Profiling developmental dynamics of aromatic amino acid fermentation in infants

Rui Su; Suzie Hoops; Islam Mabrouk; Dan Knights; Jeffrey Gerber; Sagori Mukhopadhyay; Karen Puopolo; Chi Chen

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SALIVA AND URINE METABOLOME IN KIDNEY TRANSPLANT RECIPIENTS.

Profiling developmental dynamics of aromatic amino acid fermentation in infants

Rui Su

¹,

Suzie Hoops

²,

Islam Mabrouk

¹,

Dan Knights

^{2, 3},

Jeffrey S Gerber

^{4, 5},

Sagori Mukhopadhyay

^{5, 6},

Karen Puopolo

^{6, 7},

Chi Chen

^{*

5, 6}

¹ Department of Food Science and Nutrition, University of Minnesota, Saint Paul, 55108, MN, USA
² Department of Computer Science & Engineering, University of Minnesota, Minneapolis, 55455, MN, USA
³ Biotechnology Institute, University of Minnesota, Saint Paul, 55108, MN, USA
⁴ Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, 19104, PA, USA
⁵ Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
⁶ Newborn Care at Children’s Hospital of Philadelphia, Philadelphia, 19104, PA, USA
⁷ University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA

Academic Editor: Giovanni Ribaudo

Published: 10 October 2025 by MDPI in The 4th International Electronic Conference on Metabolomics session Microbial Metabolites with Novel Functions in Diseases and Health

Abstract:

Objectives:

Aromatic amino acids (AAAs) are indispensable building blocks of protein and essential precursors of metabolic cofactors, hormones, and neurotransmitters. Owing to their stable aromatic rings, AAAs form a group of distinctive metabolites with diverse biological activities after microbial fermentation in the large intestine. The profile of microbial AAA metabolites is strongly correlated with the composition of the gut microbiome. This study aims to define the developmental dynamics of AAA fermentation in infants and its correlation with the developing gut microbiome.

Methods:

A total of 250 fecal samples were collected from 138 full-term and healthy infants at 1, 4, 12, and 24 weeks of age. Concentrations of AAA and their microbial metabolites were quantified using dansyl chloride and 2-hydrazinequinoline derivatizations coupled with liquid chromatography–mass spectrometry-based metabolomic analysis. Shotgun metagenomic sequencing was conducted to define the microbiome, especially the genes contributing to AAA fermentation.

Results:

Compared to steady increases in many free amino acids in feces from week 1 to 24, the nadirs of free AAAs were at week 4 in newborns. AAA-derived intermediates, such as 4-hydroxyphenylacetic acid (HPAA), phenylacetic acid, and 4-hydroxyphenyllactic acid, and end products such as p-cresol, 4-hydroxyphenylpropionic acid and indole-3-propionic acid, were present in feces in sequential, progressive, and selective patterns, showing gradualness and variations in the establishment of AAA microbial fermentation across human newborns. Preliminary examination of the correlations between AAA fecal metabolome and metagenomes revealed a strong association of p-cresol with the large subunit of 4-hydroxyphenylacetate decarboxylase (4-Hpd), but not with the more prevalent presence of 4-Hpd activating enzyme in newborns.

Conclusion:

Newborns undergo gradual development of microbial AAA fermentation, particularly the conversion of HPAA to p-cresol. Characterizing the microbes responsible for this development will provide useful insights for nutritional and therapeutic interventions of AAA fermentation in humans and animals.

Keywords: aromatic amino acids; metabolomics; metagenomic; microbial metabolites; microbial enzymes

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