Cancer Microbiome Sequencing Market - Global Industry Size, Share, Trends, Opportunity, and Forecast, Segmented By Component (Kits & Assays, Software, Services), By Technology (Next Generation Sequencing, Polymerase Chain Reaction), By Application (Translational Research, Clinical Diagnostics), By End User (Biotechnology & Pharmaceutical Companies, Academic & Research Institutions, Hospitals & Clinics, Others), By Region and Competition, 2020-2030F

Market Overview

The Global Cancer Microbiome Sequencing Market was valued at USD 514.74 million in 2024 and is expected to reach USD 1674.18 million by 2030 with a CAGR of 21.72% during the forecast period. The global market for Cancer Microbiome Sequencing is experiencing significant growth, driven by growing occurrences of cancer and increasing emphasis on the microbiome’s potential in the field of cancer are fueling the growth of the market. Microbiomes are the community of microorganisms that grow or exist on an environment such as saliva, skin layers, oral mucosa of human body and the gastrointestinal tract. Microbiome sequencing is a valuable tool which is used to study and analyze the microbes groups located in or out of the human body to have a better understanding of human microbes. The main aim of microbiome research is to understand the role and function of microbes in human health and disease.

The other factors supporting the market’s growth are, decreasing cost of sequencing, rise in R&D activities, exponential rise in the number of cancer cases worldwide, increasing number of clinical trials,  rise in development of novel diagnostic tools based on microbiome for supporting physicians, increasing investments by biotechnology companies, rise in demand for microbiome sequencing services for diagnosis and early detection of the diseases, rise in world population, growing awareness of the use of microbiome sequencing technology, rise in the healthcare expenditure, rising interest of researchers in understanding the role of microbiome in human health and disease, and immense potential for emerging submarkets.

Key Market Drivers

Growing Evidence That Microbiome Influences Cancer Risk, Response and Toxicity

A fundamental driver for the cancer-microbiome sequencing market is the mounting, regulator-acknowledged evidence that the human microbiome (gut, oral, intratumoral) meaningfully affects cancer risk, progression, response to therapy (especially immunotherapies), and treatment toxicity. As researchers and clinicians seek to stratify patients, predict who will respond to immune checkpoint inhibitors, or identify microbiome-based biomarkers for early detection, demand has surged for high-resolution sequencing (shotgun metagenomics, 16S rRNA profiling) and analytic pipelines that can deliver clinically actionable microbial signatures.

Public agencies and major national programs have explicitly funded such work. The NIH’s Human Microbiome Project (HMP) and subsequent non-HMP NIH investments substantially boosted the field: NIH notes that non-HMP investment in microbiome research “has increased over forty-fold” since the HMP began, spanning more than 20 NIH institutes and centers — a visible sign that public research priorities and grant support underwrite microbiome sequencing activities relevant to cancer. At the cancer-specific level, the NCI (National Cancer Institute) lists microbiome research among funded priorities and posts funding opportunities that target microbiome-based tests and mechanisms linking microbiota and anti-tumor immunity — creating direct grant demand for sequencing, biobanking and computational analysis. Those public investments not only sponsor discovery projects but also establish large, well-curated sample collections (stool, tumor tissue, blood) that require high-throughput sequencing and standardized workflows — core services provided by sequencing labs and specialized CROs.

Falling Sequencing Costs, Mature Genomic Infrastructure, And Government Genomics Initiatives Enable Scale

A second market driver is technical and infrastructural: sequencing (including whole-metagenome shotgun sequencing) has become cheaper, faster, and more accessible, while many countries have invested in genomics infrastructure and data platforms that make large-scale cancer-microbiome studies feasible. The decline in per-base sequencing costs plus improvements in library prep, automation, and cloud compute enable projects that were once impossible — e.g., population-scale microbiome cohorts, longitudinal sampling in therapy trials, and integrated host-microbe multi-omic studies. Governments are explicitly fostering genomic and bioinformatics capacity: the NIH and many national funding bodies have expanded genomic and data resources (NIH budget and genomics programs), and the EU has funded microbiome consortia and clinical translation projects (multiple EU projects received combined public funding for microbiome applications). These investments mean that clinical centers and national biobanks can partner with sequencing providers to generate standardized, regulatory-grade data on a scale.

The public funding picture underlines this enabling environment. NIH’s overall budget and institute funding (NIH ~$47.7B total operating in recent cycles; NCI funds available ~$7.2B FY2024) support genomics and translational projects that include microbiome sequencing components and data commons. The EU likewise allocated tens of millions to multi-institution microbiome projects that include clinical endpoints. Those government budget lines, and programmatic investments accelerate method standardization, shared pipelines, and public data repositories — all of which reduce barriers for commercial sequencing labs and service providers to expand capacity and offer validated workflows to cancer researchers and sponsors. In short: cheaper tech + public genomics funding + national bioinformatics platforms = scale for the cancer-microbiome sequencing market.

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Key Market Challenges

Biological Heterogeneity, Confounders and Reproducibility

A central scientific and commercial challenge is that microbiome signals in cancer are often subtle, context-dependent and easily confounded by diet, medication (notably antibiotics and proton-pump inhibitors), sample handling, geography, and host genetics. Different sequencing strategies (16S vs shotgun), extraction kits, PCR primers, and bioinformatic pipelines can yield divergent results from the same specimen. For clinical translation — e.g., a diagnostic test or companion biomarker — regulators and payers demand reproducible, robust effect sizes across populations. But the field is still grappling with cross-study reproducibility: a microbial taxon associated with response in one cohort may not replicate in another because of unmeasured confounders or technical variation.

Governments and public research programs recognize this problem and fund method development and harmonization efforts. For example, NIH funding announcements and NCI initiatives explicitly encourage standardized protocols, mechanistic studies, and validation cohorts to move findings toward clinical utility. The Human Microbiome Project and subsequent NIH portfolios highlighted method harmonization and resource sharing precisely because variability threatened scientific progress. Moreover, national screening programs (e.g., the UK colorectal screening studies that integrated microbiome assessments) show both promise and the practical difficulty of translating sequencing signals into simple clinical workflows without careful standardization and validation.

Regulatory Pathways, Clinical Validation and Reimbursement For Microbiome-Based Diagnostics and Therapeutics

The second major market challenge lies at the intersection of regulatory approval, clinical utility demonstration, and reimbursement. Microbiome-based diagnostics (tests that use sequencing to predict therapy response or detect cancer) and microbiome therapeutics (FMT, live biotherapeutic products) must satisfy rigorous regulatory standards — safety, analytical validity, clinical validity and clinical utility — to gain market access. Regulatory frameworks for diagnostics and live biological therapeutics are evolving, and there is still uncertainty about the evidentiary standards and trial designs needed for approval and payer coverage.

Public agencies are actively shaping these pathways, but guidance can be complex. The FDA and EMA have been developing approaches for microbiome therapeutics and biomarkers, and NIH/NCI funding notices encourage translational studies, yet formalized, widely-applicable qualification pathways for many microbiome biomarkers are still nascent. This regulatory uncertainty increases commercial risk: sponsors and diagnostic developers must often undertake large validation trials (with sequencing, longitudinal follow-up, and clinical endpoints) before a test can be recommended clinically. Those trials are expensive and time-consuming, and reimbursement decisions hinge on demonstration of improved patient outcomes or cost-effectiveness — endpoints that demand health-economic studies in addition to sequencing data.

Key Market Trends

Integration Of Microbiome Sequencing with Host Genomics, Immunomics And Multi-Omics

An important trend is the routine integration of microbiome sequencing with other molecular layers — host genomics (germline and somatic), tumor transcriptomics, immune profiling (TCR/BCR sequencing, cytokine assays), metabolomics and proteomics — to build composite biomarkers that outperform single-modality signatures. Cancer is a multi-factorial disease, and microbiome effects often interact with host immune tone and tumor genetics; therefore combining metagenomic data with tumor mutation burden, HLA typing, or immune cell infiltration measures yields more predictive models for response and toxicity.

Governments and public consortia are actively supporting multi-omic cancer cohorts and data platforms. NIH/NCI programs and EU projects finance integrated studies that explicitly combine microbiome sequencing with other omics and imaging, and national initiatives (biobanks, cancer data infrastructures) are creating linked datasets for discovery and validation. Such public investments accelerate methods for multi-omic integration, standardize metadata models, and create shared validation cohorts — which in turn expand demand for sequencing services that can interoperate with other omics pipelines and deliver harmonized, interoperable data products.

Clinical Translation: Companion Diagnostics, Prospective Trials And Government-Backed Validation Programs

A second clear trend is the move from retrospective discovery to prospective clinical trials and regulatory qualification — i.e., microbiome sequencing being used in protocolized ways to triage patients, guide therapy, or monitor for recurrence. Increasing numbers of government-supported and academic clinical programs are launching prospective studies that incorporate microbiome sequencing as a pre-specified stratification or exploratory endpoint. National screening programs and funded projects (for example NHS/UK and NCI-supported cohorts) have piloted microbiome-based screening adjuncts for colorectal cancer and are validating microbiome signatures in large, population-scale cohorts.

Public funding announcements and programmatic grants underscore this direction: NIH and NCI funding opportunities encourage mechanistic and translational microbiome studies; European funding supported multiple projects aiming to deliver validated clinical tools; and national research funders (e.g., Cancer Research UK with NIHR partners) are underwriting detection and early-diagnosis programmes that include microbiome sequencing validation arms. Those programs create the prospective, regulatory-grade evidence necessary for companion diagnostics and for payer evaluation.

Segmental Insights

Component Insights

Based on Component, kits & assays hold the largest market share in the global cancer microbiome sequencing market, primarily because they are essential consumables required for every sequencing workflow and are repeatedly purchased for ongoing research and clinical testing. These products include DNA/RNA extraction kits, library preparation kits, and targeted sequencing panels, which form the backbone of microbiome analysis in cancer studies. According to the U.S. National Institutes of Health (NIH), the demand for standardized and high-quality sequencing kits has grown significantly as cancer microbiome research expands, ensuring reproducibility and accuracy of results in both clinical and research applications. One of the key factors driving their dominance is that kits & assays provide ready-to-use, validated reagents that save researchers time, reduce error rates, and improve workflow efficiency. As next-generation sequencing (NGS) technology advances, companies are developing more sensitive and specific kits capable of detecting low-abundance microbial species in cancer patients, aiding in both early diagnosis and personalized treatment strategies. Furthermore, with the global rise in cancer incidence—19.3 million new cases reported worldwide in 2020 according to WHO—the need for reliable diagnostic and research tools is increasing proportionally.

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Regional Insights

Based on the region, North America holds the largest market share in the global cancer microbiome sequencing market, primarily due to its advanced healthcare infrastructure, significant research funding, and strong presence of biotechnology and genomic companies. The region benefits from substantial investments by organizations such as the U.S. National Cancer Institute (NCI), which allocated over USD 7.3 billion in 2023 for cancer research, including studies on the role of the microbiome in cancer prevention, diagnosis, and treatment. The United States and Canada have well-established genomic research centers and academic institutions actively engaged in cancer microbiome sequencing projects, supported by initiatives like the National Microbiome Initiative (NMI) launched by the U.S. government to advance microbiome science. Additionally, the availability of state-of-the-art sequencing platforms, skilled professionals, and robust regulatory frameworks facilitates faster adoption of advanced diagnostic techniques. Rising cancer prevalence also fuels the market—according to the Centers for Disease Control and Prevention (CDC), cancer remains the second leading cause of death in the U.S., with an estimated 1.9 million new cancer cases diagnosed in 2023. This high disease burden drives demand for innovative diagnostic and therapeutic approaches, including microbiome sequencing. Furthermore, strong collaborations between academic researchers, pharmaceutical companies, and contract research organizations (CROs) have accelerated clinical trials involving microbiome-targeted therapies in the region. Favorable reimbursement policies for precision medicine and genetic testing also support market expansion. Overall, the combination of a high research budget, cutting-edge technological capabilities, and a focus on personalized oncology makes North America the dominant region in the cancer microbiome sequencing market.

Key Market Players

• Illumina, Inc.
• Eurofins Scientific SE
• QIAGEN NV
• Thermo Fischer Scientific, Inc.
• Oxford Nanopore Technologies plc.
• OraSure Technologies, Inc.
• Pacific Biosciences of California, Inc.
• Psomagen, Inc
• Prescient Medicine Holdings, Inc.
• Micronoma Inc.

Report Scope:

In this report, the Global Cancer Microbiome Sequencing Market has been segmented into the following categories, in addition to the industry trends which have also been detailed below:

• Cancer Microbiome Sequencing Market, By Component:

o   Kits & Assays

o   Software

o   Services

• Cancer Microbiome Sequencing Market, By Technology:

o   Next Generation Sequencing

o   Polymerase Chain Reaction

• Cancer Microbiome Sequencing Market, By Application:

o   Translational Research

o   Clinical Diagnostics

• Cancer Microbiome Sequencing Market, By End User:

o   Biotechnology & Pharmaceutical Companies

o   Academic & Research Institutions

o   Hospitals & Clinics

o   Others

• Cancer Microbiome Sequencing Market, By Region:

o   North America

§  United States

§  Mexico

§  Canada

o   Europe

§  France

§  Germany

§  United Kingdom

§  Italy

§  Spain

o   Asia-Pacific

§  China

§  India

§  South Korea

§  Japan

§  Australia

o   South America

§  Brazil

§  Argentina

§  Colombia

o   Middle East and Africa

§  South Africa

§  Saudi Arabia

§  UAE

Competitive Landscape

Company Profiles: Detailed analysis of the major companies presents in the Global Cancer Microbiome Sequencing Market.

Available Customizations:

Global Cancer Microbiome Sequencing Market report with the given market data, TechSci Research offers customizations according to a company's specific needs. The following customization options are available for the report:

Company Information

• Detailed analysis and profiling of additional market players (up to five).

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