Global Metagenomic Sequencing Market - 2025-2033

Metagenomic Sequencing Market Metagenomic Sequencing Market reached US$ 2.31 billion in 2024 and is expected to reach US$ 9.25 billion by 2033, growing at a CAGR of 16.7% during the forecast period 2025-2033.

The global metagenomic sequencing market is poised for substantial growth driven by the rising focus on microbiome research and technological advancements in sequencing. The key trends shaping the metagenomic sequencing market are growing emphasis in clinical diagnostics, strategic partnerships and collaborations, rising usage of AI and ML for analyzing complex datasets, expansion of metagenomic sequencing applications, etc.

Metagenomic Sequencing Market Dynamics: Drivers & Restraints

The rising focus on microbiome research is driving the market growth.

There is a growing emphasis on the microbiome in the human body and its relevance in overall health and disease pathogenesis. Scientists across the world are conducting exclusive research to unravel the true link between the human gut microbiome and their role in the pathogenesis of chronic conditions like obesity, inflammatory bowel disease, mental health conditions, etc. In these activities, metagenomic sequencing plays a crucial role in analyzing the gut microbiome at the genetic level and providing information on its diversity, abundance, and functional capabilities.

The Human Gut Microbiome Project serves as a landmark example illustrating how increasing focus on microbiome research fuels the growth of the metagenomic sequencing market. By using advanced metagenomic sequencing, researchers were able to identify thousands of previously unknown bacterial species and their genetic functions.

As a result, demand for high-throughput sequencing platforms, targeted sample preparation kits, and sophisticated bioinformatics tools has surged, driving innovation and investment in the metagenomic sequencing market.

High cost of sequencing products and services may restrain the market growth

The high cost of sequencing products and services is a significant barrier to the adoption of this technology in the future. Despite technological advancements in genomic sequencing, the time for genomic sequencing has drastically reduced; the cost of these advanced technologies is substantially higher due to their complexity in nature.

For instance, the cost of a small benchtop device, for example, the PromethION 2 device by Oxford Nanopore Technologies, is US$ 89,000. This is a substantially higher investment for smaller research institutions, clinical laboratories in developing regions, and startups, slowing the widespread adoption of metagenomic sequencing technologies.

Moreover, the associated expenses of data storage, computational infrastructure, and bioinformatics analysis add to the overall cost, making it challenging for many organizations to fully leverage metagenomic sequencing despite its potential benefits.

Metagenomic Sequencing Market Segment Analysis

The global metagenomic sequencing market is segmented based on product & service, technology, application, and region.

Shotgun metagenomic sequencing in the application segment is expected to grow with the highest CAGR of 18.5% in the forecast period of 2025 to 2033.

Shotgun metagenomic sequencing refers to the sequencing of all the genetic material present in a sample, without targeting any specific gene. This method evaluates bacterial diversity and detects the abundance of microbes in various environments. It also allows studying unculturable microorganisms that are difficult or impossible to analyze. Applications of shotgun metagenomic sequencing include human microbiome analysis, genomic surveillance, environmental metagenomics, and antimicrobial resistance surveillance. It can also be used to study pathogens at a molecular level and detect resistant microorganisms.

The market for shotgun metagenomics is growing rapidly due to its expanding applications in clinical diagnostics, environmental monitoring, and biotechnology. The majority of the researchers are choosing this technology to conduct their studies because of its versatility. For instance, a research group from Nagoya University in Japan has discovered a connection between gut microbiota and Parkinson's disease using shotgun sequencing. The study published in the Springer Nature Journal in May 2024 postulated that decreased SCFAs and polyamines decrease intestinal mucus layer Decreased SCFAs and polyamines decrease intestinal mucus layer, leading to abnormal α-synuclein fibrils in neural plexus and causing neuroinflammation in Parkinson’s disease. This discovery is possible with the utilization of this advanced shotgun metagenomic sequencing.

There are several such studies, which have proven the efficacy and reliability of shotgun metagenomic sequencing for conducting research and proving that the technology is the most advanced if employed in clinical diagnostics.

Metagenomic Sequencing Market Geographical Analysis

North America dominated the metagenomic sequencing market with the highest share of 47.6% in 2024

In the North America region, the investments in healthcare advancements are substantially high, driving the research and development activities, facilitating the higher need for metagenomic sequencing products. To cater to the higher demand, key market players are constantly innovating products and subsequently launching them into the U.S. market. Moreover, the strategic partnerships to advance human microbiome research and the launch of new projects utilizing metagenomics are expected to drive the market growth.

For instance, in October 2024, Delve Bio, a pioneer in metagenomic next-generation sequencing (mNGS) for infectious diseases, and Broad Clinical Labs (BCL), the world's leading genome sequencing and testing laboratory, announced a collaboration to increase access to metagenomics for patients with neurological infections.

These activities position the North America region in a dominant position and as a global hub for metagenomic sequencing innovation and application.

Metagenomic Sequencing Market Major Players

The major players in the metagenomic sequencing market are Thermo Fisher Scientific Inc., Qiagen N.V., BGI Group, Merck KGaA, Eurofins Scientific, Illumina, Inc., Oxford Nanopore Technologies Ltd., F. Hoffmann-La Roche Ltd., Zymo Research Corporation, and PacBio, among others.

Key Development

In April 2025, Metabolon launched a new microbiome research solution, combining metagenomics sequencing and bioinformatics tools with a microbiome metabolite panel. This toolkit provides a phenotypic snapshot of microbiome activity, linking microbial functions to host physiology, immune responses, and disease progression. It offers high-quality sequencing options, a panel, and user-friendly bioinformatics tools.

In April 2024, Ginkgo Bioworks acquired AgBiome's platform assets, including 115,000 fully sequenced strains, 500 million unique gene sequences, functional data, and a development pipeline. These assets will be integrated into Ginkgo Ag Biologicals Services, expanding Ginkgo's metagenomics database and providing a deep ag biological discovery platform.