Metagenomic Sequencing Market

Metagenomic Sequencing Market Overview

The metagenomic sequencing market size is estimated to grow from USD 2.20 billion in 2024 to USD 2.55 billion in 2025 and USD 8.63 billion by 2035, representing a CAGR of 13.0% during the forecast period.

To learn more about this report, request a free sample copy

Metagenomics sequencing refers to the study of genetic materials found in environmental samples, including microbial community, and human DNA samples. The market for metagenomics sequencing has gained substantial traction due to the increasing usage for disease studies and drug development. It is worth mentioning that healthcare industry is witnessing a massive burden of chronic diseases, genetic diseases and infectious diseases. With availability of metagenomics sequencing technologies, clinicians are able to identify the root cause of disease by studying whole genome sequencing, function and molecular pattern.

Furthermore, metagenomics sequencing helps in brief study of microbial profiles that cause infectious diseases. The information collected through metagenomics sequencing technologies helps to develop a tailored drugs to target diseases. Notably, the capabilities of recognizing genome profiles has revolutionized the healthcare industry, enabling them in designing a customized approach to deal with the growing concern of diseases.

Beyond disease studies, metagenomics sequencing has been widely adopted in cancer research, ecology studies, drug discovery, virology and environmental applications. Furthermore, the rapid progress towards genomic research and availability of advanced sequencing technologies, such as PCR, shotgun sequencing, metagenomics next generation sequencing has further contributed to the growth of this industry.

Considering the opportunities in this field, many market players are accelerating their innovations, investments, partnerships and acquisition. For instance, in April 2025, Metabolon launched an advanced microbiome research solution that integrated bioinformatics tools and metagenomics sequencings with a new microbiome metabolite panel to create microbiome research toolkit.

Furthermore, the industrial players are focusing on integrating advanced analytical tools and artificial intelligence technology with metagenomics sequencing. These initiatives along with growing research on genomics is likely to maintain a long term competitiveness in metagenomics sequencing market.

Metagenomic Sequencing Market: Report Attributes

Key Report Attributes	Details
Historical Trend	Since 2020
Forecast Period	Till 2035
Market Size 2025	USD 2.55 Billion
Market Size 2035	USD 8.64 Billion
CAGR (Till 2035)	13.0%

One of the key objectives of the metagenomic sequencing market report was to estimate the current size, opportunity, and the market growth potential, over the forecast period, till 2035. We have provided informed estimates on the likely evolution of the market for the forecast period.

The global market analysis also features the likely distribution of the current and forecasted opportunity within the market across various segments, such as type of offering, type of workflow, type of technology, application area, end users, geographical regions and leading players.

In order to account for future uncertainties associated with some of the key parameters and to add robustness to our model, we have provided three metagenomic sequencing market forecast scenarios, namely conservative, base, and optimistic scenarios, representing different tracks of industry’s evolution.

With increasing research on genomics to study infection diseases and drug discovery, the demand for metagenomics sequencing technologies has significantly increased. Furthermore, the industrial players are leveraging the competitive edge to develop novel technologies for metagenomic sequencing. The future of this market will be focused on next-generation metagenomics sequencing technologies.

Recent Developments in Metagenomic Sequencing Market

Several recent developments in the field of metagenomics sequencing industry have occurred, and we outline some of these below.

• In April 2025, Karius launched Karius Focus™ | BAL (a metagenomic sequencing-based microbial cell-free DNA test) designed to identify pneumonia causing pathogens and lung infections.
• In February 2025, Ginkgo Bioworks announced a collaboration with European Health and Digital Executive Agency as a contracting authority under a joint tender of €24 million. The partnership will aim to develop point-of-care metagenomics next-generation sequencing (mNGS) solution that allows rapid turnaround diagnostics for identifying respiratory viruses.
• In February 2025, Roche revealed its new-class of next-generation sequencing technology with its novel sequencing by expansion technology.
• In January 2025, the UK launched mSCAPE (Metagenomics Surveillance Collaboration and Analysis Programme), the world’s first metagenomics initiative for rapid detection of infectious diseases in the UK.

Metagenomic Sequencing Market Segmentation Insights

The market report provides comprehensive information on metagenomics sequencing instruments and service providers who are currently active across various segments of the industry as mentioned in the table below.

Metagenomic Sequencing Market: Market Segmentation

Market Segmentations	Details
Type of Offering	Reagents and Consumables Instruments Sequencing & Data Analytics Services
Type of Workflow	Data Processing & Analysis Sequencing Sample Processing & Library Preparation
Type of Technology	Shotgun Metagenomics Sequencing 16S rRNA Sequencing Whole Genome Sequencing & De Novo Assembly Metatranscriptomics
Application Area	Ecological & Environmental Metagenomics Clinical Diagnostics Drug Discovery Biofuel Industrial Applications
End User	Pharmaceutical Companies Research Laboratories Other End Users
Geographical Regions	North America Europe Asia-Pacific Middle East and North Africa Latin America
Market In North America	US Canada Mexico
Market In Europe	France Germany Italy Spain UK Rest of Europe
Market in Asia-Pacific	China India Japan South Korea Rest of the Asia-Pacific
Market in Middle East and North Africa	Egypt Saudi Arabia United Arab Emirates
Market in Latin America	Argentina Brazil

Industry Experts on Metagenomic Sequencing Market

Metagenomics sequencing industry is rapidly evolving and continues to grow at a steady pace. We at Roche consistently working on innovating next generation sequencing technologies, said Mark Kokoris, Head of Roche's SBX Technology.

“Solving the signal-to-noise challenge is a key efficiency driver for the technology. With this capability we can flexibly operate across a range of throughput scales using the same sequencing system, which provides a significant advantage to users,” said Mark Kokoris, Head of Roche's SBX Technology.

Metagenomic Sequencing Market Share Insights

Market Share by Type of Offering

• Based on the type of offering, the global market is segmented into reagents and consumables, instruments, and sequencing & data analytics services. According to metagenomic sequencing market forecast, presently reagents and consumables hold the highest share of the market. This can be attributed to the large consumption of reagents and consumables for genomic studies in laboratories.
• Since metagenomics studies require large amounts of nucleic acid samples, the demand for reagents and consumables for purification and extraction of DNA / RNA will increase. Therefore, this segment will continue to grow at a higher CAGR during the forecast period.

Market Share by Type of Workflow

• This segment highlights the distribution of global market across different types of workflows, such as Data Processing & Analysis, Sequencing, and Sample Processing & Library Preparation. Currently, sample processing & library preparation segment holds the highest metagenomic sequencing market share. This is potentially due to the increasing research on genomics that accelerates the demand for reagents for sample preparation.
• It is worth mentioning that this segment will continue to maintain its dominance and is expected to register a higher CAGR during the forecast period. Sample processing & library preparation is a crucial part for metagenomics sequencing. Therefore, it has to be accurate to maximize the yielding of high-quality DNA for sequencing. Driven by its high demand for metagenomic analysis, this segment will continue to expand at a steady rate,

Market Share by Type of Technology

• The global market is further bifurcated across different type of technology, such as shotgun metagenomics sequencing, 16S rRNA sequencing, whole genome sequencing & de novo assembly, and metatranscriptomics. According to the metagenomic sequencing market report, currently the shotgun metagenomics segment holds the highest share of the market. Shotgun metagenomics sequencing offers rapid analysis of DNA / RNA from the sample and provides high throughput parallel sequencing of the fragmented nucleic acid.
• However, metatranscriptomics is likely to witness higher CAGR driven by the increasing adoption to study gene expression within microbes.

Market Share by Application Area

• This segment is further categorized across different application areas, such as ecological & environmental metagenomics, clinical diagnostics, drug discovery, biofuel, and industrial applications. Presently, the drug discovery segment is holding the highest share of the metagenomic sequencing market. This lucrative share is due to the increasing usage of metagenomics sequencing technologies in drug discovery and development. Notably, metagenomics sequencing technology helps to identify bioactive molecules, and novel drug targets, which is expected to drive its demand for drug discovery.
• In the long run, clinical diagnostics segment will register a higher CAGR during the forecast period. This is likely to be the widespread usage of metagenomics sequencing to understand microbial diversity, their genome and role in causing infectious diseases.

Market Share by End User

• Based on end users, the global market is distributed into pharmaceutical companies, research laboratories, and other end users. According to our metagenomic sequencing market analysis, presently research laboratories hold the dominating position in this market. This is due to the increasing research on genomics to identify disease patterns and role of genomes in diseases and drug targets manufacturing.
• It is important to highlight here that the continuous emphasis on metagenomic research is likely to fuel the demand for the next generation sequencing technologies in research laboratories. Driven by the growing research on genomics, this segment will continue to register a higher CAGR during the forecast period.

Market Share by Geographical Regions

• The global market is distributed across different geographical regions, such as North America, Europe, Asia-Pacific, Middle East and North Africa, and Latin America. It is worth mentioning that currently North America is holding the highest share (nearly 45%) of the metagenomic sequencing market. Several factors, such as government funding for research and development, increase in start-ups activity and genome sequencing advancements are the key factors for highest share.
• However, in Asia-Pacific the market for metagenomics sequencing is expected to grow at a higher CAGR during the forecast period. This is likely to be the result of increasing government initiatives to support genomic research and rising risk of infectious diseases.

Metagenomic Sequencing Market: Report Deliverables

Report Deliverables	Details
Excel Data Packs (Complimentary)	Available
Key Metagenomics Sequencing Companies Profiled	AstraZeneca Bio-Rad BGI Group Eurofins Scientific Hamilton Company Illumina Macrogen NuGEN Technologies Oxford Nanopore Technologies PerkinElmer Pacific Biosciences Promega PSomagen QIAGEN Swift Biosciences Thermo Fisher Scientific Zymo Research Takara Bio (A complete list of companies captured is available in the report)
PowerPoint Presentation (Complimentary)	Available
Customization Scope	15% Free Customization

Metagenomic Sequencing Market Major Takeaways

The “Metagenomic Sequencing Market: Industry Trends and Global Forecasts, till 2035” market report features an extensive study of the current market landscape, market size, market share, market growth, market trends, market value, market forecast, market outlook, statistics, and future opportunities future opportunities within the metagenomics sequencing industry, during the forecast period.

How does Metagenomic Sequencing Market Competitive Landscape Fragmented?

The current market landscape is highly competitive, featuring the presence of several small, mid-sized and large industrial players. Majority of the industrial players, such as Delve Bio, Pfizer, QIAGEN, and Thermo Fisher Scientific, are aiming for technological innovations.

For instance, in April 2025, Delve Bio (pioneer of metagenomic next-generation sequencing technologies) announced to share its groundbreaking mNGS test (Delve Detect) at the 2025 America Academy of Neurology Annual Meeting today in San Diego. Dele’s mNGS technology poses the ability to identify over 68,000 pathogens within a single test, offering high yielding capabilities and ability to diagnose meningitis and encephalitis. With continuous efforts for the development of novel technologies, we believe that the metagenomics sequencing market will remain competitive over the forecasted period.

Regional Analysis: Which Region Hold the Highest Share of Market for Metagenomics Sequencing?

North America Dominates the Market

In 2025, North America dominates the global metagenomic sequencing market, accounting for 40% of the revenue share. This dominance is likely to remain unchanged during the forecast period. The presence of well-established industrial players, growing research on genomics and expanding government funding on metagenomics to support the development of personalized medicine are some key growth factors. Notably, regions, specifically United States is the key spot where industrial players are focusing on innovations, and technology adaptation to accelerate disease diagnosis and treatment planning.

Europe Holds a Substantial Share

In Europe, the market for metagenomics sequencing holds a substantial share. Notably, research organizations established in countries, such as United Kingdom, Germany and France are the are focusing on microbiome research and adopting metagenomics sequencing technologies to identify infectious disease. Furthermore, robust support from regulatory agencies, such as the European Medicines Agency (EMA) will further support the market growth in this region.

Asia-Pacific: Fastest Growing Region

In Asia-Pacific, the metagenomic sequencing market is likely to register a higher CAGR during the forecast period. This expansion is driven by the rising incidence of infectious diseases and increasing research on genomics. Asian countries, such as India, Japan, and China are significantly supporting genomic research to expand its application.

What are the Metagenomic Sequencing Market Growth Drivers?

Increasing Prevalence of Infectious Diseases and Growing Research on Genomics

The global healthcare sector is experiencing a severe burden of patients with infectious diseases. According to the statistics published in Centers for Disease Control and Prevention, nearly 9.2 million cases of typhoid fever and around 3.8 million cases of paratyphoid fever are reported every year.  Metagenomics sequencing in this instance helps with microbial genome analysis, human gut health and microbiome to develop tailored therapies.

Additionally, the growing research on genomics research to understand disease causing genes and alteration in gene function has further necessitated the demand for advanced sequencing technologies. Moreover, metagenomics sequencing is widely adopted by the pharmaceutical companies for AI in drug discovery and development, which is further expected to be a key driver for the market.

What are the Key Challenges in Metagenomic Sequencing Market?

High Sequencing Cost, Stringent Regulatory Guidelines and Complexity of Sequencing

The market for metagenomics sequencing may experience several challenges, such as high cost, and stringent regulatory guidelines. Many research organizations and pharmaceutical companies, specifically with limited budget may experience challenges in utilizing cutting-edge next-generation sequencing technologies. For instance, Thermo Fisher Scientific’s Ion GeneStudio S5 Series kits may range from USD 8,260 to USD 10,250 per run or per test. Thus, high costs may limit their adoption across research laboratories and pharmaceutical industries.

Furthermore, stringent guidelines for approval and complexity of sequencing technologies may create challenges in the adoption. Moreover, lack of skilled personnel to operate sequencing technologies may hinder market progress.

What are the Top Opportunities in Metagenomics Sequencing Industry?

Expanding Next-Generation Sequencing Applications in Metagenomics for Pathogen Identification, Integration of AI, Single-Cell Metagenomics and Technological Evolution

The market for metagenomics sequencing is continually evolving driven by the growing application across various healthcare applications, such as identification of pathogens. Moreover, industrial players are aiming for integrating AI technology with next-generation sequencing platform technologies to achieve high throughput, accuracy and overall performance. In addition, the focus on single-cell metagenomics to study gene function and interaction within single cells is a key trend of this market. Furthermore, industrial players are focusing on metagenomics data standardization to enhance data security during data sharing, and metagenomics analysis across various applications.

Metagenomic Sequencing Market Report Coverage

The market report presents an in-depth analysis, highlighting the capabilities of various stakeholders in the metagenomics sequencing industry, across different geographies. Amongst other elements, the market report includes:

• An Infographic Executive Summary
• Market Landscape of Metagenomics Sequencing Instruments and Services Providers
• Company Competitiveness Analysis
• Company Profiles
• SWOT Analysis
• Market Impact Analysis
• Market Forecast Analysis

From the Author’s Desk

Author’s View on Metagenomics Sequencing Market

Metagenomics sequencing is expanding rapidly driven by the increasing demand for personalized medicine and technological innovations to identify novel biomolecules for targeting diseases. Another significant factor that is driving this industry includes adoption of next generation sequencing technologies, expanding funding on genomic research.

Glossary

• Metagenomics Sequencing: It involves the collection of genetic material and sequencing using different sequencing technologies to gain deep insight into gene function and its role in diseases.
• Next Generation Sequencing: It is a technology for sequencing large amounts of DNA or RNA parallel. Sequencing nucleic acid helps with disease diagnosis and designing personalized medicine.
• Proteomics: It refers to the study of protein structures, modification and its role in gene expression and diseases.