Metabolomics testing provides a window into a wide range of physiological processes that can be disrupted in illness and corrected with diet, nutrition, and lifestyle interventions. When combining metabolic markers with stool testing, a more complete picture of a patient’s metabolic and immune systems emerges. It provides more information about the gut microbiome: gut bacteria imbalance (dysbiosis), fungal imbalance, if someone is an equol-producer or not, and the dietary products that are being acted upon by the microbiome. As metabolomics research advances, scientists will continue to characterize core metabolic signatures associated with specific diseases. Clinicians can intervene when metabolic perturbations are first detected on metabolomic testing- long before frank disease presents itself.
What is a Metabolomics Test?
Metabolomics is the study of the set of metabolites of a cell, organism, or tissue. These are small biochemical substances that are used by and produced by the body during daily activities. The patterns seen on a metabolomics test are individual to each person and impacted by lifestyle. By analyzing these small molecules, we can identify a person’s individual signature and see problems in biochemistry before standard blood tests show abnormal findings.
Organic acids and other small molecules are intermediate compounds that can define the efficient flow of pathways and substrates such as amino acids to reveal the level of inputs, which together establish the functional status of key areas of health.
Metabolomics is ideally suited for functional medicine, as it seeks to analyze each person’s individual biochemical milieu and determine how it may be promoting or preventing healthy function. Integrative and functional medicine practitioners are looking for root causes that may be causing chronic illness or symptoms – and these root causes can start with metabolic disturbances.
Shifting the Paradigm from Organic Acid Testing to Applied Metabolomics
Thirty years ago, organic acids were a revolutionary way to look at cell metabolism. Today, we are entering a new age that carries organic acid and amino acid testing into the future, where metabolomic signatures are the new face of personalized medicine.
Metabolomics tests, such as the OMX® test, help to identify a patient’s metabolic signature by providing a systems-biology perspective of key metabolic pathways. Practitioners are able to follow an amino acid through its biochemical pathway and see its end products, which helps detect imbalances in the pathway. Further, metabolomic testing includes relevant enzymes and cofactors related to key biomarkers, making it possible to trace the web of interconnections in the metabolome and develop customized treatments.
Metabolomics Testing Offers Insight into the Gut Microbiome
We can’t talk about the human metabolome without talking about metabolites from the gut microbiome. In fact, over 10% of the human metabolome is directly associated with gut microbial metabolism.1 Bacterial metabolites can harm the host2 or they can enhance biological activity and promote health of the host.4
“While over 10% of the human metabolome is directly associated with the gut microbial metabolism, specific metabolites are largely uncharacterized. Therefore, methods for the identification and quantification of microbiota-associated metabolites in biological fluids such as urine or plasma are necessary in order to elucidate the molecular basis of host-microbiota interaction.”3
Microbes eat what we eat: amino acids, sugar, carbohydrates, fiber, fats, or polyphenols. 95% of the dietary polyphenols that you eat pass along to the colon where they are fermented by gut microorganisms, oftentimes improving their bioactivity.1 The best example of bacterial metabolism improving the bioactivity of a polyphenol is equol, which benefits hormone balance, cardiovascular health, and cancer risk. More on equol below.
Figure 1. A schematic depiction of how the polyphenol, naringenin, is metabolized by the human-microbial superorganism. Dietary polyphenols and their metabolic byproducts undergo phase I and phase II detoxification, they are absorbed into systemic circulation, they interact with organs and tissues, and they are excreted in urine. Figure used with permission.4
Metabolomics is an exciting new frontier in human health. Testing the metabolome for gut bacterial (and fungal) byproducts helps us understand the whole picture of the human-microbe “superorganism.” These urine microbial markers can complement and enhance insights from comprehensive stool analysis.
Note that organic acid testing of microbial metabolites must be interpreted in the context of the diet. The presence of a microbial organic acid is not only a sign that gut bacteria are making it, but also that the dietary precursors are available in the gut to be acted upon by those microbes.
The following biomarkers offer insight into microbial function and have human clinical studies to back up their relevance.
4-Hydroxyphenylacetic acid is a microbial byproduct of tyrosine, tyramine, and polyphenols such as those found in wine or green tea. 4-hydroxyphenylacetic acid was the most abundant urinary polyphenol in a study of 475 people and its presence was attributed entirely to microbiota.4 Bacteria believed to produce 4-hydroxyphenylacetic acid are:6
- Arthrobacter species5
- Bacillus species5
- Halomonas species5
- Clostridium species
- Klebsiella species
- Proteus species
- Pseudomonas species
In one study of children, higher 4-hydroxyphenylacetic acid was associated with Giardia lamblia, ileal resection, and small intestine bacterial overgrowth. Researchers noted it as a useful small intestinal bacterial overgrowth (SIBO) screening tool.6 Levels of this urinary polyphenol were 1.4 times higher in men than women.4
Indoleacetic acid (or indole-3-acetic acid) is one of the predominant tryptophan microbial metabolites in the intestine. Indoleacetic acid is recognized as a marker of microbial activity.3 Indoleacetic acid levels have been found to be high in some patients with autism spectrum disorder.7
These gut bacteria are believed to produce indoleacetic acid:
- Bacillus subtillis3
- Pseudomonas aeruginosa3
- Clostridium species8
- Clostridium sporogenes9
- Lactobacillus species8
Microbes in the gut are instrumental in tryptophan metabolism. They can impact serotonin, kynurenine, and indole metabolites such as indoleacetic acid, with subsequent effects on brain function. Authors suggest this could be one mechanism underlying the gut-brain axis. They suggest treating the gut microbiota as a strategy to correct brain function and tryptophan metabolism.8
Homovanillic acid (HVA) is commonly known as the human breakdown product of dopamine. However, homovanillic acid is also a significant microbial urine metabolite.10
Urine homovanillic acid was one of the highest microbial metabolites found in a human study of dietary polyphenols intake. Levels of HVA were attributed to microbiota and endogenous synthesis. Levels of HVA were higher in men, in subjects who ate more calories, and in patients who had eaten polyphenols from apples, pears, or olives around the time of the test.4 Quercetin intake can cause very high elevations of urine HVA.13
These organisms may produce HVA:11
- Klebsiella spp.
- Serratia spp.
- Klebsiella pneumoniae
- Pseudomonas aeruginosa
Equol is a product of bacterial metabolism on isoflavones (a type of polyphenol) from soy. Reductase enzymes secreted by the gut microbiota convert daidzein into equol. Only 20-30% of people in Western countries are equol producers, whereas 40-60% of people in Asian countries are equol producers. All animals tested so far can produce equol.12 Consumption of soy isoflavones alone does not mean someone is an equol producer. It depends on their gut microbiome.16
Aside from its role as a marker of microbial activity in the gut, equol has beneficial health impacts. Equol can modify blood and urine estradiol levels. It is associated with a reduced risk of developing female hormone-related diseases such as breast cancer, hot flashes, and bone loss.1 It has been associated with decreased risks of prostate and colon cancers and cardiovascular diseases.13
“There is evidence that equol is more bioactive than its parent isoflavone [daidzein] in a range of areas including estrogenic and anti-estrogenic activity, antioxidant capacity and potential anti-cancer effects. Studies of equol producers versus non-producers have suggested that equol production may be important in determining benefits of soy consumption in terms of bone health, menopausal symptoms, and breast cancer, although the data are not consistent.”14
These species can produce equol:(12,13)
- Adlercreutzia equolifaciens
- Asaccharobacter celatus
- Bacteroides ovatus
- Bifidobacterium breve
- Bifidobacterium longum
- Catenibacterium spp.
- Clostridium spp.
- Eggerthella spp.
- Finegoldia magna
- Lactobacillus mucosae
- Lactobacillus paracasei
- Lactobacillus sakei/graminis
- Lactococcus garvieae
- Pediococcus pentosaceus
- Slackia equolifaciens
- Slackia isoflavoniconvertens
- Slackia spp.
- Streptococcus intermedia
New Markers in Metabolomic Testing Offer Enhanced Insight into Patient Health
Metabolomics testing offers so much more than just information about the gut microbiome. It also measures metabolism, neurohormones, detoxification, glucose regulation, oxidative stress, and more.
Cortisol – Urine cortisol can give practitioners information about their patient’s stress response. Cortisol and hypothalamic-pituitary-adrenal axis function is certainly a piece of the puzzle for many patients with mood disorders and sleep dysfunction.15 A high cortisol may nudge practitioners to run a 4-point salivary cortisol test as they see fit.
Glucose – Urine glucose indicates how patients process their diet and gives practitioners a peek at sugar metabolism or glycolysis. Levels should be low but may elevate in diabetes, kidney disease, pregnancy, or in patients with hereditary abnormalities.16 If glucose is elevated, the microalbumin in the kidney section can give you further insight into kidney health.
Kynurenine/Tryptophan Ratio (KTR) – This is a ratio created from two critical components of the tryptophan pathway (pictured above). When this ratio is high, it indicates that activity of the cytokine-sensitive enzyme, indoleamine 2,3 dioxygenase (IDO), is increased – pulling tryptophan down the pathway and increasing kynurenine production. A higher KTR is associated with systemic inflammation and has been associated with higher body mass index, obesity, inflammation, renal failure and chronic kidney disease (CKD), cancer, AIDS, sepsis, pregnancy, reduced cognition, and cardiovascular disease. Further, the KTR is regarded as a marker for biological aging.17
Microalbumin – Imagine checking for early kidney damage while running a patient’s organic acids test. Urine microalbumin is a standard clinical laboratory test that practitioners can now access as part of a metabolomics work-up. If microalbumin is present consistently in urine, it is associated with early-stage kidney disease.18
What Types of Patients Benefit from Metabolomic Testing?
A metabolomics test is often used to identify a healthy patient’s baseline metabolomic profile, which can be included in yearly health evaluations. Metabolomic evaluation can also be helpful in patients with chronic health conditions because it gives practitioners information about their patient’s underlying biochemical pathways, including:
- Glucose metabolism and ketones
- Mitochondrial markers
- Fatty acid metabolism
- Neurotransmitter metabolites
- Amino acid metabolism
- Inflammatory markers
- Collagen breakdown
- B vitamins
- Dietary indicators
- Oxidative stress
- Kidney health
- Microbial metabolites
Conditions That May Benefit from Metabolomics Testing:
- Alzheimer’s Disease
- Autism Spectrum Disorder
- Autoimmune/Immune Activation
- Bipolar Disorder
- Bowel Disorders/Disease
- Brain Fog/Mental Focus
- Cardiovascular Disease
- Chronic Fatigue
- Exercise Intolerance
- High Blood Pressure
- Impaired Digestion
- Inborn Errors of Metabolism
- Inflammatory Conditions
- Insomnia/Sleep Disturbances
- Insulin resistance/Prediabetes/Diabetes
- Liver Disease
- Microbial Processing
- Nutritional Insufficiencies
- Parkinson’s Disease
- Poor muscle Mass
- Skin Conditions
- Toxicity or Detoxification Challenge
- Unexplained Chronic Illnesses
- Weight Loss Resistance
About the OMX™ Organic Metabolomics test from Diagnostic Solutions Laboratory
The OMX™ Organic Metabolomics test from Diagnostic Solutions Laboratory evaluates organic acids, amino acids, and other key compounds to provide practitioners with a deep-dive look into a patient’s metabolome. In addition to neurotransmitters, glucose metabolism, inflammation, methylation, glutathione, and oxidative stress, metabolomics testing expands on the microbial metabolome. Useful for a wide range of patient conditions, metabolomic testing allows clinicians to more easily identify biochemical deviations that can underlie—and even precede—disease.
- Clifford MN. Diet-derived phenols in plasma and tissues and their implications for health. Planta medica. Dec 2004;70(12):1103-14. doi:10.1055/s-2004-835835
- Armand L, Andriamihaja M, Gellenoncourt S, Bitane V, Lan A, Blachier F. In vitro impact of amino acid-derived bacterial metabolites on colonocyte mitochondrial activity, oxidative stress response and DNA integrity. Biochimica et biophysica acta General subjects. Aug 2019;1863(8):1292-1301. doi:10.1016/j.bbagen.2019.04.018
- Pavlova T, Vidova V, Bienertova-Vasku J, et al. Urinary intermediates of tryptophan as indicators of the gut microbial metabolism. Anal Chim Acta. Sep 22 2017;987:72-80. doi:10.1016/j.aca.2017.08.022
- Zamora-Ros R, Achaintre D, Rothwell JA, et al. Urinary excretions of 34 dietary polyphenols and their associations with lifestyle factors in the EPIC cohort study. Sci Rep. Jun 7 2016;6:26905. doi:10.1038/srep26905
- Liebgott PP, Amouric A, Comte A, Tholozan JL, Lorquin J. Hydroxytyrosol from tyrosol using hydroxyphenylacetic acid-induced bacterial cultures and evidence of the role of 4-HPA 3-hydroxylase. Res Microbiol. Dec 2009;160(10):757-66. doi:10.1016/j.resmic.2009.09.015
- Chalmers RA, Valman HB, Liberman MM. Measurement of 4-hydroxyphenylacetic aciduria as a screening test for small-bowel disease. Clin Chem. Oct 1979;25(10):1791-4.
- Gevi F, Zolla L, Gabriele S, Persico AM. Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism. Molecular autism. 2016;7:47. doi:10.1186/s13229-016-0109-5
- Gao K, Mu CL, Farzi A, Zhu WY. Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain. Adv Nutr. May 1 2020;11(3):709-723. doi:10.1093/advances/nmz127
- Agus A, Planchais J, Sokol H. Gut Microbiota Regulation of Tryptophan Metabolism in Health and Disease. Cell Host Microbe. Jun 13 2018;23(6):716-724. doi:10.1016/j.chom.2018.05.003
- Bitner BF, Ray JD, Kener KB, et al. Common gut microbial metabolites of dietary flavonoids exert potent protective activities in beta-cells and skeletal muscle cells. J Nutr Biochem. Dec 2018;62:95-107. doi:10.1016/j.jnutbio.2018.09.004
- Chernevskaya E, Beloborodova N, Klimenko N, et al. Serum and fecal profiles of aromatic microbial metabolites reflect gut microbiota disruption in critically ill patients: a prospective observational pilot study. Crit Care. Jun 8 2020;24(1):312. doi:10.1186/s13054-020-03031-0
- Mayo B, Vázquez L, Flórez AB. Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects. Nutrients. Sep 16 2019;11(9)doi:10.3390/nu11092231
- Iino C, Shimoyama T, Iino K, et al. Daidzein Intake Is Associated with Equol Producing Status through an Increase in the Intestinal Bacteria Responsible for Equol Production. Nutrients. Feb 19 2019;11(2)doi:10.3390/nu11020433
- Rowland I, Gibson G, Heinken A, et al. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. Feb 2018;57(1):1-24. doi:10.1007/s00394-017-1445-8
- Steen NE, Methlie P, Lorentzen S, et al. Altered systemic cortisol metabolism in bipolar disorder and schizophrenia spectrum disorders. J Psychiatr Res. May 2014;52:57-62. doi:10.1016/j.jpsychires.2014.01.017
- Sivanand S, Viney I, Wellen KE. Spatiotemporal Control of Acetyl-CoA Metabolism in Chromatin Regulation. Trends Biochem Sci. Jan 2018;43(1):61-74. doi:10.1016/j.tibs.2017.11.004
- Badawy AA. Kynurenine Pathway of Tryptophan Metabolism: Regulatory and Functional Aspects. International journal of tryptophan research : IJTR. 2017;10:1178646917691938. doi:10.1177/1178646917691938
- McGrath K, Edi R. Diabetic Kidney Disease: Diagnosis, Treatment, and Prevention. Am Fam Physician. Jun 15 2019;99(12):751-759.
By: Cass Nelson-Dooley, MS
Cass Nelson-Dooley, MS, studied medicinal plants in the rain forests of Panama, in 2003 as a Fulbright Scholar, and then launched a career in science and natural medicine. She researched the pharmacology of medicinal plants at the University of Georgia and AptoTec, Inc. She has over 15 years of experience teaching doctors about integrative and functional laboratory results.
At Diagnostic Solutions Laboratory, she analyzes GI-MAP stool tests and develops educational tools. Ms. Nelson-Dooley owns Health First Consulting, LLC, a medical writing, patient education, and consulting firm that serves the integrative and functional medicine industry. Ms. Nelson-Dooley is the author of Heal Your Oral Microbiome and authored chapters in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine.