Gut and Microbiome Metabolites

Precision Metabolomics Services


Microbial metabolism plays a key role in human and animal health, influencing immune regulation, nutrient absorption, and energy balance. Metabolites produced by gut microbes, such as short-chain fatty acids, bile acid derivatives, and aromatic compounds, act as signaling molecules that affect host physiology and disease susceptibility.

Our targeted microbiome metabolite analyses quantify a broad spectrum of gut-derived compounds to provide detailed insight into microbial activity and its interaction with host metabolism. These analyses support studies in microbiome research, nutrition, metabolic health, and systems biology, and can be combined with amino acid, bile acid, and lipid panels for a comprehensive metabolic overview.

If you’d like to learn more, we are happy to discuss your project and help you get the most out of your metabolomics analysis.


Let’s discuss your project


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Guiding you from sample to biology

Our metabolomics specialists collaborate with you from the earliest project stages. We start with an initial consultation to understand your biological questions, study design, and sample types. Based on your research focus, we help select the most suitable microbiome-related panels and combinations to capture relevant metabolic pathways.



Get a Project Estimate

We provide customized project estimates and timelines aligned with your study design and experimental scope. Contact us for a free consultation to discuss your analytical strategy and learn how Biogenity can support your microbiome metabolomics workflow.


Sample preparation and sample analysis

Optimized workflows for diverse lipid classes

Microbiome-related metabolites vary widely in chemical properties and stability. We use optimized and validated Standard Operating Procedures (SOPs) designed for high reproducibility and compound preservation during extraction and storage.

Supported matrices include

  • Biological fluids: plasma, serum, urine, saliva, fecal water
  • Microbiome samples: feces, gut content, intestinal fluids
  • Cells and tissues: tissue biopsies, cell cultures, microbial extracts
  • Model systems: animal models, fermentation experiments, and dietary studies

All sample preparation workflows are tailored to preserve volatile, polar, and non-polar metabolites, ensuring accurate representation of microbial activity.

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Our microbiome metabolite analyses combine targeted LC-MS/MS and GC-MS/MS platforms to cover a wide range of gut-derived compounds. High-resolution instrumentation provides excellent sensitivity and reproducibility for volatile and non-volatile metabolites.


Our gut and microbiome metabolites panels

Short-Chain Fatty Acids

Quantifies acetate, propionate, butyrate, and branched-chain fatty acids, providing insights into microbial fermentation and host energy metabolism. Ideal for studies of gut health, dietary fiber utilization, and microbiome functionality.



Bile Acids and Derivatives

Profiles primary and secondary bile acids along with conjugates and microbial derivatives. Enables assessment of gut–liver axis activity and microbial influence on lipid and cholesterol metabolism.

Indoles and Aromatic

Measures tryptophan-derived metabolites such as indole, indole-3-acetic acid, and p-cresol, reflecting microbial amino acid catabolism and host–microbe signaling interactions.



Volatile and Semi-Volatile Metabolites

Detects a wide array of volatile metabolites including alcohols, aldehydes, and organic acis, providing an additional layer of metabolic fingerprinting in gut or fermentation samples.

Gut and microbiome metabolism combo options

Core metabolomics combo

Combines Amino Acids and Derivatives, Energy Metabolism, and Lipid Profiling panels for a comprehensive baseline of central metabolism.



Regulatory Metabolomics Combo

Integrates Amino Acids and Derivatives, Energy Metabolism, and Lipid Mediators panels to study signaling and regulation.

Microbiome-Linked Combo

Includes Short-Chain Fatty Acids, Bile Acids, and Indoles to connect host metabolism with microbial activity.



Environmental & Impact Combo

Combines Fatty Acids, Bile Acids, and PFAS analysis to assess how environmental factors influence metabolism.

Do you want to learn more? We are happy to assist
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Data analysis, including report, figures, and tables

Advanced data analysis by metabolomics experts

At Biogenity, our experts manage the complete data analysis workflow for your microbiome metabolite studies, allowing you to focus on interpreting biological mechanisms. We handle every step from data filtering and normalization to advanced statistical evaluation and pathway analysis. Our team ensures your data are accurate, reproducible, and publication-ready.



!! Visualize lipid pathways and regulation

Reports include quantitative results, QC summaries, and interactive pathway visualizations. These tools highlight microbial pathways and metabolites that differ between conditions, helping you understand how microbial activity and host metabolism are interconnected.

Delivery and discussion

Delivery, post-consultation and discussion

At the conclusion of our metabolomics analysis, we ensure a seamless transition from discovery to application. We deliver detailed reports and data, followed by a post-delivery consultation to discuss your study's insights and findings.


What to expect during post-consultation

  • Explanation of the different steps in the sample analysis
  • Discussion of the data
  • Explanation of the different steps in the data analysis
  • Q&A to the report(s)

Together, we ensure that you have the best prerequisite for your further research. The consultation can also be used to explore the next step, whether you are looking to expand the project with additional omics studies or validate the results.


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