Metabolomics

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 and process. These metabolites directly interact with our human physiology to promote health or cause 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 techniques, our services allow you to collaborate directly with scientists who specialize in metabolic profiling for different applications. Our team can advise you on analytical chemistry and suitable methods for your study, provide technical information on the analysis, and perform advanced data processing and analysis.  

We offer versatile packages for metabolic profiling that suit your needs. Our platform offers both untargeted and targeted analysis options using gas chromatography (GC) or liquid chromatography (LC) coupled with a mass spectrometry (MS) detector. Our instruments include leading platforms as Thermo Scientific Exploris 240/120, Bruker TimsTOF pro and various Agilent and Leco GC-MS systems.

Untargeted metabolomics 

Untargeted metabolomics provides global detection of broad compound classes produced by the host and the microbiome 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:

Microbial metabolites

Microbial metabolites refer to the small molecules produced by microorganisms and have various roles and significance. They provide a detailed snapshot of the metabolic status of microbial communities and offer insights into the biochemical pathways and processes of the microorganisms to enable an understanding of how microbes interact with their environment, utilize resources, respond to external stimuli and potential implications for driving health and disease. Our untargeted methods include analysis of common microbial metabolites such as TMAO, bile acids, tryptophan, tryptophan-derived metabolites, acylcarnitines, amino acids, citric acid cycle compounds, phosphatidylcholine and carnitine.

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

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.

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 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 specific classes and can detect a wide variety of other metabolites. To ensure the broadest coverage, all samples are processed using both positive and negative ionization modes, thereby capturing a comprehensive range of compounds. This approach is important in uncovering the metabolic capabilities of microbial communities, identifying biomarkers of microbial activity, and understanding 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: 

SCFA panel
  • Acetic acid aka acetate (HMDB0000042)
  • Butanoic acid aka butyrate (HMDB0000039)
  • Heptanoic acid (HMDB0000666)
  • Hexanoic acid aka caproic acid (HMDB0000535)
  • Pentanoic acid aka valerate, valeric acid (HMDB0000892)
  • 2-methylpropanoic acid aka isobutyrate, isobutyric acid (HMDB0001873)
  • 3-Methylbutanoic acid aka isovalerate, isovaleric acid (HMDB0000718)
  • Formic acid aka formate (HMDB0000142)
  • Propanoic acid aka propionate (HMDB0000237)
  • 4-Methylpentanoic acid aka isocaproic acid (HMDB0000689)
Bile acid panel
  • β-Muricholic acid (HMDB0000865)
  • Chenodeoxycholic acid (HMDB0000518)
  • Cholic acid aka cholate (HMDB0000619)
  • Deoxycholic acid aka deoxycholate (HMDB0000626)
  • Glycocholic acid (HMDB0000138)
  • Glycolithocholic acid (HMDB0000698)
  • Glycoursodeoxycholic acid (HMDB0000708)
  • Glycodeoxycholic acid (HMDB0000631)
  • Hyocholic acid (HMDB0000760)
  • Hyodeoxycholic acid (HMDB0000733)
  • Lithocholic acid aka lithocholate (HMDB0000761)
  • α-Muricholic acid (HMDB0000506)
  • Tauro-α-Muricholic acid (HMDB0258742)
  • Tauro-β-Muricholic acid (HMDB0000932)
  • Taurochenodeoxycholic acid (HMDB0000951)
  • Taurocholic acid (HMDB0000036)
  • Taurodeoxycholic acid aka taurodeoxycholate (HMDB0000896)
  • Taurohyodeoxycholic acid
  • Taurolithocholic acid (HMDB0000722)
  • Taurolithocholic acid sulfate (HMDB0002580)
  • Tauroursodeoxycholic acid (HMDB0000874)
  • Ursodeoxycholic acid (HMDB0000946)
  • ω-Muricholic acid (HMDB0000364)
  • Isolithocholic acid (HMDB0000717)
  • 12-Ketolithocholic acid (HMDB0000328)
Total fatty acid panel
  • ⍺-Linolenic acid (HMDB0001388)
  • 11,14-Eicosadienoic acid (HMDB0244372)
  • 13,16-Docosadienoic acid (HMDB0244521)
  • Arachidic acid (HMDB0002212)
  • Arachidonic acid (HMDB0001043)
  • cis-10-Heptadecenoic acid (HMDB0060038)
  • cis-10-Pentadecenoic acid (HMDB0304816)
  • cis-11-Eicosenoic acid (HMDB0002231)
  • Decanoic acid aka caprate, capric acid (HMDB0000511)
  • Dihomo-⍺-linolenic acid (HMDB0060039)
  • Dihomo-γ-linoleic acid (HMDB0002925)
  • Docosahexaenoic acid (HMDB0002183)
  • Docosanoic acid (HMDB0000944)
  • Docosapentaenoic acid (HMDB0006528)
  • Dodecanoic acid (HMDB0000638)
  • Eicosapentaenoic acid (HMDB0001999)
  • Elaidic acid (HMDB0000573)
  • Erucic acid (HMDB0002068)
  • Heneicosanoic acid (HMDB0002345)
  • Heptadecanoic acid (HMDB0002259)
  • Linoleic acid (HMDB0000673)
  • Linolelaidic acid (HMDB0006270)
  • Myristic acid (HMDB0000806)
  • Myristoleic acid (HMDB0002000)
  • Nervonic acid (HMDB0002368)
  • Octadecanoic acid (HMDB0000827)
  • Oleic acid (HMDB0000207)
  • Palmitic acid (HMDB0000220)
  • Palmitoleic acid (HMDB0003229)
  • Pentadecanoic acid (HMDB0000826)
  • Tetracosanoic acid (HMDB0002003)
  • Tricosanoic acid (HMDB0001160)
  • Tridecanoic acid (HMDB0000910)
  • Undecanoic acid (HMDB0000947)
  • γ-Linolenic acid (HMDB0003073)
Tryptophan panel
  • 2,3-Pyridinedicarboxylic acid (HMDB0000232)
  • 2-Picolinic acid (HMDB0002243)
  • 3-(4-hydroxyphenyl)propionic acid (HMDB0002199)
  • 3-Methylindole (HMDB0000466)
  • Anthranilic acid (HMDB0001123)
  • Indole (HMDB0000738)
  • Indole-3-acetic acid (HMDB0000197)*
  • Indole-3-acrylic acid (HMDB0000734)
  • Indole-3-butyric acid (HMDB0002096)
  • Indole-3-propionic acid (HMDB0002302)
  • Indole-3-pyruvic acid (HMDB0060484)*
  • Tryptamine (HMDB0000303)
  • 2-Oxoglutaric acid (HMDB0000208)
  • 5-Aminovaleric acid (HMDB0003355)
  • Alanine (HMDB0000161)
  • Asparagine (HMDB0000168)
  • Aspartic acid (HMDB0000191)
  • cis-Aconitic acid (HMDB0000072)
  • Citric acid (HMDB0000094)
  • Cystine (HMDB0000192)
  • Fumaric acid aka fumarate (HMDB0000134)
  • Glutamic acid aka glutamate (HMDB0000148)
  • Glutamine (HMDB0000641)
  • Glycine (HMDB0000123)
  • Histidine (HMDB0000177)
  • Isocitric acid (HMDB0000193)
  • Isoleucine (HMDB0000172)
  • Lactic acid aka lactate (HMDB0000190)
  • Leucine (HMDB0000687)
  • Lysine (HMDB0000182)
  • Malic acid (HMDB0000156)
  • Methionine (HMDB0000696)
  • Ornithine (HMDB0000214)
  • Phenylalanine (HMDB0000159)
  • Phosphoenolpyruvic acid (HMDB0000263)
  • Proline (HMDB0000162)
  • Serine (HMDB0000187)
  • Succinic acid aka succinate (HMDB0000254)
  • Threonine (HMDB0000167)
  • Tryptophan (HMDB0000929)
  • Tyrosine (HMDB0000158)
  • Valine (HMDB0000883)

*NOTE: Indole-3-acetic acid and indole-3-pyruvic acid co-elute; their peaks can therefore not be resolved and they cannot be quantified individually. These compounds are marked with a ‘*’ in compounds detected/quantified section.

Amino acids and TCA cycle intermediates panel
  • 2-Oxoglutaric acid (HMDB0000208)
  • 5-Aminovaleric acid (HMDB0003355)
  • Alanine (HMDB0000161)
  • Asparagine (HMDB0000168)
  • Aspartic acid (HMDB0000191)
  • cis-Aconitic acid (HMDB0000072)
  • Citric acid (HMDB0000094)
  • Cystine (HMDB0000192)
  • Fumaric acid aka fumarate (HMDB0000134)
  • Glutamic acid aka glutamate (HMDB0000148)
  • Glutamine (HMDB0000641)
  • Glycine (HMDB0000123)
  • Histidine (HMDB0000177)
  • Isocitric acid (HMDB0000193)
  • Isoleucine (HMDB0000172)
  • Lactic acid aka lactate (HMDB0000190)
  • Leucine (HMDB0000687)
  • Lysine (HMDB0000182)
  • Malic acid (HMDB0000156)
  • Methionine (HMDB0000696)
  • Ornithine (HMDB0000214)
  • Phenylalanine (HMDB0000159)
  • Phosphoenolpyruvic acid (HMDB0000263)
  • Proline (HMDB0000162)
  • Serine (HMDB0000187)
  • Succinic acid aka succinate (HMDB0000254)
  • Threonine (HMDB0000167)
  • Tryptophan (HMDB0000929)
  • Tyrosine (HMDB0000158)
  • Valine (HMDB0000883
Human Milk Oligosaccharides (HMOs)

Most HMOs are measured as prebiotics in formula or as compounds in breastmilk. Contact us to discuss the range of HMOs that best fit your study goals.

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. 

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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