Understanding the Gut Microbiome Through the Lens of the OMX Organic Metabolomics Test

Introduction – Metabolites from 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 The Diagnostic Solutions GI-MAP^® stool test makes it possible to directly identify and measure the quantities of bacteria and fungi in the stool. But the OMX™ Organic Metabolomics test allows you to look at the gut bacteria from a different angle — from their byproducts or metabolites. When taken together, these two tests give you a more complete picture of a person's gut microbiome.

 

The gut microbiome has been described as an organ — and a metabolic organ at that. Indeed, 95% of the dietary polyphenols that you eat pass along to the colon where they are fermented by gut microorganisms.²

Bacterial metabolites can harm the host³ or they can enhance biological activity and promote health of the host.⁴ The best example of bacterial metabolism improving the bioactivity of a polyphenol is equol, which benefits hormone balance, cardiovascular health, and cancer risk.
 

"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 [99]. 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."⁴

 
Microbes eat what we eat: amino acids, sugar, carbohydrates, fiber, fats, or polyphenols. You will see on the OMX Quick Reference Guide that the microbes that make an organic acid metabolite are listed as well as what they use from the diet to make it — amino acids, for example. This means that 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.

 
 

"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."¹

Testing and Treatment Considerations

The OMX test is ideal for patients who have a wide range of symptoms affecting not only the gut, but also neurologic, metabolic, detoxification, or oxidative stress systems, as shown here. Use the OMX test in conjunction with the GI-MAP stool test for patients complaining of gut symptoms such as constipation, diarrhea, gas, bloating, reflux, distension, irritable bowel syndrome, or inflammatory bowel disease.

When urine OMX microbial markers are high, along with dysbiosis symptoms, consider treatment with a 5R protocol. High levels of microbial metabolites might be addressed this way:

• Evaluate and optimize the diet — encourage a whole foods diet, low in sugar and refined carbohydrates, balanced in protein, and high in fiber.
• Promote the gut microbiome — give fiber, probiotics, and prebiotics, as tolerated.
• Improve digestion to eliminate microbial overgrowth — support with digestive enzymes, betaine HCl, and good mealtime habits that promote rest, relaxation, and chewing.
• Herbal antimicrobial agents — may be used to lower bacterial and fungal dysbiosis, as needed.

When OMX microbial metabolites are elevated, but the patient has no dysbiosis symptoms, query the patient on their diet. Higher intake of polyphenols or protein could increase levels of the markers. Also consider gentle interventions such as optimizing the diet, supporting healthy gut mucosa, enhancing digestion, and building the beneficial bacteria of the gut microbiome with probiotics, prebiotics, and fiber. Address other abnormalities on the test.

If the OMX bacterial metabolites are all normal or low this is generally considered a positive finding. It suggests no bacterial or fungal overgrowth. However, look for signs that your patient may have poor dietary intake of protein and plant-based polyphenols. Amino acids and polyphenols are food sources for the microbes that might be in short supply if bacterial metabolites are low.

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Gut Bacteria Metabolites on the OMX Organic Metabolomics Test

The table below summarizes the microbial markers found on the OMX test and the microbes that produce them. Most markers are found in the "Microbial Metabolites" section of the report. Others can be found elsewhere on the report. Continue reading below for a full description of each organic acid, research behind it, and its clinical relevance.

OMX Urine Marker	Microbial Producers	Dietary Sources	If Low or Normal	If High
4-Hydroxyphenylacetic acid	Arthrobacter species6 Bacillus species6 Halomonas species6 Clostridium species Klebsiella species Proteus species Pseudomonas species	Tyrosine, tyramine, and polyphenols	Generally considered a positive finding. Suggests low bacterial or fungal overgrowth. A pattern of lows, however, may point to poor intake of polyphenols or amino acids.	Evaluate intake of dietary sources. If gut dysbiosis symptoms are present, consider a 5R protocol including improving the diet, promoting beneficial gut bacteria, enhancing digestion, and antimicrobial agents if needed. Compare with findings from GI-MAP.
Indoleacetic acid	Bifidobacterium1 Bacteroides1 Bacillus subtillis1 Pseudomonas aeruginosa1 Clostridium species7 Clostridium sporogenes8 Lactobacillus species7	Tryptophan	Same as above. See: 4-Hydroxyphenylacetic acid	Same as above. See: 4-Hydroxyphenylacetic acid
Phenylacetic acid Found in the "Phenylalanine Metabolism" section of the OMX report	Bacteroides spp.9 Bifidobacterium lactis Clostridium barlettii Escherichia coli Eubacterium hallii Lactobacillus gasseri	Phenylalanine, polyphenols	Same as above. See: 4-Hydroxyphenylacetic acid	Same as above. See: 4-Hydroxyphenylacetic acid
3,4-Dihydroxyhydrocinnamic acid	Clostridium10,11 orbiscindens Escherichia coli Bifidobacterium lactis Lactobacillus gasseri Eubacterium ramulus Enterococcus avium	Polyphenols – flavonoids	Same as above. See: 4-Hydroxyphenylacetic acid	Same as above. See: 4-Hydroxyphenylacetic acid
3,5-Dihydroxybenzoic acid	Mixture of unspecified gut microbiota	Polyphenols, hydroxybenzoates	Same as above. See: 4-Hydroxyphenylacetic acid	Same as above. See: 4-Hydroxyphenylacetic acid
4-Hydroxybenzoic acid	Clostridium saccarogumia Eubacterium ramulus Akkermansia muciniphila	Polyphenols, anthocyanidins	Same as above. See: 4-Hydroxyphenylacetic acid	Same as above. See: 4-Hydroxyphenylacetic acid
Benzoic acid and Hippuric acid	Escherichia coli4 Bifidobacterium lactis4 Lactobacillus gasseri4 Collinsella12 These are general microbiota markers. The species that make them are not widely published.	Polyphenols	Same as above. See: 4-Hydroxyphenylacetic acid	Same as above. See: 4-Hydroxyphenylacetic acid
Homovanillic acid Found in the "Phenylalanine Metabolism" section of the report	Klebsiella spp.13 Serratia spp. Klebsiella pneumoniae Pseudomonas aeruginosa	Polyphenols from apples, pears, or olives. Quercetin.	Same as above. See: 4-Hydroxyphenylacetic acid	Same as above. See: 4-Hydroxyphenylacetic acid
Equol	Adlercreutzia equolifaciens14,15 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	Soy isoflavones	Indicates poor intake of soy isoflavones and/or the person is not an equol-producer.	Indicates patient is an equol-producer and eats soy isoflavones in the diet. High levels may have benefits for bones, cardiovascular, and endocrine systems.
Arabinitol	D-arabinitol is produced by:16 Candida albicans Candida parapsilosis Candida tropicalis Arabinitol can be produced by: Debaryomyces Pichia Zygosaccharomyces	Arabinose, glucose, or glycerol.	Generally considered a positive finding. Suggests low bacterial or fungal overgrowth.	If consistent with fungal overgrowth symptoms, consider a 5R protocol with dietary restriction of sugars and starches, promoting beneficial gut bacteria and fungi, enhancing digestion, and antifungal agents if needed.
D-Lactate and L-Lactate Found in the "Glycolysis" section of the OMX report	Aerococcus17 Bacillus coagulans18 Carnobacterium17 Enterococcus17,19 Lactobacillus species17 Lactococcus species17 Leuconostoc species17 Oenococcus species17 Pediococcus species17 Streptococcus17,19 Weissella species17	Carbohydrates	Same as above. See: Arabinitol	If consistent with gut dysbiosis symptoms, consider a 5R protocol including improving the diet (especially limiting carbs), promoting beneficial gut bacteria, enhancing digestion, and antimicrobial agents if needed. Compare with findings from GI-MAP.

 

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Gut Bacteria Byproducts of Amino Acid Fermentation

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.¹¹ Bacteria believed to produce 4-hydroxyphenylacetic acid are:²⁰

• Arthrobacter species⁶
• Bacillus species⁶
• Halomonas species⁶
• 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.²¹ Levels of this urinary polyphenol were 1.4 times higher in men than women.¹¹

 

"The most abundant urinary polyphenols detected in our [human] study were phenolic acids formed by the microbiota: 4- and 3-hydroxyphenylacetic acids, 3,4-dihydroxyphenylacetic acid, protocatechuic acid (and their O-methylated metabolites: homovanillic acid and vanillic acid, respectively), 4-hydroxybenzoic acid, 3,5- and 3,4-dihydroxyphenylpropionic acids, and, 3,5-dihydroxybenzoic acid, with median excretion levels ranging from 3.4 to 157 μmol/24 h."¹¹

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Indoleacetic acid (or indole-3-acetic acid) is one of the predominant tryptophan microbial metabolites in the intestine. Indoles are organic chemical structures found in nature and made by gut microbiota. Indoleacetic acid is recognized as a marker of microbial activity.¹ Indoleacetic acid levels were high in patients with autism spectrum disorder.²²

These gut bacteria are believed to produce indoleacetic acid:

• Bifidobacterium¹
• Bacteroides¹
• Bacillus subtillis¹
• Pseudomonas aeruginosa¹
• Clostridium species⁷
• Clostridium sporogenes⁸
• Lactobacillus species⁷

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.⁷

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Phenylacetic acid (found in the "Phenylalanine Metabolism" section of the OMX report)

Phenylacetic acid is a breakdown product of phenylalanine and can increase when phenylalanine hydroxylase is impaired. It can be produced by fermentation of phenylalanine by Bacteroides spp.⁹ It can also be created from metabolism of polyphenols by gut microbes.^4,23 Phenylacetic acid is one of the main phenolic metabolites found at high levels in stool.⁴ It has been positively associated with Crohn's disease and negatively with F. prausnitzii.^24,25 Phenylacetic acid was negatively associated with Clostridium cluster XIVa and positively associated with Lactobacillus spp.²⁶

Microbes that make phenylacetic acid include:⁴

• Bacteroides spp.⁹
• Bifidobacterium lactis
• Clostridium barlettii
• Escherichia coli
• Eubacterium hallii
• Lactobacillus gasseri

 

Gut Bacteria Products of Polyphenol Metabolism

3,4-Dihydroxyhydrocinnamic acid (also known as 3,4-dihydroxyhydrocinnamate or 3,4-dihydroxyphenylpropionate) is a major metabolite of microbiota acting on polyphenols, found in human urine.¹¹ 3,4-dihydroxycinnamic acid has antioxidant properties and can inhibit secretion of pro-inflammatory cytokines.

Microbes that produce 3,4-dihydroxyhydrocinnamic acid are:^10,11

• Bifidobacterium lactis
• Clostridium orbiscindens
• Enterococcus avium
• Escherichia coli
• Eubacterium ramulus
• Lactobacillus gasseri

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3,5-Dihydroxybenzoic acid (3,5-DHBA) is a microbial metabolite of polyphenols and hydroxybenzoates. It is high in human urine as a result of microbial activity on dietary polyphenols. 3,5-dihydroxybenzoic acid is considered a dietary biomarker of non-white bread and cereal intake.¹¹ Levels of 3,5-DHBA in the stool increase after red wine intake, pointing to bacterial metabolism of red wine polyphenols.²⁷ A mixture of fecal microbiota acted on black tea to produce 3,5-dihydroxybenzoic acid in cell studies.²⁸

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4-Hydroxybenzoic acid, or p-hydroxybenzoic acid, is a phenolic derivative of benzoic acid. It is found in all living species, from bacteria to plants to humans. 4-Hydroxybenzoic acid is produced when Clostridium saccharogumia and Eubacterium ramulus act on anthocyanidins such as malvidin.⁴ In a human study looking at microbial polyphenol metabolites, 4-hydroxybenzoic acid was one of the most abundant polyphenols found in urine.¹¹ It correlated with level of education and was lower in subjects with no or only primary education.

4-Hydroxybenzoic acid increased on a low FODMAP diet, and was found to be positively associated with Firmicutes, Verrucomicrobia, and Akkermansia muciniphilia, and negatively with Actinobacteria.²⁹ Coenzyme Q₁₀ is synthesized in multiple steps from the precursor 4-hydroxybenzoic acid.

Microbes that make 4-hydroxybenzoic acid include:

• Clostridium saccarogumia
• Eubacterium ramulus
• Akkermansia muciniphila

"Deployment of in vitro gut models, humanized mouse models, and human intervention trials, in combination with deployment of metabolomics and microbiomics, is a prerequisite for unraveling the role of colonic microbiota in the bioconversion of polyphenols."

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Benzoic acid and hippuric acid — these two urine metabolites travel together. They are well-known byproducts of bacterial metabolism on dietary polyphenols. Benzoate and hippurate as microbial byproducts have been detected in cell studies, animal studies, and human studies. After treatment with antimicrobials, the levels of these byproducts decrease in urine, attesting to the role of the microbiota in their production.^30,31

Examples of polyphenol-containing foods that can produce urine benzoic acid and hippuric acid include: fruit juice, tea, wine, cinnamon, cloves, tomatoes, berries, plums, apples, and cranberries. For example, an increased intake of cranberry polyphenols resulted in an increase in benzoic acid. The increase was individual and likely partially dependent on the gut microbiome.³² Benzoic acid can also be found in processed foods, especially because it is an antimicrobial preservative.

The human body converts benzoic acid to hippuric acid for excretion. Phenolic compounds are converted to benzoic acid, conjugated with glycine and excreted as hippuric acid.³³ Glycine and pantothenic acid are needed for this reaction.

Hippuric acid is known as a gut-derived metabolite commonly associated with a "healthy phenotype." It is a key differentiator between the urine metabolic profiles of lean versus obese or diabetic people. It is decreased in diabetes and obesity and increases after bariatric surgery. Increased levels of Collinsella correlated with higher urinary hippurate.¹² Collinsella was found to correlate with urinary hippurate in an animal model.

Microbes that produce benzoic acid and/or hippuric acid:

• Escherichia coli⁴
• Bifidobacterium lactis⁴
• Lactobacillus gasseri⁴
• Collinsella¹²

Benzoic acid and hippuric acid are general microbiota markers. The species that make them are not widely known or published.

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Homovanillic acid (HVA) is commonly known as the human breakdown product of dopamine and is found in the "Phenylalanine Metabolism" and "Stress & Mood" sections on the OMX report. However, homovanillic acid is also a significant microbial urine metabolite.³⁴

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.¹¹ Quercetin intake can cause very high elevations of urine HVA.³⁵

These organisms may produce HVA:¹³

• Klebsiella spp.
• Serratia spp.
• Klebsiella pneumoniae
• Pseudomonas aeruginosa

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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. Daidzein is a phytoestrogen found in soybeans and other legumes with an almost identical chemical composition to mammalian estrogens. 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.¹⁵ Consumption of soy isoflavones alone does not mean someone is an equol producer. It depends on their gut microbiome.¹⁴

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.⁴ It has been associated with decreased risks of prostate and colon cancers and cardiovascular diseases.¹⁴

These species can produce equol:^14,15

• 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

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Fungal Metabolism Markers

Arabinitol can be found in two forms, as L-arabinitol or D-arabinitol, in human serum and urine. There are some native yeast strains, such as Candida, Debaryomyces, Pichia, and Zygosaccharomyces possessing the ability to biotransform arabinose, glucose, or glycerol to arabinitol.^36,37 Elevations of arabinitol should be evaluated for intestinal fungal overgrowth. A ratio of D-arabinitol to L-arabinitol was shown to be elevated with invasive candidiasis in children and in infants infected with C. albicans. Serum D-arabinitol to creatinine ratio correlated with antifungal treatment response in 10 out of 10 adults with cancer.³⁸ Some studies show that serum D-arabinitol can be detected earlier than Candida growth in blood cultures and may therefore be useful for monitoring clinical response to treatment.¹⁶

• D-arabinitol is produced by:¹⁶
  • Candida albicans
  • Candida parapsilosis
  • Candida tropicalis
• Arabinitol can be produced by:
  • Debaryomyces
  • Pichia
  • Zygosaccharomyces

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Other Microbial Byproducts Found on the OMX Report

Lactic acid producing bacteria (found in the "Glycolysis" section of the OMX test) D-Lactate and L-Lactate — Lactic acid is made by a wide range of bacteria, yeast, and filamentous fungi.¹⁸ Lactic-acid-producing bacteria can make L(+)-lactic acid, D(-)-lactic acid, the racemate DL-lactate, or a combination of these.¹⁷ L-lactic acid is called lactic acid on the OMX report. When D-lactic acid elevates in urine, it can cause a severe type of metabolic acidosis known as D-lactic acidosis. It can present with neurological symptoms such as confusion, memory loss, or poor cognition. It has been observed in animals and humans.¹⁹

High urinary D-lactic acid usually occurs due to gastrointestinal dysfunction. It has primarily been reported in patients with short bowel syndrome who have had removal of a section of the small bowel. Changes to the small bowel set the stage for difficulty metabolizing carbohydrates, which can lead to excessive bacterial fermentation in the colon, producing D-lactate. In rare situations, the production of D-lactate can exceed a person's ability to metabolize D-lactate, leading to high circulating levels of D-lactate which can be absorbed in the brain and cause encephalopathy.¹⁹ Both urine L-lactic acid and D-lactic acid were elevated in those with irritable bowel disease.³⁹ In one case report of short bowel syndrome, probiotic therapy was able to suppress D-lactate producing bacteria.⁴⁰ Probiotic therapy with D-lactate-producing microbes are not believed to pose a concern for anyone except those with short bowel syndrome¹⁷17 or malabsorption syndromes.⁴¹

Other contributors to urine D-lactate are the human methylglyoxal (MGO) pathway and/or ingestion of preformed D-lactate through fermented foods. MGO is a precursor of glycation of proteins and DNA which is converted into D-lactate when it is detoxified.

These gut bacteria can produce D-lactate, L-lactate, or a mixture:

• Aerococcus (L-lactate)¹⁷
• Bacillus coagulans (L-lactate)¹⁸
• Carnobacterium (L-lactate)¹⁷
• Enterococcus (L-lactate)^17,19
• Lactobacillus species D-lactate (L-lactate and DL-lactate)¹⁷
  • Probiotic species that can produce D-lactate include: L. acidophilus, L. gasseri, L. delbrueckii subsp. bulgaricus, L. fermentum, L. lactis, L. brevis, L. helveticus, L. plantarum and L. reuteri.
• Lactococcus species (L-lactate)¹⁷
• Leuconostoc species (D-lactate)¹⁷
• Oenococcus species (D-lactate)¹⁷
• Pediococcus species (L-lactate and DL-lactate)¹⁷
• Streptococcus (L-lactate)^17,19
• Weissella species (D-lactate and DL-lactate)¹⁷

 

 

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