Microbiome Sequencing Service Market Report 2025

The microbiome sequencing service market size has grown rapidly in recent years. It will grow from $2.07 billion in 2024 to $2.43 billion in 2025 at a compound annual growth rate (CAGR) of 17.3%. Growth during the historic period was driven by increased interest in human microbiota research, higher prevalence of gastrointestinal disorders, greater awareness of antibiotic resistance, wider use of microbiome studies in disease diagnostics, and stronger collaborations among research institutions.

The microbiome sequencing service market size is expected to see rapid growth in the next few years. It will grow to $4.54 billion in 2029 at a compound annual growth rate (CAGR) of 16.9%. Growth in the forecast period is expected to result from the rising emphasis on precision nutrition, increasing demand for microbiome-based therapeutics, stronger consumer focus on preventive healthcare, expanding use of microbiome data in drug discovery, and broader adoption of microbiome testing in clinical settings. Key trends for the forecast period include progress in metagenomic sequencing methods, development of microbiome-based diagnostic solutions, advancements in bioinformatics tools for data analysis, growth in the integration of multi-omics approaches, and the emergence of personalized microbiome-based therapies.

The increasing prevalence of gut-related diseases is expected to drive the growth of the microbiome sequencing service market. Gut-related diseases refer to conditions affecting the gastrointestinal (GI) tract, including the stomach, intestines, and other associated organs such as the liver and pancreas. The rising incidence of these diseases can be attributed to lifestyle and dietary changes, such as increased consumption of processed foods and reduced fiber intake, which disrupt the balance of gut microbiota. Microbiome sequencing services aid in the management of these diseases by providing detailed insights into the composition of gut microbes, making it crucial for diagnosing and monitoring gastrointestinal conditions. These services help identify microbial imbalances, enabling targeted interventions that improve personalized treatment and overall gut health management. For example, in June 2025, the UK Health Security Agency reported a 27% increase in Campylobacter cases, from 96.1 to 122 per 100,000 population, between 2022 and 2024. As a result, the growing prevalence of gut-related diseases is contributing to the expansion of the microbiome sequencing service market.

Key companies in the microbiome sequencing service market are focusing on developing advanced automated solutions, such as metagenomics sequencing technologies. These automated systems enable the sequencing and analysis of microbial communities with minimal manual intervention, ensuring high accuracy, reproducibility, and scalable throughput. For instance, in July 2024, MGI Tech Co. Ltd., a biotechnology company based in China, launched the Human Microbiome Metagenomics Sequencing Package. This fully integrated system combines automated sample pretreatment, nucleic acid extraction, library preparation, sequencing, and data analysis, supporting high-throughput and cost-efficient microbiome research. Its validated performance on a large number of human stool samples ensures reproducibility and accuracy, setting a new standard for large-scale human microbiome studies.

In May 2025, Mapmygenome India Limited, a genomics and diagnostics company based in India, acquired Microbiome Insights Inc. to expand its microbiome sequencing and analysis capabilities. This acquisition aims to strengthen Mapmygenome’s presence in the North American market and enhance its offerings in personalized health, genomics, and research services. Microbiome Insights Inc., based in Canada, specializes in microbiome sequencing services.

Major players in the microbiome sequencing service market are Eurofins Scientific LLC, Illumina Inc., Charles River Laboratories, QIAGEN N.V., Mérieux NutriSciences Corporation, OraSure Technologies Inc., Zifo RnD Solutions, Novogene Co. Ltd., Oxford Nanopore Technologies Plc, Macrogen Inc., Zymo Research Corporation, CD Genomics, Molzym GmbH & Co. KG (Gradian Diagnostics), Baseclear BV, Psomagen Inc., Mapmygenome, Rancho Biosciences LLC, Boster Biological Technology Ltd., Clinical Microbiomics, and Microba Life Sciences Limited.

North America was the largest region in the microbiome sequencing service market in 2024. Asia-Pacific is expected to be the fastest-growing region in the forecast period. The regions covered in microbiome sequencing service report are Asia-Pacific, Western Europe, Eastern Europe, North America, South America, Middle East and Africa. The countries covered in the microbiome sequencing service market report are Australia, Brazil, China, France, Germany, India, Indonesia, Japan, Russia, South Korea, UK, USA, Canada, Italy, Spain.

Note that the outlook for this market is being affected by rapid changes in trade relations and tariffs globally. The report will be updated prior to delivery to reflect the latest status, including revised forecasts and quantified impact analysis. The report’s Recommendations and Conclusions sections will be updated to give strategies for entities dealing with the fast-moving international environment.

The sudden escalation of U.S. tariffs and the consequent trade frictions in spring 2025 are severely impacting the healthcare sector, particularly in the supply of critical medical devices, diagnostic equipment, and pharmaceuticals. Hospitals and healthcare providers are facing higher costs for imported surgical instruments, imaging equipment, and consumables such as syringes and catheters, many of which have limited domestic alternatives. These increased costs are straining healthcare budgets, leading some providers to delay equipment upgrades or pass on expenses to patients. Additionally, tariffs on raw materials and components are disrupting the production of essential drugs and devices, causing supply chain bottlenecks. In response, the industry is diversifying sourcing strategies, boosting local manufacturing where possible, and advocating for tariff exemptions on life-saving medical products.

A microbiome sequencing service is a specialized scientific process that examines the genetic material of microbial communities found in biological or environmental samples such as the gut, skin, or soil. It is applied to identify, measure, and describe microorganisms in order to gain insights into their composition, diversity, and functional roles.

The core components of microbiome sequencing include sample preparation, sequencing and library preparation, and data analysis. Sample preparation focuses on processing collected biological material to maintain quality and purity for sequencing. The technologies used include sequencing by ligation, sequencing by synthesis, shotgun sequencing, targeted gene sequencing, RNA sequencing, and others. These services are utilized in fields such as autoimmune disorders, cancer, and gastrointestinal disorders, supporting end users such as pharmaceutical and biotechnology companies, academic institutions, and research organizations.

The microbiome sequencing service market research report is one of a series of new reports that provides microbiome sequencing service market statistics, including microbiome sequencing service industry global market size, regional shares, competitors with a microbiome sequencing service market share, detailed microbiome sequencing service market segments, market trends and opportunities, and any further data you may need to thrive in the microbiome sequencing service industry. This microbiome sequencing service market research report delivers a complete perspective of everything you need, with an in-depth analysis of the current and future scenario of the industry.

The microbiome sequencing service market includes revenues earned by entities through microbiome biomarker discovery, host-microbiome interaction analysis, microbial strain identification, metatranscriptomic profiling, metaproteomic analysis, metabolomic profiling, microbiome-based diagnostics development, and microbiome therapeutics support services. The market value includes the value of related goods sold by the service provider or included within the service offering. Only goods and services traded between entities or sold to end consumers are included.

The market value is defined as the revenues that enterprises gain from the sale of goods and/or services within the specified market and geography through sales, grants, or donations in terms of the currency (in USD unless otherwise specified).

The revenues for a specified geography are consumption values and are revenues generated by organizations in the specified geography within the market, irrespective of where they are produced. It does not include revenues from resales along the supply chain, either further along the supply chain or as part of other products.

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