# The role of gut microbes in production of aromatic carboxaldehydes

**Authors:** Manish Kumar, Rachel Son, Sarah M. Preston, Robert W. P. Glowacki, Kelley M. Carr, Jiyeon Kim, Jin Z. Ma, Philip P. Ahern, Jan Claesen, Naseer Sangwan, Florian Rieder, Ina Nemet

PMC · DOI: 10.1080/19490976.2026.2632979 · Gut Microbes · 2026-02-21

## TL;DR

Gut microbes produce aromatic carboxaldehydes like I3A and 4HBA, which are linked to health benefits, and their levels drop when gut microbes are reduced.

## Contribution

A new method to detect and quantify aromatic carboxaldehydes from gut microbes is developed and validated.

## Key findings

- Fecal levels of I3A and 4HBA decrease after gut microbiota depletion in humans and mice.
- Crohn's disease patients have lower fecal I3A and 4HBA compared to controls.
- Multiple commensal microbes can produce aromatic carboxaldehydes in culture.

## Abstract

Gut microbes play an important role in maintaining our health through the alteration of available nutrients and by the production of small molecules/metabolites. Indole-3-carboxaldehyde (I3A) is an aromatic carboxaldehyde (ArA) synthesized by gut microbes from the aromatic amino acid tryptophan, and has been mechanistically linked to antitumor activity, intestinal homeostasis, and metabolic syndrome. However, the capacity of gut microbes to produce other ArAs and their associations with host health remains largely unexplored due to a lack of methods for their detection and quantification. A stable isotope dilution mass spectrometry method for quantifying ArAs from all four aromatic amino acids (benzaldehyde (BA), 4-hydroxybenzaldehyde (4HBA), and 4-imidazolecarboxaldehyde (4IA) in addition to I3A) based on derivatization with 3-methoxyphenylhydrazine was developed and validated. Fecal levels of I3A and 4HBA were reduced in both human and mouse feces after a cocktail of nonabsorbable antibiotics depleted the gut microbiota, while the same treatment reduced BA in humans and 4IA in mice. Further, we identified multiple commensals with the capacity to produce selected ArAs in culture and showed that individuals with Crohn's disease, but not in those with ulcerative colitis, have lower fecal levels of I3A and 4HBA, relative to non-inflammatory bowel disease controls.

## Linked entities

- **Chemicals:** Indole-3-carboxaldehyde (PubChem CID 10256), benzaldehyde (PubChem CID 240), BA (PubChem CID 243), 4-hydroxybenzaldehyde (PubChem CID 126), 4HBA (PubChem CID 125), 4-imidazolecarboxaldehyde (PubChem CID 76428), 4IA (PubChem CID 10820), 3-methoxyphenylhydrazine (PubChem CID 423605)
- **Diseases:** Crohn's disease (MONDO:0005011), ulcerative colitis (MONDO:0005101), metabolic syndrome (MONDO:0000816)

## Full-text entities

- **Genes:** Ahr (aryl-hydrocarbon receptor) [NCBI Gene 11622] {aka Ah, Ahh, Ahre, In, bHLHe76}, Ltf (lactotransferrin) [NCBI Gene 17002] {aka Csp82, Lf, MMS10R, Ms10r}, PAK3 (p21 (RAC1) activated kinase 3) [NCBI Gene 5063] {aka ARA, MRX30, MRX47, OPHN3, PAK-3, PAK3beta}, AWAT2 (acyl-CoA wax alcohol acyltransferase 2) [NCBI Gene 158835] {aka ARAT, DC4, DGAT2L4, MFAT, WS}, AHR (aryl hydrocarbon receptor) [NCBI Gene 196] {aka FVH3, RP85, bHLHe76}, Crp (C-reactive protein, pentraxin-related) [NCBI Gene 12944]
- **Diseases:** intestinal disorders (MESH:D007410), chronic (MESH:D002908), UC (MESH:D003093), IBD (MESH:D015212), heart failure (MESH:D006333), colitis (MESH:D003092), gastrointestinal disorders (MESH:D005767), CD (MESH:D003424), hematologic diseases (MESH:D006402), MRM (MESH:D000069076), malignancy (MESH:D009369), dysbiosis (MESH:D064806), liver, renal, lung or metabolic disorders (MESH:D008171), renal failure (MESH:D051437), metabolic syndrome (MESH:D024821), inflammatory disorder (MESH:D007249)
- **Chemicals:** indole-3 acetic acid (MESH:C030737), H2 (MESH:D006859), I3A (MESH:C012381), Trp (MESH:D014364), polysorbate-80 (MESH:D011136), tryptamine (MESH:C030820), sodium acetate (MESH:D019346), neomycin (MESH:D009355), SCFA (MESH:D005232), dextrose (MESH:D005947), serotonin (MESH:D012701), phenylpyruvic acid (MESH:C031606), CO2 (MESH:D002245), vitamin B12 (MESH:D014805), L-cysteine (MESH:D003545), amino acid (MESH:D000596), HM (MESH:C100283), MgSO4 (MESH:D008278), L-arginine (MESH:D001120), Phe (MESH:D010649), starch (MESH:D013213), bile acid (MESH:D001647), ammonium citrate (MESH:C481046), 4-hydroxyphenylacetic acid (MESH:C008070), 3MPH hydrochloride (-), NaHCO3 (MESH:D017693), indole-3-lactic acid (MESH:C024139), HCl (MESH:D006851), gentamicin (MESH:D005839), acetic acid (MESH:D019342), CaCl2 (MESH:D002122), hemin (MESH:D006427), erythromycin (MESH:D004917), kanamycin (MESH:D007612), hydrazone (MESH:D006835), water (MESH:D014867), sodium thioglycollate (MESH:C017487), Tyr (MESH:D014443), ArAs (MESH:D016718), phenolic acid (MESH:C017616), vancomycin (MESH:D014640), K2HPO4 (MESH:C013216), N2 (MESH:D009584), BA (MESH:C032175), His (MESH:D006639), phenylacetic acid (MESH:C025136), (C, (MESH:D002244), metronidazole (MESH:D008795), ciprofloxacin (MESH:D002939), acetonitrile (MESH:C032159), NaCl (MESH:D012965), menadione (MESH:D024483), methanol (MESH:D000432), aromatic amino acids (MESH:D024322), formic acid (MESH:C030544), 4-hydroxybenzaldehyde (MESH:C011483)
- **Species:** Flavonifractor sp. (species) [taxon 2049025], Flavonifractor plautii (species) [taxon 292800], Limosilactobacillus reuteri (species) [taxon 1598], gut metagenome (species) [taxon 749906], Dorea sp. (species) [taxon 2040332], Lactobacillus johnsonii (species) [taxon 33959], Staphylococcus (genus) [taxon 1279], Blautia faecis (species) [taxon 871665], Faecalibacterium prausnitzii (species) [taxon 853], Lentinula sp. R (species) [taxon 1445722], Homo sapiens (human, species) [taxon 9606], Eubacterium sp. (species) [taxon 142586], Rodentia (rodent, order) [taxon 9989], Turicibacter (genus) [taxon 191303], Dorea longicatena (species) [taxon 88431], Blautia caecimuris (species) [taxon 1796615], Bacteroides stercoris (species) [taxon 46506], Allocoprococcus comes (species) [taxon 410072], Fusicatenibacter saccharivorans (species) [taxon 1150298], Bacillus sp. T (species) [taxon 1071724], Bacteroides thetaiotaomicron (species) [taxon 818], Clostridia (class) [taxon 186801], Curtobacterium (genus) [taxon 2034], Paenibacillus (genus) [taxon 44249], Clostridium sp. (species) [taxon 1506], Collinsella aerofaciens (species) [taxon 74426], Mus musculus (house mouse, species) [taxon 10090], Bacteroides caccae (species) [taxon 47678], Alistipes onderdonkii (species) [taxon 328813], Dorea formicigenerans (species) [taxon 39486], Petrachloros mirabilis (species) [taxon 2918835], Enterococcus sp. (species) [taxon 35783]
- **Cell lines:** C57BL/6J — Mus musculus (Mouse), Transformed cell line (CVCL_C0MW)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12928648/full.md

## References

52 references — full list in the complete paper: https://tomesphere.com/paper/PMC12928648/full.md

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Source: https://tomesphere.com/paper/PMC12928648