Global Metagenomics Market Grows Steadily at a CAGR of 12.05%

Introduction

A key aspect fostering the growth of the global metagenomics market is its increasing use in non-clinical fields such as agriculture, environmental science, and industrial biotechnology. In agriculture, metagenomics is used to study soil microbial communities, helping to boost crop productivity, enhance disease resistance, and minimize the reliance on chemical inputs. In environmental science, it supports the detection of microbial pollutants, assessment of ecosystem changes, and research related to climate change.

In the industrial domain, metagenomics plays a crucial role in identifying novel enzymes used in the production of biofuels, bioplastics, and in bioremediation processes. Moreover, the rising interest in microbiome-driven solutions across the food, cosmetics, and nutraceutical sectors is propelling market expansion. Technological breakthroughs in sequencing methods, such as long-read and nanopore technologies, are enhancing precision, lowering costs, and enabling real-time data analysis. These advancements are making metagenomics more widely accessible, strengthening its adoption across multiple industries and supporting sustained global market growth.

Market Dynamics

Growing prevalence of infectious and chronic diseases drives the global market

The surging prevalence of both chronic and infectious diseases is a major aspect augmenting the expansion of the metagenomics market. Metagenomic techniques allow for in-depth microbial analysis, providing vital insights into disease development, diagnosis, and treatment strategies. These methods are especially useful for exploring the role of gut microbiota in chronic conditions and for detecting pathogens in infectious diseases.

• According to the World Health Organization (WHO), chronic diseases such as cardiovascular disorders, cancer, diabetes, and chronic respiratory illnesses were responsible for 74% of global deaths in 2021. Additionally, the WHO’s 2023 report indicated that tuberculosis (TB) remained the leading cause of death from infectious diseases, with an estimated 1.25 million deaths and over 10 million new cases worldwide.

With increasing demand for fast, precise, and culture-independent diagnostic tools, metagenomics is gaining prominence in both clinical and public health settings.

Public-private partnerships and funding create tremendous opportunities

The global market is experiencing robust growth, driven by increasing public-private partnerships and dedicated funding efforts. These collaborations play a fundamental role in advancing research, enhancing clinical applications, and developing cutting-edge infrastructure for metagenomic sequencing and analysis. Stakeholders, including governments, research organisations, and private enterprises, are working together to strengthen real-time pathogen detection and deepen microbiome insights. Moreover, the integration of next-generation sequencing with AI-based data analysis is boosting capabilities in diagnostics, disease surveillance, and treatment strategies.

• For example, in December 2024, the UK Health Security Agency (UKHSA), in collaboration with the NHS, Genomics England, and Oxford Nanopore, launched the mSCAPE (Metagenomics Surveillance Collaboration and Analysis Programme). Backed by a £50 million investment from Novo Holdings, the initiative aims to implement rapid clinical detection of respiratory pathogens and antimicrobial resistance within six hours across 30 NHS sites using long-read metagenomic sequencing.

Such efforts are expected to spur technological advancements and support the global expansion of the metagenomics market.

Regional Analysis

North America holds a dominant share in the global metagenomics market, driven by advanced healthcare infrastructure, robust research funding, and the presence of major biotech firms. The U.S. leads with extensive microbiome research initiatives, such as the NIH’s Human Microbiome Project, which has accelerated the integration of metagenomic tools in clinical settings. In 2024, Canada’s Genome Canada launched new funding for environmental and agri-food metagenomics, supporting projects that analyze soil microbiota to enhance crop yield and sustainability. 

The region’s high prevalence of lifestyle-related disorders like obesity and inflammatory bowel diseases has further intensified the focus on gut microbiome studies. Additionally, North American startups like BiomeSense Inc. and DayTwo are leveraging AI-powered microbiome diagnostics, indicating a growing trend in precision health. Strategic collaborations between universities, tech firms, and healthcare providers continue to support innovation in metagenomic research and applications.

Key Highlights

• The global metagenomics market size was valued at USD 2.34 billion in 2024 and is estimated to grow from USD 2.62 billion in 2025 to reach USD 6.52 billion by 2033, growing at a CAGR of 12.05% during the forecast period (2025–2033).

• By product, the global metagenomics market is segmented into kits & reagents, sequencing & data analytics services, and instruments. The kits & reagents segment dominated the market.

• By technology, the market is categorized into shotgun metagenomic sequencing, 16S rRNA sequencing, whole genome sequencing, and other omics technologies. The shotgun metagenomic sequencing segment contributed the largest market share.

• By workflow, the market is divided into pre-sequencing, sequencing, and data analysis. The sequencing segment contributed the largest market share.

• By application, the market includes clinical diagnostics, environmental metagenomics, industrial applications, agricultural applications, drug discovery and development, and others.The environmental metagenomicssegment dominated the market.

• North America is the highest shareholder in the global market.

Competitive Players

1. Illumina,Inc.
2. Thermo Fisher Scientific, Inc.
3. QIAGEN N.V.
4. Agilent Technologies, Inc.
5. PerkinElmer, Inc.
6. Oxford Nanopore Technologies plc
7. BGI Group
8. Eurofins Scientific
9. F. Hoffmann-La Roche Ltd
10. Bio-Rad Laboratories, Inc.

Recent Developments

• In June 2025, Phase Genomics, Inc., launched ProxiMeta Starter and Elite Bundles, bringing Hi‑C metagenomics within reach for diverse research users. The Starter Bundle is ideal for early-career researchers (up to two samples) with support and guaranteed library prep success. The Elite Bundle caters to experienced labs, offering deep sequencing and in-house Hi‑C assembly for up to eight samples.

Segmentation

1. By Product
   1. Kits & Reagents
   2. Sequencing & Data Analytics Services
   3. Instruments
2. By Technology
   1. Shotgun Metagenomic Sequencing
   2. 16S rRNA Sequencing
   3. Whole Genome Sequencing
   4. Other Omics Technologies
3. By Workflow
   1. Pre-sequencing
   2. Sequencing
   3. Data Analysis
4. By Application
   1. Clinical Diagnostics
   2. Environmental Metagenomics
   3. Industrial Applications
   4. Agricultural Applications
   5. Drug Discovery and Development
   6. Others
5. By Regions
   1. North America
   2. Europe
   3. Asia-Pacific
   4. Latin America
   5. The Middle East and Africa