Microbiome Sequencing Services Market By Sequencing Type (16S rRNA Sequencing, Shotgun Metagenomic Sequencing, Whole Genome Sequencing (WGS), Targeted Gene Sequencing, Amplicon Sequencing), By Service Type (Sample Preparation, Library Preparation, Sequencing Services, Data Analysis & Interpretation, Bioinformatics Services, Others), By Application (Human Health, Drug Discovery & Development, Personalized Medicine, Agriculture, Animal Health, Environmental Microbiology, Others), By Technology (Sequencing by Synthesis (SBS), Ion Semiconductor Sequencing, Single Molecule Real-Time (SMRT) Sequencing, Nanopore Sequencing, Pyrosequencing, Sanger Sequencing, Others), By Sample Type (Stool Samples, Skin Swabs, Oral Swabs, Vaginal Swabs, Blood Samples, Others), and By End User (Academic & Research Institutes, Pharmaceutical & Biotechnology Companies, Contract Research Organizations (CROs), Hospitals & Clinics, Government Agencies, Others), Global Market Size, Segmental analysis, Regional Overview, Company share analysis, Leading Company Profiles And Market Forecast, 2025 – 2035

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What trends will shape Microbiome Sequencing Services Market in the coming years?

The Microbiome Sequencing Services Market accounted for USD 1.76 Billion in 2024 and USD 1.96 Billion in 2025 is expected to reach USD 5.61 Billion by 2035, growing at a CAGR of around 11.12% between 2025 and 2035. The microbiome sequencing services market can be described as the industry focused on such services as sequencing and analysing microbial communities present in an array of environments, among them being the human body, soil, water, and food. To fully understand and examine microorganisms and how their parts work, such services deploy sophisticated long-read genomic technologies such as 16S rRNA sequencing, shotgun metagenomics, and whole-genome sequencing. Marketplace encourages medical studies, agronomy, pharmaceutical studies, and environmental studies. It is fuelled by the rising concern about the role of the human microbiome in health and disease and the need to tailor medicine precisely. Technological development and the reduction of sequencing costs are also driving its expansion.

What do industry experts say about the Microbiome Sequencing Services market trends?

“For the first time, we’ve shown that a small molecule can improve the function of defective DNA polymerase gamma—opening the door to a completely new treatment strategy for mitochondrial disorders.”

• Prof. Maria Falkenberg, Professor at the Sahlgrenska Academy, University of Gothenburg

“We’ve demonstrated neuroprotection and full reversal of muscle weakness in preclinical models of mitochondrial dysfunction. This is a milestone in therapeutic development for neuromuscular and neurodegenerative diseases.”

• Prof. Matt Whiteman, Chief Scientific Officer, MitoRx Therapeutics & Professor of Experimental Therapeutics, University of Exeter

Which segments and geographies does the report analyze?

What are the key drivers and challenges shaping the Microbiome Sequencing Services market?

How does rising chronic disease prevalence boost microbiome sequencing demand?

Chronic illnesses that are increasingly becoming common, like type 2 diabetes, obesity, and inflammatory bowel disease (IBD), contribute significantly to the rate of need for microbiome sequencing services. According to the World Health Organisation, there are more than 537 million adults with diabetes globally, and the levels are likely to grow unwarrantedly in the next few decades. In the same way, the rate of occurrence of IBD has been increasing in the whole world, especially in the developed world. These are closely associated with alterations in the gut microbiome that affect metabolism, immune homeostasis, and inflammation.

The goal of the Human Microbiome Project by the U.S. National Institutes of Health (NIH) was to shed more light on these relations and create specific treatments. Through the sequencing of the microbiome of patients, researchers and clinicians will be able to find the signatures of the disease-inducing microbiomes to know how to diagnose the disease earlier and treat the patient as an individual. This scientific knowledge presents a higher investment in the microbiome investigation and sequencing infrastructure, and it is important to note that the global chronic disease burden can be managed effectively with the help of microbiome analysis.

Will increasing government funding accelerate microbiome research and service expansion?

A major factor to enhance the pace of microbiome research and to massively increase the sequencing services includes allocating increased government funding to it. As one example, the U.S. National Institutes of Health (NIH) gave the start to the Human Microbiome Project, in which many hundreds of millions of dollars are going to be spent on mapping the microbial communities of the human body. This massive undertaking had a profound impact on the efforts to define the relationship between the microbiome, health, and disease, and demonstrates that committed government funding drives scientific innovation.

NIH grants also maintain microbiome-oriented research centres in universities and allow the development of diagnostics and therapeutics. In India, more investment by the government in biotechnology, such as the Genome India Project, helps in high-level genome sequencing, which adds to the microbiome research. These publicly funded initiatives create the basic infrastructure, generate partnerships, and make high-throughput sequencing technologies that, in many cases, are simply economically out of reach without government funding. Overall, this type of funding hastens innovation, stimulates service growth, and fills in the gap between basic scientific research and clinical practice.

Are data privacy concerns slowing adoption of microbiome sequencing techniques?

Microbiome sequencing methods run up against the data privacy issue, as the process of collecting and interpreting microbial DNA is, in many cases, associated with sensitive personal health data. A study released in 2022 by the National Institutes of Health (NIH) revealed that more than 60% of the research participants were concerned about the misuse and misdirection of their microbiome data, and they feared its usage in this way. The NIH All of Us Research Program has reported on the issues of participant consent and data security regarding both genomic and microbiome information, arguing that the issue of privacy concerns can discourage participation and data sharing.

The National Science Foundation (2020) emphasised that non-uniform data governance structures and inadequate regulatory rules form obstacles for researchers and medical professionals to securely handle microbiome data. With the proposed European Health Data Space regulation, European efforts are geared towards enhancing data privacy regulations as a way of promoting confidence among the public. On balance, these justified privacy implications evince the necessity to adjust the data security level and discernible policies to persuade more contributors towards embracing microbiome sequencing in research and clinical practice.

Will partnerships between biotech firms expand microbiome sequencing service reach?

Alliances among biotech companies will bring with them vast potential for the scale of microbiome sequencing services by the pooling of technological skills, research capabilities, and resources. For instance, the U.S. National Microbiome Initiative (NMI) is an intersectoral approach to advance microbiome research and its utilisation in human health, agriculture, or the environment. Such partnerships, the National Institutes of Health (NIH) states, encourage innovation of sequencing technologies and data analysis pipelines, if pursued, making microbiome sequencing more available and less expensive.

Universities and government laboratories tend to collaborate with biotech businesses to convert research results into technologies that can be delivered on a large scale. The wider geographical dissemination of microbiome sequencing becomes possible owing to such partnerships, where it can access the underserved or target new markets in different regions. The synergies aid in realising amplified changes and performances in the spheres of clinical diagnostics, personalised medicine, and environmental surveillance, and eventually increase the microbiome sequencing market range and potential worldwide.

How might emerging markets drive growth for microbiome sequencing technologies?

Microbiome sequencing technologies are expected to grow, especially in emerging markets, as there has been a rise in investments in biotechnology research and improvement of healthcare infrastructure. For instance, the Department of Biotechnology at the Indian government has been aggressively investing in microbiome-related efforts via its National Microbiome Mission, with the objective of creating microbial diversity in the areas of health and agricultural development. The National Institutes of Health (NIH) in the U.S. stated that international partnerships with nations such as China and India have enhanced the study of microbiomes due to the increased possibilities of studying microbiomes by expanding sequencing technologies in those countries.

Government-sponsored programs have resulted in the collection of microbial genomic data (over 6 billion records) by the National Microbiology Data Centre of China. These initiatives of emerging economies, with government support, are helping bridge the access divide to high-technology sequencing platforms and information, expanding innovation and the market. The increased focus on microbiome research to inform public health issues and crop productivity will likely strengthen the pace of sequencing service uptake and commercialisation in these markets.

What are the key market segments in the Microbiome Sequencing Services industry?

Based on the Sequencing Type, the Microbiome Sequencing Services Market has been classified into 16S rRNA Sequencing, Shotgun Metagenomic Sequencing, Whole Genome Sequencing (WGS), Targeted Gene Sequencing, and Amplicon Sequencing. The most obvious and popular technique in the microbiome sequencing services market is 16S rRNA sequencing. It has been in dominance due to its affordability, rapidness, and appropriateness in microbial community profiling, especially in research and diagnostics in clinics. This technique can effectively identify the taxon of bacteria and archaea by targeting the well-conserved region of the 16S ribosomal RNA gene. It does not demand the computational bluntness and the data storage of the whole genome or shotgun sequencing, and it is affordable in a wide variety of applications. They nonetheless specify that 16S rRNA is the sequencing of choice to study microbiomes at scale.

Based on the Service Type, the Microbiome Sequencing Services Market has been classified into Sample Preparation, Library Preparation, Sequencing Services, Data Analysis & Interpretation, Bioinformatics Services, and Others. The most vivid section of the Microbiome Sequencing Services Market is sequencing services. Since sequencing services are the main stake of the microbiome analysis process, they create the strongest demand, as without these services, the raw genetic data on microbial samples will be irreducibly absent. Driven by the soaring application of high-throughput platforms such as Illumina and the improvement in the development of sequencing technologies, scientists and organisations are dependent on proficient sequencing providers. The dominance of this segment can also be explained by the increase in research in human health, agriculture, and environmental microbiomes, in which correct and efficient sequencing is required in order to perform downstream analysis.

Which regions are leading the Microbiome Sequencing Services market, and why?

The North America microbiome sequencing services market is leading due to developed healthcare infrastructure, research and development capacity, and the adoption of next-generation sequencing technologies. The area has a high number of well-established biotechnology and pharmaceutical firms that are currently investing their efforts in microbiome research and development to continue using it in personalised medicine, disease diagnostics, and treatment. This is also innovated by government funding and academic collaborations.

The rise in the realisation of the importance of the microbiome to human health has contributed to a rise in the need for precision health solutions. This is because the market has key players and regulatory support that would enable it to experience a favourable environment. Dominance of genomics and extensive data analytics capability in North America also provides it with a competitive advantage. The increasing occurrence of chronic diseases and lifestyle disorders only further adds to the interest in microbiome-based interventions. The collaboration of research institutes and commercial organisations is a strategic partnership that contributes to the increased availability of services and market penetration.

The Asia Pacific microbiome sequencing services market is growing because of multiple factors interrelated with each other. Surging investments in biotechnology and life sciences, coupled with rapid improvements in the healthcare infrastructure, have sparked the growth of demand for microbiome research. Genomic research and personalised medicine are well on the way in countries such as China, Japan, South Korea, and India, where both the government and private sectors have invested funds.

Increasing population, large numbers of chronic diseases, and increased awareness about the part microbiota play in health are also fuelling market growth. Further, the availability of expertise in the scientific community, affordable services, and conducive regulatory conditions make the region a destination for international partnerships. The growth in the market is also enhanced by the rise in the implementation of next-generation sequencing (NGS) technologies and local manufacturing capacities. With this changing environment, Asia Pacific will be a key centre of innovation and development in microbiome sequencing.

What does the competitive landscape of the Microbiome Sequencing Services market look like?

The microbiome sequencing services market is registering strong growth owing to the rising research in the areas of human health, agriculture, and the environmental sector. The industry leaders, including CosmosID, Novogene, Diversigen, and Microba, have gained a foothold in the market due to their latest technology of sequencing and broad data interpretation.

The recent trends are a strategic alliance and the growth in service portfolio to incorporate multi-omics across the service spectrum and to gain knowledge on complex microbial communities. Novogene has recently enhanced its sequencer equipment to allow better accuracy and improved turnaround time, with sunnier Diversigen to new locations around the globe to meet increasing demand in North America and Europe. Moreover, firms such as Biome Makers are also incorporating AI-powered analytics to give greater detail into the microbiomes of soils and plants. In sum, innovation and alliances are essential to have a competitive advantage in this dynamic market.

Microbiome Sequencing Services Market, Company Shares Analysis, 2024

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Which recent mergers, acquisitions, or product launches are shaping the Microbiome Sequencing Services industry?

• In June 2025, the FDA granted Fast Track and Rare Pediatric Disease designations to MNV-201 for Pearson syndrome. The move supported the upcoming pivotal trial. It also boosted Minovia’s preparations for going public. The designations highlighted the therapy’s potential for a serious rare condition.
• In April 2025, the FDA cleared Minovia’s second IND for MNV-201, an autologous stem-cell therapy enriched with donor mitochondria. The approval allowed it to proceed to a Phase II trial for pediatric Pearson syndrome. Early data from the first-generation version showed stabilization in growth metrics. It also showed improvements in disease scale scores.

Report Coverage:

By Sequencing Type

• 16S rRNA Sequencing
• Shotgun Metagenomic Sequencing
• Whole Genome Sequencing (WGS)
• Targeted Gene Sequencing
• Amplicon Sequencing

By Service Type

• Sample Preparation
• Library Preparation
• Sequencing Services
• Data Analysis & Interpretation
• Bioinformatics Services
• Others

By Application

• Human Health
• Drug Discovery & Development
• Personalized Medicine
• Agriculture
• Animal Health
• Environmental Microbiology
• Others

By Technology

• Sequencing by Synthesis (SBS)
• Ion Semiconductor Sequencing
• Single Molecule Real-Time (SMRT) Sequencing
• Nanopore Sequencing
• Pyrosequencing
• Sanger Sequencing
• Others

By Sample Type

• Stool Samples
• Skin Swabs
• Oral Swabs
• Vaginal Swabs
• Blood Samples
• Others

By End User

• Academic & Research Institutes
• Pharmaceutical & Biotechnology Companies
• Contract Research Organizations (CROs)
• Hospitals & Clinics
• Government Agencies
• Others

By Region

North America

• U.S.
• Canada

Europe

• U.K.
• France
• Germany
• Italy
• Spain
• Rest of Europe

Asia Pacific

• China
• Japan
• India
• Australia
• South Korea
• Singapore
• Rest of Asia Pacific

Latin America

• Brazil
• Argentina
• Mexico
• Rest of Latin America

Middle East & Africa

• GCC Countries
• South Africa
• Rest of the Middle East & Africa

List of Companies:

• CosmosID
• uBiome
• Second Genome
• GenoBiome
• Novogene
• Diversigen, Inc.
• Biome Makers
• Microba
• MO BIO Laboratories
• SeqBiome
• DNA Genotek
• Microbiome Insights Inc.
• Genewiz
• Eurofins Scientific
• BaseClear

Frequently Asked Questions (FAQs)