United States Microbiome Sequencing Services Market By Technology (Sequencing by Ligation (SBL), Sequencing by Synthesis (SBS), Shotgun Sequencing, Targeted Gene Sequencing, Others), By Application (Gastrointestinal Diseases, Infectious Diseases, CNS Diseases, Oncology, Others), By Region, By Competition Forecast & Opportunities 2021-2031F

Forecast Period	2027-2031
Market Size (2025)	USD 621.73 Million
CAGR (2026-2031)	8.79%
Fastest Growing Segment	Infectious Diseases
Largest Market	Midwest
Market Size (2031)	USD 1030.71 Million

Market Overview

The United States Microbiome Sequencing Services Market will grow from USD 621.73 Million in 2025 to USD 1030.71 Million by 2031 at a 8.79% CAGR. Microbiome sequencing services encompass the comprehensive genomic analysis of microbial communities residing within biological samples, utilizing advanced technologies such as Next-Generation Sequencing to identify and characterize microorganisms for clinical, research, and industrial applications. The United States market is significantly driven by the plunging costs of genomic analysis and the increasing integration of microbiome profiles into personalized medicine and therapeutic strategies. According to the Biocodex Microbiota Institute, in 2025, 60% of surveyed individuals expressed a willingness to undergo microbiota testing for general health monitoring, underscoring the rising consumer demand that supports the sector's rapid expansion.

Despite this positive trajectory, the market faces a substantial challenge regarding the lack of standardization in data analysis and regulatory frameworks. The variability in bioinformatic pipelines and the absence of harmonized reference databases create inconsistencies in results across different service providers, complicating the regulatory validation process and potentially delaying the broader clinical adoption of microbiome-based diagnostics.

Key Market Drivers

Robust Federal Funding and Grants for Genomic and Microbiome Research significantly propel the United States market by providing essential capital for high-risk, high-reward studies that underpin commercial applications. Government agencies are increasingly prioritizing the elucidation of microbial roles in health, directly subsidizing the sequencing costs for academic and institutional projects which eventually transition into clinical solutions. According to the University of South Florida, January 2025, in the 'Microbiome Grants' update, the National Institutes of Health (NIH) structured specific funding opportunities with a combined direct cost budget limit of $275,000 over a two-year period, incentivizing granular research into microbial function. This consistent financial injection de-risks early-stage discovery, allowing sequencing providers to secure stable contracts from grant-funded research bodies, thereby stabilizing revenue streams amidst broader economic fluctuations.

Accelerated Outsourcing of Sequencing by Pharmaceutical and Biotechnology Firms serves as a primary catalyst, as drug developers shift away from maintaining expensive in-house genomic facilities in favor of specialized external providers. This trend is amplified by the need for advanced bioinformatic interpretation and the integration of multi-omics data which specialized vendors can deliver more efficiently. According to Microba Life Sciences, August 2025, in the '2025 Annual Report', the company reported that group revenue grew to $15.7 million, a 30% increase driven largely by the accelerating adoption of their testing products and services. Furthermore, strategic collaborations are reinforcing this ecosystem; according to Ginkgo Bioworks, November 2025, in a partnership announcement, the company launched a five-year initiative with the University of Illinois to develop phage-based therapies, highlighting the reliance on external platforms for complex microbial engineering.

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Key Market Challenges

The lack of standardization in data analysis and regulatory frameworks constitutes a critical impediment to the growth of the United States Microbiome Sequencing Services Market. When bioinformatic pipelines and reference databases vary significantly across service providers, the resulting genomic data often lacks the reproducibility required for clinical and regulatory validation. This inconsistency prevents pharmaceutical companies and healthcare providers from confidently relying on sequencing outputs for diagnostic or therapeutic decision-making. Consequently, the inability to compare results across different laboratories creates a bottleneck in the development pipeline, forcing stakeholders to delay commercial investments and stalling the transition of microbiome research from academic exploration to scalable medical application.

This fragmentation directly impacts market revenue by limiting the utility of sequencing data for high-value clinical trials and regulatory submissions. The magnitude of this operational friction is evident in recent industry surveys. According to the Pistoia Alliance, in 2024, 48% of life science experts surveyed identified the lack of metadata standardization as a primary barrier to utilizing experimental data effectively. Such statistical evidence highlights that even as sequencing costs fall, the value of the service is diminished by data quality issues. As long as these discrepancies persist, regulatory bodies remain cautious in approving microbiome-based diagnostics, thereby restricting the total addressable market for sequencing services and dampening the sector's overall expansion.

Key Market Trends

The utilization of long-read sequencing technologies is fundamentally reshaping the United States market by overcoming the resolution limitations of traditional short-read methods. Service providers are increasingly deploying platforms capable of spanning complex repetitive genomic regions, which enables the precise identification of microbial strains and structural variants essential for functional profiling. This technical shift from genus-level identification to strain-level tracking is validated by the rapid uptake of high-throughput long-read devices in commercial laboratories. According to Oxford Nanopore Technologies, March 2025, in the 'Annual results for the year ended 31 December 2024' report, revenue from the PromethION product range grew 55.8% to £75.9 million in 2024, highlighting the industry's aggressive transition toward producing more complete and contiguous microbial genomes for advanced research applications.

Simultaneously, the application of sequencing in oncology and immunotherapy is establishing the microbiome as a critical biomarker for cancer treatment outcomes. Clinicians and pharmaceutical partners are integrating gut microbiome profiling into oncological workflows to stratify patients for immune checkpoint inhibitor therapies and to develop bacteria-derived adjunctive treatments. This integration of microbial data into broader cancer care pipelines is driving substantial revenue growth for genomic profiling companies that offer comprehensive multi-modal data analysis. According to Tempus AI, February 2025, in the 'Reports Fourth Quarter and Full Year 2024 Results' press release, the company's Genomics division generated $120.4 million in revenue in the fourth quarter of 2024, underscoring the escalating demand for precision medicine platforms that increasingly encompass the tumor-microbiome axis.

Segmental Insights

Within the United States microbiome sequencing services market, the infectious diseases segment is recognized as the fastest-growing category. This expansion is primarily driven by the increasing necessity for genomic analysis to identify pathogens that traditional culture methods cannot detect. The rising prevalence of complex infections has accelerated the demand for sequencing to support precise diagnosis and treatment strategies. Furthermore, ongoing research funded by the National Institutes of Health regarding microbial interactions continues to validate sequencing applications, encouraging clinical laboratories to adopt these services for monitoring disease outbreaks and antibiotic resistance.

Regional Insights

The Midwest United States stands as the leading region in the Microbiome Sequencing Services Market, driven by a dense concentration of elite research institutions and advanced clinical infrastructure. This dominance is anchored by the collaborative efforts of the Microbiome Center, which unites expertise from the University of Chicago, the Marine Biological Laboratory, and the Argonne National Laboratory to accelerate microbial discovery. Furthermore, the region benefits from a robust ecosystem that seamlessly integrates agricultural and human health research, fostering rapid commercialization of sequencing technologies. This unique convergence of academic excellence and expanding laboratory capabilities establishes the Midwest as the primary hub for industry innovation.

Recent Developments

• In October 2024, Clinical Microbiomics entered into a definitive agreement to acquire the Research Services business unit of Microba Life Sciences. This transaction was a significant consolidation in the global and US microbiome services market, transferring Microba's service operations in North America and the Asia-Pacific region to Clinical Microbiomics. The deal was designed to allow Microba to focus on its core diagnostic and therapeutic activities while expanding Clinical Microbiomics' global infrastructure and client base. The acquisition included the transition of key laboratory and business development staff, further strengthening the acquirer's position as a leading contract research organization dedicated to multi-omics and microbiome research services.
• In June 2024, Zymo Research launched the ZymoBIOMICS Oral Microbiome Standard to improve the accuracy and reproducibility of microbiome profiling workflows. This new product was designed to serve as a defined mock community standard, mimicking the complexity of the human oral microbiome. It comprised a scientifically validated mixture of bacterial species commonly found in the oral cavity, allowing researchers to benchmark their DNA extraction, library preparation, and sequencing processes. The launch addressed a significant need in the market for reliable reference materials, ensuring that sequencing service providers and research labs could generate consistent and comparable data across different studies and platforms.
• In April 2024, Ginkgo Bioworks expanded its service capabilities by acquiring the platform assets of AgBiome, including a massive collection of sequenced microbial strains. This acquisition integrated over 115,000 fully sequenced strains and more than 500 million unique gene sequences into Ginkgo Ag Biologicals Services. The transaction allowed the company to enhance its unified metagenomics database, providing customers with deeper insights for biological discovery and development. By incorporating these rich data assets, the company aimed to accelerate the creation of new agricultural biological products and offer more robust microbiome sequencing and screening services to its partners in the agricultural and biotechnology sectors.
• In March 2024, CosmosID announced a strategic collaboration with Resilient Biotics, a biotechnology company focused on respiratory immunotherapies. This partnership aimed to advance the understanding of the respiratory tract microbiome by leveraging CosmosID's high-resolution genomic sequencing and bioinformatics capabilities. The collaboration focused on analyzing the complex microbial communities within the respiratory system using Resilient Biotics' extensive collection of respiratory tract bacterial strains. By combining these assets, the companies sought to generate high-quality genomic data to support the discovery of novel therapeutic candidates and diagnostic markers, thereby addressing a critical gap in respiratory health research and service offerings.

Key Market Players

• Illumina Inc
• Thermo Fisher Scientific Inc
• PacBio (Pacific Biosciences of California Inc)
• Oxford Nanopore Technologies
• CD Genomics
• Diversigen Inc
• Second Genome Inc
• CosmosID Inc
• Zymo Research Corp
• GenomeDx Biosciences

By Technology	By Application	By Region
Sequencing by Ligation (SBL) Sequencing by Synthesis (SBS) Shotgun Sequencing Targeted Gene Sequencing Others	Gastrointestinal Diseases Infectious Diseases CNS Diseases Oncology Others	Northeast Midwest South West

Report Scope:

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

• United States Microbiome Sequencing Services Market, By Technology:

• Sequencing by Ligation (SBL)
• Sequencing by Synthesis (SBS)
• Shotgun Sequencing
• Targeted Gene Sequencing
• Others

• United States Microbiome Sequencing Services Market, By Application:

• Gastrointestinal Diseases
• Infectious Diseases
• CNS Diseases
• Oncology
• Others

• United States Microbiome Sequencing Services Market, By Region:

• Northeast
• Midwest
• South
• West