these microbes to host physiology. The solution allowed researchers to select various sequencing methods and depths to seamlessly merge metagenomics with phenotypic insights. The Chief Business Officer of Metabolon noted that this synergy provided deeper microbiome insights than either approach could offer individually, positioning the company as a unified source for integrated multi-omics data.
• In October 2024, Delve Bio announced a strategic partnership with Broad Clinical Labs to expand access to metagenomic next-generation sequencing (mNGS) for the diagnosis of infectious diseases. This collaboration was established to leverage the high-throughput capabilities and clinical expertise of Broad Clinical Labs to scale the commercialization of Delve Bio’s pathogen-agnostic platform. The technology was designed to identify a wide range of bacteria, fungi, parasites, and viruses in a single test, providing definitive answers for complex cases such as meningitis and encephalitis. The partnership aimed to accelerate the availability of rapid, hypothesis-free diagnostics for patients suffering from severe neurological infections.
• In April 2024, Clinical Microbiomics introduced its advanced long-read sequencing services, tailored to meet the rigorous requirements of clinical, academic, and industrial research. This new offering provided comprehensive capabilities for 16S, ITS, and 18S rRNA sequencing, as well as isolate and shotgun metagenomics, delivering industry-leading read lengths and quality scores. The expanded portfolio allowed for the reconstruction of high-quality metagenome-assembled genomes, offering a more complete resolution of microbial ecosystems. The Chief Executive Officer of Clinical Microbiomics stated that these enhanced capabilities would redefine the standards for microbial analysis and enable deeper insights into host-microbiome interactions.
• In February 2024, PacBio launched the HiFi Prep Kit 96 and HiFi Plex Prep Kit 96, which were designed to provide automated and scalable library preparation solutions for high-throughput sequencing. These new products enabled researchers to process up to 1,536 samples in a single sequencing run, delivering a significant reduction in costs and workflow time. The company highlighted that these advancements would transform large-scale sequencing projects across critical fields such as microbial genomics and agrigenomics. By improving the efficiency of library preparation, PacBio aimed to facilitate broader adoption of high-fidelity long-read sequencing for complex applications, including the analysis of diverse microbial communities.

Key Market Players

• BGI Genomics Co Ltd.
• Eurofins Scientific SE
• Illumina Inc.
• Macrogen, Inc.
• Oxford Nanopore Technologies plc.
• Pacific Biosciences of California, Inc.
• PerkinElmer Inc.
• QIAGEN N.V.
• Swift Biosciences Inc.
• Thermo Fisher Scientific Inc.

By Product and Service	By Technology	By Application	By Region
Reagents & consumables Instruments Services	Shotgun metagenomic sequencing 16S rRNA sequencing Whole genome sequencing & de novo assembly Meta transcriptomics	Drug discovery Ecological & environmental metagenomics Clinical diagnostics Biofuel Industrial applications	North America Europe Asia Pacific South America Middle East & Africa

Report Scope:

In this report, the Global Metagenomics Sequencing Market has been segmented into the following categories, in addition to the industry trends which have also been detailed below:

• Metagenomics Sequencing Market, By Product and Service:

• Reagents & consumables
• Instruments
• Services

• Metagenomics Sequencing Market, By Technology:

• Shotgun metagenomic sequencing
• 16S rRNA sequencing
• Whole genome sequencing & de novo assembly
• Meta transcriptomics

• Metagenomics Sequencing Market, By Application:

• Drug discovery
• Ecological & environmental metagenomics
• Clinical diagnostics
• Biofuel
• Industrial applications

• Metagenomics Sequencing Market, By Region:

• North America
• United States
• Canada
• Mexico
• Europe
• France
• United Kingdom
• Italy
• Germany
• Spain
• Asia Pacific
• China
• India
• Japan
• Australia
• South Korea
• South America
• Brazil
• Argentina
• Colombia
• Middle East & Africa
• South Africa
• Saudi Arabia
• UAE