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Microbiome Panel

Metabolites that Translate Microbial Activity into Host Impact

A highly-curated metabolomics panel that screens for more than 800 key small molecules to accelerate microbiome discovery. 

  • Vetted Microbiome Metabolites
  • Easily Integrate with Metagenomics Data
  • Powerful Informatics Tools
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Request a quote, get detailed information on sample types, or learn how metabolomics can accelerate your research.

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Microbiome Research as a Key Driver in the Future of
Human and Animal Health

Microbiome research is now established as one of the most crucial areas of scientific exploration, as it uncovers the profound influence microorganisms have on host health, disease, treatment response and overall well-being. The microbiome’s capacity to generate a vast repertoire of metabolites has profound implications for health and disease. These microbial metabolites are key mediators of microbiome-host interactions, influencing various physiological and pathological processes.

To help researchers understand the functional outputs of microbiome activity, Metabolon designed a carefully curated panel of metabolites that reports on microbiome activity. The Microbiome Panel screens for more than 800 microbiome-associated metabolites that were vetted in scientific literature as microbiome-relevant, covering key biology that span dozens of chemical classes. Short Chain Fatty Acids are measured with rigorous absolute quantitation within the Microbiome Panel, enabling comparison of these microbially-derived and clinically relevant biomarkers to values reported in the literature. Collectively, these metabolites report on key outputs of microbial activity, moving beyond just characterizing the microbial community composition of a sample into measuring the molecules they produce that influence host physiology.

Top Microbiome Panel Pathways

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Short Chain Fatty Acids – with absolute quantitation

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Bile Acids – Primary and Secondary

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Tryptophan (Indole) Metabolites

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Amino Acid Metabolites Including Aromatic Compounds

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Diet and Drug Metabolites

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Antibiotics and Xenobiotics

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70 additional pathways..

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Short Chain Fatty Acids – with absolute quantitation

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Bile Acids – Primary and Secondary

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Tryptophan (Indole) Metabolites

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Amino Acid Metabolites Including Aromatic Compounds

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Diet and Drug Metabolites

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Antibiotics and Xenobiotics

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70 additional pathways..

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Tailored Microbiome Solutions

Metagenomics Options for Integration with Metabolomics

Metabolon offers flexible metagenomics sequencing options – including amplicon sequencing, shotgun sequencing at various read depths and a bring your own approach– for microbial community profiling tailored to your research goals. These sequencing options are available to pair with the Global Discovery Panel or the Microbiome Panel. Metagenomic sequencing reveals the composition and genetic potential of the microbial community, while metabolomics captures the functional outputs that influence host biology. Together, these approaches combine for a comprehensive, synergistic view of microbiome activity and its impact on the host.

    Metagenomic Sequencing
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    Integrated Bioinformatics Platform

    Comprehensive Insights at the Click of a Button

    Results from the Microbiome Panel are delivered in Metabolon’s Integrated Bioinformatics Platform (IBP) with user-friendly and powerful capabilities to analyze data and generate publication-quality figures. Clients who opt to include a metagenomics sequencing option as part of the Microbiome Research Solution can access the Microbiome Analysis Tool that transforms raw sequencing data to integrated metabolomics and metagenomics insights not available when either data stream is analyzed separately.

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    Demo our Platform$
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    Comprehensive Data

    Project Deliverables that Advance Your Research Objectives

    Metabolon produces high-quality metabolomics datasets by implementing rigorous quality control (QC) measures at every step of the data generation process as part of adherence to an ISO 9001:2015-certified quality management system, enabling researchers to move forward confidently with analysis. Microbiome Panel projects receive a Client Data Table (CDT) with abundances of panel of metabolites detected in samples. Delivered data include metabolites named by matching acquired LC-MS data against our industry-leading library of authenticated standards for Level 1 identifications, with metabolites organized into pathways with other associated chemical annotations. Metagenomics data generated through Metabolon also undergoes a comprehensive QC evaluation before delivery in the IBP.

     

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    Expert Hands

    Your Biological Research Partner

    With 25 years of experience, Metabolon has completed more than 10,000 projects and been cited in more than 3,500 scientific publications. With a team of high-impact PhD-level metabolomics and bioinformatics experts, we have the collective skill, knowledge, and experience to help researchers uncover novel discoveries, advance biological understanding, and achieve clinical and commercial success. This experience culminates in offering interpretation report options that focus on metabolomics data alone or insights derived from the integration of metabolomics and metagenomics data streams to jump-start your research.

    Working With Us
    Why Metabolon?$
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    Featured Resources

    Learn more about our Microbiome Panel and the impacts metabolomics has made on various research areas. Explore more resources here.

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    eBrochure: Global Discovery Panel

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    Guide to Successful Metabolomics Study Design

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    Why Metabolomics: Your Guide to Metabolomics

    GET STARTED

    Talk with an expert

    Request a quote, get detailed information on sample types, or learn how metabolomics can accelerate your research. Find our contact details are here.

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    References

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    2. Bryant, J.A., et al., The impact of an oral purified microbiome therapeutic on the gastrointestinal microbiome. Nat Med, 2026. 32(1): p. 186-196

    3. McGovern, B .H., et al., SER-109, an Investigational Microbiome Drugto Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial. Clin Infect Dis, 2021. 72(12): p. 2132-2140.

    4. Feuerstadt, P., et al., SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection. N Engl J Med, 2022. 386(3): p. 220-229.

    5. Hu, Z., et al., Targeted metabolomics reveals novel diagnostic biomarkers for colorectal cancer. Mol Oncol, 2025. 19(6): p. 1737-1750.

    6. Butler, F.M., et al., Vegetarian Dietary Patterns and Diet-Related Metabolites Are Associated With Kidney Function in the Adventist Health Study-2 Cohort. J Ren Nutr, 2025.

    7. Stanford, J., et al., Metabolomic Profiling and Diet Quality Scoring in a Randomized Crossover Trial of Healthy and Typical Dietary Patterns. Mol Nutr Food Res, 2025 . 69(23): p. e70271.

    8. O’Connor, L.E., et al., Metabolomic Profiling of an Ultraprocessed Dietary Pattern in a Domiciled Randomized Controlled Crossover Feeding Trial. J Nutr, 2023. 153(8): p. 2181-2192.

    9. Fritsch, D.A., et al., Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea. BMC Vet Res, 2022. 18(1): p. 245.

    10. Leal, L.N., et al., Preweaning nutrient supply improves lactation productivity and reduces the risk of culling in Holstein cows. J Dairy Sci, 2025. 108(6): p. 5875-5888.

    11. Ahsin, M., et al., Soil and pasture health underlie improved beef nutrient density determined by untargeted metabolomics in Southern US grass finished beef systems. NPJ Sci Food, 2025. 9(1): p. 151.

    12. Yin, W., et al., Plasma lipid profiling across species for the identification of optimal animal models of human dyslipidemia. J Lipid Res, 2012. 53(1): p. 51-65.

    13. Porter, F .D., et al., Cholesterol oxidation products are sensitive and specific blood-based biomarkers for Niemann-Pick C1 disease. Sci Transl Med, 2010. 2(56): p. 56ra81.

    14. Needham, B .D., et al., Plasma and Fecal Metabolite Profiles in Autism Spectrum Disorder. Biol Psychiatry, 2021. 89(5): p. 451-462

    15. Li, C., et al., Estradiol and mTORC2 cooperate to enhance prostaglandin biosynthesis and tumorigenesis in TSC2-deficient LAM cells. J Exp Med, 2014. 211(1): p. 15-28.

    16. Green, P.G., et al., Metabolic flexibility and reverse remodelling of the failing human heart. Eur Heart J, 2025. 46(25): p. 2422-2433.

    17. Maekawa, H., et al., SGLT2 inhibition protects kidney function by SAM-dependent epigenetic repression of inflammatory genes under metabolic stress. J Clin Invest, 2025. 135(19).

    18. Wu, D., et al., Integrated screens reveal that guanine nucleotide depletion, which is irreversible via targeting IMPDH2, inhibits pancreatic cancer and potentiates KRAS inhibition. Gut, 2026.

    19. Schwerdtfeger, L.A., et al., Gut microbiota and metabolites are linked to disease progression in multiple sclerosis. Cell Rep Med, 2025. 6(4): p. 102055.

    20. Wu, H., et al., Microbiome-metabolome dynamics associated with impaired glucose control and responses to lifestyle changes. Nat Med, 2025. 31(7): p. 2222-2231.

    21. Jacobs, J.P., et al., Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement. Microbiome, 2021. 9(1): p. 236.

    22. Pietzner, M., et al., Plasma metabolites to profile pathways in noncommunicable disease multimorbidity. Nat Med, 2021. 27(3): p. 471-479.

    23. Faquih, T.O., et al., Robust Metabolomic Age Prediction Based on a Wide Selection of Metabolites. J Gerontol A Biol Sci Med Sci, 2025. 80(3).

    24. Scherer, N., et al., Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits. Nat Genet, 2025. 57(1): p. 193-205.

    25. Holmes, Z.C., et al., Untargeted metabolomic analysis of human milk from healthy mothers reveals drivers of metabolite variability. Sci Rep, 2024. 14(1): p. 20827.

    26. Titz, B., et al., Implications of Ocular Confounding Factors for Aqueous Humor Proteomic and Metabolomic Analyses in Retinal Diseases. Transl Vis Sci Technol, 2024. 13(6): p. 17.

    27. Bloom, S.M., et al., Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation. Nat Microbiol, 2022. 7(3): p. 434-450.

    28. Leimer, E.M., et al., Lipid profile of human synovial fluid following intra-articular ankle fracture. J Orthop Res, 2017. 35(3): p. 657-666.