Metagenomic Sequencing Market Size & Outlook, 2025-2033

Metagenomic Sequencing Market Size

The global metagenomic sequencing market size was valued at USD 2198.13 million in 2024 and is anticipated to grow from USD 2582.8 million in 2025 to reach USD 9384.12 million in 2033, growing at a CAGR of 17.5% during the forecast period (2025–2033). 

Metagenomics is a biological approach in genomics that analyzes mixed genomic materials derived from a community of organisms using metagenomic sequencing. This approach gives detailed information on species diversity and abundance, functional genes, evolutionary relationships, population structure, and environmental factor correlation networks. Although these processes were developed for clinical diagnostics, drug discovery, biofuel, and industrial applications, they are now being employed for other purposes. Metagenomics allows researchers to study creatures difficult to culture in the lab because most microbes have never been cultured.

"Metagenomic sequencing" refers to a thorough examination of all species retrieved from the environment. Microbes in various settings can be discovered and measured using metagenomic sequencing. It Is also an opportunity to research unculturable bacteria and learn about their biological potential. Some of the factors that drive the market growth include advancements in metagenomic sequencing, significant applications of metagenomics in various fields, initiatives and funding from government and private bodies for large-scale sequencing projects, and a decline in the cost of sequencing.

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Metagenomic Sequencing Market Growth Factors

Development in Metagenomic Sequencing

Technological advancements have allowed metagenomic sequencing platforms to make significant progress in recent years. Due to many factors such as low input sample concentration requirements, lack of experimental bias in microarrays, and others, DNA sequencing is far more helpful and advantageous than traditional microarrays. The introduction of massive parallelization of sequencing operations has skyrocketed the overall number of produced sequence reads per run. Scientists worldwide are looking for a platform that decreases the amount of pre-sequencing stages, ensures precise sequences with lengthy reads (MB to GB) produced each run, works on a DNA molecule without pre-amplification and has excellent read accuracy.

Thus, scientists focus on developing advanced sequencing platforms. For instance, in January 2019, GenBank assigned accessions with a stable 6-letter whole genome shotgun (WGS) accession prefix and a minimum of 9 digits. In 2021, the number of sequence records in each release of GenBank was 243, and the whole genome shotgun sequence was 1,590,670,459. Since DNA sequencing is primarily associated with metagenomics studies, advancements regarding the same are set to contribute to market growth.

Significant Applications of Metagenomics in Various Fields

Metagenomics is essential in genomics; it has applications in bioremediation, ecological and environmental metagenomics, clinical diagnostics, drug development, and industrial use. Pathogen detection via unbiased next-generation sequencing is possible with clinical diagnostic metagenomics. Metagenomic sequencing and bioinformatics technology have recently boosted the adoption of metagenomics-based precision diagnostic procedures. Furthermore, function-based screenings can aid in the discovery of new proteins such as antibiotics by purifying, cloning, and expressing DNA taken from the desired organism in a heterologous host. As a result, a wide range of applications contributes to market growth.

Restraining Factor

End-User Budget Constraints in Developing Countries

One of the significant challenges metagenomic sequencing experiments face is end-user budget constraints in some developing countries. In addition, the economic and social impact of genomic medicine and research in developing countries hinder the market growth. According to the ARXIV organization, only big research institutions with large funding programs, usually from developed countries, can undertake such projects, leaving developing countries behind in this field as these countries cannot afford expensive next-generation sequencers (NGS). This hinders the market growth.

Market Opportunity

Availability of Cloud Computing for Data Management

With growing knowledge in developing economies, the need for metagenomic sequencing methodologies has grown in scientific communities worldwide. On the other hand, cloud computing offers a tormenting option for on-demand access to computational resources for metagenomic sequencing. Furthermore, in bioinformatics and computational biology, an essential local alignment search tool (BLAST) on accurate metagenomics data in a cloud setting to determine the viability of metagenomic sequencing approaches, BLAST is one of the premier applications. It is assumed to consume the majority of resources in that area. Hence, an opportunity such as the availability of cloud computing for data management drives the growth of the global metagenomic sequencing market.

Regional Insights

North America holds the most dominant share of the market. It is estimated to reach an expected value of USD 2,035 million by 2030 at a CAGR of 17%. North America is studied across three major countries: the US, Canada, and Mexico. The region held the largest market share of 42.33% in the global metagenomic sequencing market in 2021, owing to its stronghold on deoxyribonucleic acid (DNA) sequencing technologies due to continuous improvement and availability and accessibility of DNA sequencing in this region.

Several global manufacturers of DNA sequencing, platforms, equipment, and technologies are highly active in North America, especially in the US. For instance, key market players, such as Illumina, Inc., Thermo Fisher Scientific Inc., and others, have their corporate presence. Hence, most DNA sequencing products and platforms are first launched in the US and then distributed to other regions of the world.

The key market players strive to introduce affordable DNA sequencing technologies in the North American market. This has provided momentum to the global metagenomics market in this region, enabling further investigation of microbial ecology. Moreover, the North American market has witnessed tremendous developments regarding the utilization of metagenomics products and technologies in biotechnology, which are expected to make way for new avenues and provide numerous growth opportunities for the expansion of the market.

Asia-Pacific Metagenomic Sequencing Market Trends

Asia-Pacific is the fastest-growing market. It is estimated to reach an expected value of USD 1,270 million by 2030 at a CAGR of 19%. The Asia-Pacific market is studied across Japan, China, Australia, India, and the rest of Asia-Pacific. Asia-Pacific possesses immense potential for the growth of metagenomics, which is attributed to the surge in the focus of healthcare professionals on drug discovery and development in the biotechnology industry. In addition, the rise in the accessibility of novel advanced sequencing technologies across the countries in this region is expected to contribute to the highest growth rate during the forecast period.

Moreover, research, innovation, and developments related to DNA sequencing have fueled the growth of metagenomic studies in the Asia-Pacific region. Further, an increase in the collaborations between developed and developing economies working in microbiome and metagenomics is set to boost the growth of the Asia-Pacific market. For instance, in February 2016, GenomeAsia 100K, a non-profit consortium, announced its proposal to sequence 100,000 individuals. This plan initially included a population from twelve South Asian countries and at least seven North and East Asian countries.

The program's supporters included genomics companies such as Macrogen Inc. (Korea) and Illumina Inc. (US). The primary goal of this program was to increase the number of precision medicine applications for Asian patients. Moreover, China has focused on its precision medicine program based on sequencing, which is expected to boost the demand for metagenomics products and technologies across the Asia-Pacific region.

Product and Service Insights

The market is divided into reagents and consumables, instruments, and services. The services segment dominated the market. It is estimated to reach an expected value of USD 3,830 million by 2030 at a CAGR of 17.6%. Higher usage of metagenomic sequencing services and analysis and data interpretation solutions is attributable to the increased market growth.

The segment of the reagents and consumables is the second-largest market based on product and service. It is estimated to reach an expected value of USD 785 million by 2030 at a CAGR of 18.5%. The use of reagents and consumables has increased in recent years due to lower metagenomic sequencing error margins. For example, in 2021, QIAGEN N.V. released artus SARS-CoV-2 Prep&Amp UM Kit, a liquid-based reagent for SARS-CoV-2 testing.

Technology Insights

The market is divided into shotgun metagenomic sequencing, 16S rRNA sequencing, whole-genome sequencing and de novo assembly, and metatranscriptomics. The 16S rRNA sequencing segment dominated the market. It is estimated to reach an expected USD 2,300 million by 2030 at a CAGR of 17.6%. 16S rRNA gene sequencing is commonly used to identify, classify, and quantify microbes within complex biological mixtures such as environmental and gut samples. 

Several manufacturers have introduced newer techniques combined with the 16S rRNA metagenomic sequencing, which helps combat the conventional issues faced earlier. The researchers have now studied the coupling of 16S rRNA PCR with next-generation sequencing, which has enabled the study of many samples at a low cost. 16SrRNA gene sequencing service can be used to identify and classify species in microbial samples.

Furthermore, adding Internal Transcribed Spacer (ITS) in combination with 16S rRNA is expected to help provide a cost-effective technique to identify strains that may not be found using traditional methods. With the increase in antimicrobial resistance, the need to identify the mutated microbes has increased. This is anticipated to help the market gain traction during the forecast period.

Application Insights

The market is classified into drug discovery, ecological and environmental metagenomics, clinical diagnostics, biofuel, and industrial applications. The drug discovery segment dominated the market. It is estimated to reach an expected value of USD 2,120 million by 2030 at a CAGR of 18.3%. The emergence of advanced metagenomic sequencing technologies and their application in the analysis of microbial population genomes has introduced a new area of scientific research in metagenomic sequencing.

The rapid progress in metagenomic sequencing has enabled direct access to the genomes of pathogenic microorganisms for drug discovery. The global threat of drug-resistant pathogens continues to increase with increasing years; new strategies such as metagenomic sequencing are required to accelerate and advance the drug discovery process. Factors such as the development and commercialization of drug discovery for unknown pathogenic organisms are expected to drive the growth of the drug discovery segment in the coming years.

List of key players in Metagenomic Sequencing Market

1. BGI Genomics Co., Ltd.
2. Oxford Nanopore Technologies Ltd
3. Eurofins Genomics
4. Illumina, Inc.
5. Macrogen Inc.
6. Pacific Biosciences of California, Inc.
7. PerkinElmer Inc.
8. QIAGEN N.V.
9. Swift Biosciences Inc.
10. Thermo Fisher Scientific Inc.

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Recent Developments

• June 2021 - Illumina announced an agreement with the Belgian Genetic Centers to evaluate whole-genome sequencing (WGS) for the diagnosis of patients with intellectual disabilities (ID) and developmental disorders (DD).
• April 2021 - Illumina announced a partnership with Kartos Therapeutics, Inc. to co-develop a tumor protein (TP53) companion diagnostic (CDx) based on Illumina's comprehensive genomic profiling content assay, TruSight Oncology. It will expand the TruSight Oncology offerings into hematologic malignancies of illumine
• February 2021 - PacBio announced that Children's Mercy Kansas City increased its investment in highly accurate HiFi sequencing with four new Sequel IIe Systems to add to its two existing Sequel IIe Systems.
• December 2020- Eurofins launched ARTIC Next Generation Sequencing (NGS) service. ARTIC SARS-CoV-2 Whole Genome Sequencing service includes NGS and detailed reporting for universal end-to-end surveillance of pandemic development.