Metabolomics is the large-scale study of small molecules known as metabolites, which aims to capture the multiple metabolic processes occurring in a biological system. Metabolite profiling provides a real-time snapshot of these metabolic processes when the sample was collected. 

Metabolomics provides an indispensable tool for microbiome research by illuminating the functional output of microbial communities. For understanding how the microbiome interacts with the human host, we need not only to look at the microbes, but also the metabolites they produce, which are directly interacting with our human physiology to promote health or cause disease.  

The human microbiome is known to produce or process a myriad of different compounds – many of which affect human health, behavior and disease. To understand these intricate connections, we offer metabolomics and data analysis services through our specialized team at MS-Omics. Whether you are new to metabolomics or experienced in the analysis techniques, our services allow you to collaborate directly with scientists who specialize in metabolic profiling for different applications. Our team can advise you on suitable methods for your study, provide technical information on the analysis, and advise on analytical chemistry and advanced data handling.  

We offer versatile packages for metabolic profiling that suit your needs – and with a quick turnaround time. Our platform offers both untargeted and targeted analysis options and uses gas chromatography (GC) or liquid chromatography (LC) coupled with a mass spectrometry (MS) detector. Our instruments include leading platforms from Thermo Scientific Q Exactive HF LC-MS/MS and Agilent Q GC-MS.

Untargeted metabolomics 

With untargeted metabolomics, we can identify a wide range of compound classes that play crucial roles in microbial metabolism and host-microbe interactions. While the specific composition may vary depending on the sample type and experimental conditions, here are some of the relevant compound classes commonly detected: 

Amino acids and derivatives

Amino acids serve as building blocks for proteins and participate in various metabolic pathways. Their analysis can provide insights into microbial protein synthesis, nitrogen utilization, and nutrient availability.

Tryptophan metabolites

They include indole and its derivatives, which modulate host immune responses and gut barrier function. Tryptamine and serotonin derivatives impact host neurobiology and gut-brain communication. Kynurenine pathway metabolites are associated with inflammation, neurodegeneration, and psychiatric disorders. Additionally, tryptophan-derived AhR ligands play a role in immune regulation and gut health. Analyzing these metabolites provides insights into microbial-host interactions and their implications for health and disease.

Organic acids and short-chain fatty acids

Organic acids, including short-chain fatty acids (SCFAs) like acetate, propionate, and butyrate, are metabolic byproducts of microbial fermentation. These metabolites have been associated with important host-microbe interactions, including gut health, immune modulation, and energy metabolism.

Lipids and lipid derivatives

Lipids are crucial components of microbial cell membranes and play roles in signalling, energy storage, and inflammation modulation. Analysis of lipid metabolites can provide insights into microbial membrane composition, lipid metabolism, and potential interactions with host lipid metabolism.

Nucleotides and nucleosides

Nucleotides and nucleosides are involved in various cellular processes, including DNA and RNA synthesis, signalling, and energy transfer. Their detection can provide information on microbial nucleotide metabolism and potential interactions with host nucleotide pools.

Secondary metabolites

Microbes are prolific producers of secondary metabolites, including antibiotics, toxins, and signalling molecules. Identifying these compounds can offer insights into microbial community dynamics, competitive interactions, and potential functional roles in the microbiome ecosystem. 

It’s important to note that untargeted metabolomics approaches are not limited to these classes and can detect a wide variety of other metabolites as well. The comprehensive analysis of these compound classes through untargeted metabolomics helps researchers uncover the metabolic capabilities of microbial communities, identify biomarkers of microbial activity, and understand the intricate interplay between the microbiome and host health. 


Targeted metabolomics 

In addition to our untargeted metabolomics services, we provide a set of targeted panels for dedicated analysis of: 

  • Short Chain Fatty Acids (SCFAs) – Targeted method to quantify fatty acids including: Acetic acid, Formic acid, Propanoic acid, 2-Methylpropanoic acid, Butanoic acid
  • Amino Acids and Organic Acids
  • Bile Acids 
  • Human Milk Oligosaccharides (HMOs) 

The specific methods used for microbiome-metabolomics depend on the information you intend to uncover from your samples.


Tell us about your project 

In microbiome studies, metabolomics data provide crucial information for investigating mechanisms. Contact us today to discuss how metabolomics analysis can complement your metagenomics data and enhance your overall knowledge about the microbiome. 

Visit the dedicated MS-Omics website for more information on our metabolomics capabilities. 

Combining the power of metabolomics and metagenomics

Read more about our multi-omics solutions for integrating metabolomics data with metagenomics data.

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