Targeted Metabolomics Services

Short-chain fatty acids (SCFAs)

Updated 06/06/2023

What is measured?

Formate (Frm), acetate (Ace), propionate (Pro), butyrate (But), isobutyrate (iBut), valerate (Vlr), isovalerate (iVlr) and α-methylbutyrate (aMB) .
Method(s): GC-MS/MS.

What are short-chain fatty acids (SCFAs)?

Formate holds a unique position among the SCFAs since has a critical role in one-carbon metabolism, primarily as a source of one-carbon groups for the synthesis of 10-formyl-tetrahydrofolate (10-fTHF). 10-fTHF is a substrate for purine synthesis, and after further reduction of the one-carbon group, may serve as a substrate for thymidylate synthesis and for homocysteine remethylation. Serum formate shows a positive association with serum folate and with potential metabolic precursors (serine, methionine, tryptophan, choline) and an inverse association with vitamin B12 (1).
Acetate, propionate and butyrate are SCFAs produced from non-digestible complex carbohydrates (dietary fibre) in the gut during microbial fermentation, whereas the branched-chain SCFAs, isobutyrate , isovalerate and α-methylbutyrate, are bacterial-produced metabolites of amino acids. Acetate is the most abundant (50-70 %) followed by propionate and butyrate. They are absorbed into the systemic circulation, and each SCFA exerts specific metabolic effects, and may mediate beneficial but also adverse health effects.
SCFAs, in particular butyrate, are anti-inflammatory, expand the pool of intestinal regulatory T cells, protect against allergic sensitization, mitigate production of reactive oxygen species, are essential for gut integrity, and exert antiproliferative effects on cancer cells. Butyrate’s effects on the immune system are mediated through the inhibition of class I histone deacetylases and activation of G-protein coupled receptors: GPR109A, GPR41 and GPR43. SCFAs increase insulin secretion (via GPR41/43), and low gut-derived SCFAs have been suggested to be associated with type II diabetes, insulin resistance, obesity and NAFLD (2).
In a recent seminal review article, the authors recommend measurement of circulating SCFAs in human studies, since the SCFAs in faeces may not be an accurate measure of SCFA production or exposure (3).

Important note on contamination

Contamination from chemicals, additives and blood collection tubes with formate and acetate in particular is widespread. For example, we observed contamination of sealing O-rings in one brand of cryopreservation tubes with formate (1). Others have reported on the presence of acetate and propionate in EDTA K2 tubes, and propionate and butyrate in tubes containing polyacrylamide gel (4).


To investigate the metabolomic signature of human diseases.

Specimen, collection and processing

Matrix: Serum.
Volume: Minimum volume is 60 µL, but 200 µL is optimal and allows reanalysis.
Preparation and stability: Samples should be put on ice immediately after collection and stored at -80 °C.


Frozen, on dry ice. (for general instruction on transportation, click here)

Reported values, interpretation

Frm: 8-100 µmol/L; Ace: 5-300 µmol/L; Pro: 1-13 µmol/L; But: 1-30 µmol/L; iBut: 0.7-6 µmol/L; Vlr: 0.2-1 µmol/L; iVlr: 0.3-3 µmol/L; aMB: 0.3-3 µmol/L.
Intraclass correlation coefficient (ICC): na.


1. Brosnan, J. T., Mills, J. L., Ueland, P. M., Shane, B., Fan, R., Chiu, C.-Y., Pangilinan, F., Brody, L. C., Brosnan, M. E., Pongnopparat, T., & Molloy, A. M. (2018). Lifestyle, metabolite, and genetic determinants of formate concentrations in a cross-sectional study in young, healthy adults. Am J Clin Nutr, 107, 345-354.
2. Blaak, E. E., Canfora, E. E., Theis, S., Frost, G., Groen, A. K., Mithieux, G., Nauta, A., Scott, K., Stahl, B., van Harsselaar, J., van Tol, R., Vaughan, E. E., & Verbeke, K. (2020). Short chain fatty acids in human gut and metabolic health. Benef Microbes, 11, 411-455.
3. Eslick, S., Thompson, C., Berthon, B., & Wood, L. (2021). Short-chain fatty acids as anti-inflammatory agents in overweight and obesity: a systematic review and meta-analysis. Nutr Rev, nuab059.
4. Deroover, L., Boets, E., Tie, Y., Vandermeulen, G., & Verbeke, K. (2017). Quantification of plasma or serum short-chain fatty acids: Choosing the correct blood tube. J Nutrition Health Food Sci, 5, 1-6.

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Amino acids, amino acid catabolites, acylcarnitines, TCA metabolites, ketone bodies, AGEs

Kynurenines, ratio-derived metabolites, proteins

SCFAs, indoles, choline metabolites, amino acid derived

B-vitamins, functional markers, and methyl donors, fat-soluble vitamins, essential amino acids, meat & fish intake, tobacco use & coffee intake
Biomarkers (n)

Amino acids: Alanine, Arginine, Asparagine, Aspartic acid, Glutamic acid, Glutamine, Glycine, Histidine, Isoleucine, Kynurenine, Leucine, Lysine, Methionine, Ornithine, Phenylalanine, Proline, Sarcosine, Serine, Threonine, Total cysteine, Tryptophan, Tyrosine, Valine

Amino acid catabolites: 2-Aminoadipic acid, 2-Hydroxybutyrate, 3-Hydroxysiobutyrate, α-Hydroxyglutaric acid, β-Alanine, β-Aminoisobutyrate, β-Hydroxy B-methylbutyric acid, Phenylacetylglutamine

Acylcarnities: BB, C0, C2, C3, C3-DC, C4, C4-OH, C4-DC, iC5, C5-DC, C5:1, C6, C8, C10, C12, C14, C14-OH, C16, C16-OH, C18, C18-OH, C18:1, C18:2

TCA metabolites: α-Ketoglutarate, Citrate, Fumarate, Isocitrate, Lactate, Malate, Pyruvate

Ketone bodies: Acetoacetate, 3-Hydroxybutyrate

AGEs: Carboxyethyllysine, Carboxymethyllysine


Kynurenines: 3-hydroxykynurenine, 3-hydroxyanthranilic acid, Anthranilic acid, Kynurenine, Kynurenic acid, Nicotinic acid, Nicotinamide, N1-methylnicotinamide, Picolinic acid, Quinaldic acid, Quinolinic acid, Xanthurenic acid


Proteins: C-Reactive protein, Calprotectin, Serum Amyloid A

Ratio-derived: Kynurenine/tryptophan ratio, PAr index (PLP, PL, PA)


SCFAs: Acetate, Butyrate, Formate, Isobutyrate, Isovalerate, Propionate, Valerate, α-Methylbutyrate

Indoles: 3-Indoxyl sulfate, Imidazole propionate, Indole-3-acetamide, Indole-3-acetate, Indole-3-aldehyde, Indole-3-lactate, Indole-3-propionate

Choline metabolites: Choline, Betaine, DMG, TMAO

Amino acid derived: Phenylacetylglutamine


B-vitamins, functional markers, and methyl donors: 4-Pyridoxic acid, Betaine, Choline, Cobalamin, Flavin mononucleotide, Folate, Methylmalonic acid, N1-methylnicotinamide, Nicotinamide, Nicotinic acid, Pyridoxal, Pyridoxal 5-phosphate, Pyridoxine, Riboflavin, Thiamine, Thiamine monophosphate, Total homocysteine

Fat-soluble vitamins: 25-hydroxy vitamin D2, 25-hydroxy vitamin D3, α-Tocopherol (Vit. E), All-trans retinol (Vit. A), Phylloquinone (Vit. K1), y-Tocopherol (Vit. E)

Essential amino acids: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine

Meat and fish intake: 1-Methylhistidine, 3-Methylhistidine, B-Alanine, Creatine, Creatinine, TMAO

Tobacco use and coffee intake: Cotinine, Trans-3-hydroxycotinine, Trigonelline

Volume (μl)
Analytical techniques
GC- and LC-MS/MS
GC- and LC-MS/MS
GC- and LC-MS/MS
Turnaround time (weeks)

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