Aromatic Amino Acid Metabolites: Molecular Messengers Bridging Immune-Microbiota Communication

Abstract

Aromatic amino acid (AAA) metabolites, derived from tryptophan, phenylalanine, and tyrosine through coordinated host and microbial metabolism, have emerged as critical modulators of immune function. We examine the complex journey of AAAs from dietary intake through intestinal absorption and metabolic transformation, highlighting the crucial role of host-microbe metabolic networks in generating diverse immunomodulatory compounds. This review provides a unique integrative perspective by mapping the molecular mechanisms through which these metabolites orchestrate immune responses. Through detailed analysis of metabolite-receptor and metabolite-transporter interactions, we reveal how specific molecular recognition drives cell type-specific immune responses. Our comprehensive examination of signaling networks—from membrane receptor engagement to nuclear receptor activation to post-translational modifications— demonstrates how the same metabolite can elicit distinct functional outcomes in different immune cell populations. The context-dependent nature of these molecular interactions presents both challenges and opportunities for therapeutic development, particularly in inflammatory conditions where metabolite signaling pathways are dysregulated. Understanding the complexity of these regulatory networks and remaining knowledge gaps is fundamental for advancing metabolite-based therapeutic strategies in immune-mediated disorders.

INTRODUCTION

The human gut microbiota plays a fundamental role in shaping and maintaining immune homeostasis through complex bidirectional interactions with the host immune system. These microorganisms produce various bioactive metabolites that act as essential mediators in host-microbe communication, influencing both local and systemic immune responses (1,2). Recent advances have revealed that microbiota-derived metabolites significantly influence immune cell function through specific molecular mechanisms. These interactions modulate metabolic programming, gene expression, and cellular function, ultimately affecting immune cell differentiation, activation, and effector functions (3). Dysregulation of these pathways has been implicated in various immune-mediated disorders, including inflammatory bowel disease (IBD), autoimmune conditions, and allergic diseases (4,5), highlighting their clinical significance and potential as therapeutic targets.

Among the diverse array of microbiota-derived metabolites, those derived from aromatic amino acids (AAAs)—tryptophan (Trp), phenylalanine (Phe), and tyrosine (Tyr)— have emerged as critical modulators of immune function. While these compounds have traditionally been recognized for their roles in protein synthesis and as precursors for neurotransmitters (6), recent research has unveiled that AAA catabolism directly influences immune responses through specific molecular mechanisms. These include activation of membrane receptor-mediated signaling cascades, nuclear receptor-mediated signaling pathways, post-translational modification, and reprogramming of cellular metabolism (7,8). Despite their relatively low abundance, these findings have generated renewed interest in AAA-derived metabolites as important immunomodulatory agents essential for maintaining intestinal and systemic immune homeostasis.

Recent research has revealed sophisticated molecular pathways through which AAA metabolites coordinate microbial metabolism and host immune responses (9). However, several fundamental questions remain unresolved, particularly regarding how multiple metabolic pathways interact in different cellular contexts and disease states. This review provides a unique perspective on AAA metabolite-mediated immune regulation by integrating multiple levels of molecular interactions between host and microbes. We examine how dietary AAAs are transformed through coordinated host and microbial metabolic networks to generate diverse immunomodulatory compounds and provide a comprehensive analysis of their mechanisms, focusing on how ligand-specific receptors and transporters contribute to context-appropriate immune responses.

These ligand-specific transporters and receptors enable precise control of both innate and adaptive immunity in a cell type-dependent manner (10). Understanding these molecular mechanisms is particularly crucial for therapeutic development, as altered AAA metabolite profiles correlate with disease severity and show promise in modulating pathogenic immune responses in conditions like IBD (4). However, the same metabolic pathway can have opposing effects in different disease contexts, highlighting the need for careful consideration in therapeutic targeting. This integrated perspective of host-microbe-metabolite interactions is fundamental for developing more effective targeted interventions that can achieve appropriate immune modulation in specific disease contexts.

AAAs AND THEIR METABOLITES: OVERVIEW AND ABSORPTION

AAAs (Trp, Tyr, and Phe) are characterized by their distinctive aromatic ring structures, which enable protein structure stabilization and metabolic functions through their unique chemical properties (11). These essential molecules follow a complex pathway from dietary intake to biological function, involving coordinated processes of digestion, absorption, and metabolic transformation by both host and microbial systems.

Dietary sources and digestion

Trp and Phe are essential amino acids that must be obtained through diet, while Tyr can be synthesized endogenously from Phe. These AAAs are abundant in protein-rich foods and fermented products such as sauerkraut and kimchi (12,13). Fermented foods provide direct sources of AAA metabolites, including phenyllactate, 4-hydroxyphenyllactate and indole-3-lactate, which support immune homeostasis, neurogenesis, and enteric nervous system (ENS) maturation (14,15,16,17,18).

The gastrointestinal (GI) tract processes both dietary and endogenous proteins through a sophisticated digestive system. Initial protein breakdown yields small peptides, followed by further digestion at the brush border of intestinal epithelial cells (IECs) (19). This process achieves highly efficient amino acid absorption, with approximately 90% absorption by the time digestive contents reach the ileum (20).

Absorption

The efficient absorption of AAAs is accomplished through sophisticated transport systems composed of various transporters at IECs that are spatially organized at apical and basolateral membranes (21). In the small intestine, the primary neutral amino acid transporter B⁰AT1 (Slc6a19) at the apical membrane operates through a Na⁺-dependent mechanism in complex with angiotensin converting enzyme II to accept all neutral amino acids, branched-chain amino acids, and methionine (22). Additional apical transporters include ASCT2 (Slc1a5), a bidirectional neutral amino acid transporter; b^0,+AT (Slc7a9)/rBAT complex, which exchanges cationic with neutral amino acids (K_M 100-300 μM); and TAUT (Slc6a6), which facilitates Phe transport (23). The basolateral membrane contains 3 key transporters operating synergistically: 1) LAT2 (Slc7a8), an obligatory amino acid antiporter facilitating the exchange of all neutral amino acids except proline; 2) LAT4 (Slc43a2), a low-affinity facilitative uniporter (K_M ≈ 4 mM) specific for Phe, leucine, isoleucine, valine, and methionine; and 3) TAT1 (Slc16a10), a H⁺-dependent facilitative uniporter selective for aromatic amino acids (K_M 2.5-7 mM). Additionally, LAT1 (Slc7a7)/4F2hc complex mediates the exchange of neutral amino acids and Na⁺ for cationic amino acids (Fig. 1) (24,25).

Figure 1. Microbial and host transport mechanisms for aromatic amino acids in the intestine. Schematic overview of dietary aromatic amino acids (Trp, Phe, Tyr) transport at the intestinal host-microbe interface. Upper panel: Microbial utilization showing specialized transporters and de novo biosynthesis through shikimate pathway. Lower panel: Host absorption mechanisms in the intestinal epithelium, with the small intestine achieving >90% dietary protein uptake through coordinated apical and basal transport systems, while the large intestine processes remaining 2%–7% of unabsorbed proteins and microbial-derived amino acids.

AA⁰, neutral amino acids; AA⁺, cationic amino acids; PEP, phosphoenolpyruvate; E4P, erythrose 4-phosphate; PP pathway, pentose phosphate pathway.

In the large intestine, distinct transport systems handle the remaining 2%–7% of dietary proteins and amino acids derived from microbial metabolism and endogenous sources. Key apical transporters include ATB^0,+ (Slc6a14), which accepts both neutral and cationic amino acids with high affinity (K_M 6-600 μM), in addition to ASCT2 (Slc1a5) and TAUT (Slc6a6). At the basolateral membrane, SNAT2 (Slc38a2) facilitates the uptake of neutral amino acids with Na⁺ (Fig. 1) (24).

The expression and activity of these transporters are regulated through complex coordinated mechanisms, including spatial gradients of expression along the intestine, temporal control by diurnal rhythm and feeding patterns, and post-translational modifications like phosphorylation. The distinct transport mechanisms work in concert to ensure efficient amino acid absorption and homeostasis in IECs (24).

Microbial utilization of AAAs

The intestinal lumen serves as a shared metabolic environment where host absorption and microbial metabolism of AAAs occur simultaneously. Microbes utilize AAAs through multiple pathways: direct uptake of dietary AAAs, de novo biosynthesis, and metabolism of host-derived substrates. Despite efficient small intestinal absorption, a small fraction of dietary amino acids appears to escape assimilation and becomes available for microbial utilization. Microbes have evolved sophisticated transport systems for AAA uptake. In Escherichia coli, these include the high-affinity Trp permease Mtr, low-affinity Trp permease TnaB, Tyr-specific permease TyrP, and high-affinity Phe permease PheP. Additionally, the general permease AroP and ATP-binding cassette (ABC) transporters facilitate uptake of all three AAAs (26,27,28,29). Other species utilize distinct transporters, such as the Trp permease MhsT identified in Bacillus halodurans (30).

Beyond dietary sources, the host contributes to the amino acid pool through the production of endogenous substrates, particularly glycoproteins such as mucins (31). Some gut bacteria possess the shikimate pathway for de novo AAA biosynthesis, which proceeds through chorismate as a central intermediate. This biosynthetic capability allows certain microbes to thrive independent of dietary AAA availability (32). The bacterial-derived AAAs can be excreted through efflux pumps, like YddG in E. coli, which could affect AAA pools in the gut (33). However, as the extent of activity and the level of bacterial AAA synthesis remain unclear, dietary intake remains the primary source of AAAs for host intake (Fig. 1) (32). The interplay between incomplete absorption, host-derived endogenous substrates, and bacterial de novo AAA synthesis dynamically affects AAA availability in the gut, which further influences microbial community structure and metabolism.

A comparative analysis of blood plasma metabolites between germ-free (GF) and conventional mice has revealed profound differences in AAA metabolism. Trp and Tyr levels are elevated more than 1.4-fold in GF mice, while products of bacterial AAA metabolism, including indoxyl-sulfate, phenyl sulfate, p-Cresol sulfate, and phenylpropionylglycine, are exclusively present in conventional mice (34). These findings highlight the significant impact of gut microbiota on AAA metabolism and availability.

METABOLISM OF AAAs

The metabolic fate of AAAs involves complex networks that generate diverse bioactive compounds. The sophisticated interplay between dietary intake, host metabolism, and microbial processing creates a dynamic system that profoundly influences immune regulation and intestinal homeostasis.

Host metabolic pathways

Following absorption through the small intestinal epithelium, AAAs either enter systemic circulation for distribution to various organs or undergo immediate metabolism in intestinal tissues, establishing distinct yet interconnected metabolic pathways (Fig. 2).

Figure 2. Integrated metabolic network of aromatic amino acid catabolism by host and gut microbiota. Metabolic pathways of aromatic amino acids in the gut microbiota and host cells characterized to date. Blue arrows indicate microbial pathways with representative enzyme names shown in blue, while black arrows and enzymes represent host metabolic processes.

Trp metabolism

Host Trp metabolism proceeds through two principal pathways: kynurenine and serotonin. The kynurenine pathway represents the major route, accounting for approximately 95% of Trp catabolism in the liver (35). This pathway is regulated by three key enzymes that show distinct tissue distribution patterns. Trp 2,3-dioxygenase expression remains specific to the liver, while indoleamine 2,3-dioxygenase (IDO)1 and its paralog IDO2 show broader tissue distribution (36). These enzymes have emerged as critical immunoregulatory molecules (37). IDO1 expression and activity, which are influenced by gut microbiota, serve as a crucial link between immune modulation and microbial regulation of host metabolism. Increased IDO1/2 enzymatic activity leads to a higher kynurenine-to-Trp ratio, which has been reported in various inflammatory diseases and cancers associated with elevated IFN-γ levels (38). The inflammatory response driving IDO1 activation may originate from microbial interactions, highlighting the complex pathways through which microbes influence immune modulation (39).

The serotonin pathway produces crucial signaling molecules including serotonin (5-hydroxytryptamine) that influence multiple physiological systems. This pathway begins with tryptophan hydroxylases (TPH1/2) converting Trp to 5-hydroxytryptophan, followed by decarboxylation via DOPA decarboxylase (DDC) to produce serotonin. The tissue distribution of these enzymes shows clear compartmentalization: TPH1 predominates in peripheral tissues, while TPH2 functions primarily in the central nervous system. Notably, approximately 90%–95% of serotonin production occurs in the intestinal enterochromaffin cells, with additional significant quantities synthesized within the ENS. Since serotonin cannot cross the blood-brain barrier, this gut-derived serotonin serves as a major source for peripheral organs, where it exerts its physiological functions through specific receptor-mediated pathways (40). Beyond its traditional role as a neurotransmitter, serotonin and its metabolites play crucial roles in immune regulation, including T cell activation and dendritic cell (DC) maturation (40). Additionally, serotonin serves as a precursor for melatonin, a hormone essential for circadian rhythm regulation and immune modulation (41).

Phe metabolism

The primary fate of Phe is its conversion to Tyr through phenylalanine hydroxylase (PAH) (42), an enzyme requiring tetrahydrobiopterin (BH4) as a cofactor (43). This conversion occurs primarily in the liver and kidney, providing the majority of the body’s Tyr requirements. The physiological significance of this pathway is evidenced by phenylketonuria, a genetic disease caused by PAH deficiency that leads to elevated Phe concentrations and subsequent severe neurological and developmental complications. Phe can also undergo transamination to phenylpyruvate or decarboxylation to phenethylamine, but these represent minor pathways under normal physiological conditions (44,45). Phe and its derived compounds serve as important regulators of gut barrier function, and Phe itself can directly modulate immune cells function through specific signaling pathways (46).

Tyr metabolism

Tyr serves as a crucial precursor for several physiologically important molecules, primarily in the biosynthesis of dopamine, catecholamines, and melanin. In both intestine and brain, Tyr metabolism begins with Tyr hydroxylase converting Tyr to levodopa (L-3,4-dihydroxyphenylalanine), which subsequently undergoes decarboxylation by DDC to produce dopamine (35). Dysfunctional dopamine signaling in the brain is a hallmark of various neurological disorders, notably schizophrenia and Parkinson’s disease. The gut plays a crucial role in neurotransmitter production, contributing over half of the body’s dopamine production through both host and bacterial pathways (47). Dopamine receptors, extensively expressed throughout the intestinal tract, regulate various functions including intestinal motility, ion transport, mucus secretion, and mucosal blood flow. In specific tissues, particularly the brain, dopamine undergoes further modification by dopamine beta-hydroxylase and phenylethanolamine N-methyltransferase to produce L-noradrenaline and L-adrenaline, respectively. Beyond neurotransmitter synthesis, Tyr also serves as a substrate for melanin biosynthesis through tyrosinase-mediated pathways, contributing to skin, hair, and eye pigmentation, as well as thyroid hormone production (48).

Microbial metabolic pathways

Recent advances in microbiome research have revealed the extensive and specific capacity of gut bacteria to generate unique bioactive compounds from AAAs. These metabolic networks show remarkable complexity and specificity in terms of bacterial species involvement and metabolite production patterns (Fig. 2).

Trp-derived metabolites

The bacterial metabolism of Trp exemplifies the complexity of microbial metabolic capabilities. Multiple bacterial species catalyze the conversion of Trp into various indole derivatives through specific enzymatic cascades. These pathways generate intermediate compounds such as indole, indole-3-acetamide, tryptamine, indole-3-acetaldehyde, and indole-3-pyruvate, which can undergo further transformation to produce final metabolites including indole-3-acetate, indole-3-aldehyde, and indole-3-propionate. Notably, specific bacterial phyla are associated with metabolic pathways; for instance, Proteobacteria are primarily responsible for indole-3-acetamide production, while Firmicutes contribute to the formation of tryptamine and indole-3-pyruvate (49,50,51). Indole, a primary metabolite in this pathway, functions as a well-characterized signaling molecule in microbial communities, affecting bacterial behaviors such as spore formation, plasmid stability, drug resistance, biofilm formation, and virulence (52). Other metabolites, including indole-3-lactate and indole-3-ethanol (tryptophol), have recently been discovered to have anti-fungal and anti-bacterial activity, suggesting their role in microbial community regulation (53,54,55,56).

The bacterial contribution to serotonin metabolism in the gut represents another significant pathway. Several gut bacteria, including Staphylococcus aureus, Clostridium perfringens, Klebsiella grimontii, and Staphylococcus epidermis can produce serotonin, although the exact enzymatic pathways remain unidentified (57). This bacterial production is especially significant in the neonatal gut, where nearly half of bacterial isolates from the small intestine demonstrate serotonin-producing capability (57). Additionally, intestinal bacteria can modulate serotonin availability through β-glucuronidase-mediated deconjugation of host-derived serotonin (58).

Phe-derived metabolites

The microbial metabolism of Phe demonstrates similar complexity and specificity. Different bacterial species orchestrate the conversion of Phe into various metabolites including phenylpyruvate, phenylacetate, phenyllactate, and phenylpropionate. This metabolic network shows clear species-specific patterns: Bacteroides ovatus and Bacteroides fragilis predominantly produce phenylpyruvate, while Clostridium species specialize in phenylacetate formation. Some metabolites, such as phenylacetate, are produced by multiple bacterial species across different phyla, while others like phenyllactate and phenylpropionate are produced by a more limited range of bacteria, with Bifidobacterium species being significant contributor (4). Phenethylamine, produced through bacterial decarboxylation of Phe, has gained particular attention for its effects on mood, energy, and attention regulation, earning its designation as ‘endogenous amphetamine’ (59,60). The physiological roles of many other Phe-derived metabolites remain to be fully elucidated, highlighting an important area for future research.

Tyr-derived metabolites

The bacterial conversion of Tyr yields several bioactive compounds through diverse metabolic pathways (9). Key metabolites include tyramine, 4-hydroxyphenylpyruvate, 4-hydroxyphenylacetate, 4-hydroxyphenyllactate, and p-Cresol. The production of these compounds follows distinct phylogenetic patterns, with Firmicutes specializing in tyramine production and Proteobacteria contributing significantly to 4-hydroxyphenylpyruvate formation. Among these metabolites, p-Cresol has attracted particular attention due to its influence on the immune system, though its potential genotoxicity in the colon necessitates careful investigation of the underlying molecular mechanisms (61).

Host-microbe interactions in AAA metabolism

The interplay between host and microbial metabolism of AAAs involves sophisticated regulatory mechanisms operating at multiple levels, from direct substrate competition to complex metabolic networks. Understanding these interactions is crucial for comprehending the physiological impact of AAA metabolism on immune function and host homeostasis.

Competition for substrates

The intestinal lumen serves as a shared metabolic space where host absorption and microbial metabolism compete for available AAAs (62,63). This competition has significant physiological consequences; intestinal and circulatory AAA levels are notably lower in microbiota-colonized mice compared to GF counterparts. Recent study has identified specific gut microbes and their metabolic genes that efficiently deplete amino acids in the intestine, demonstrating the substantial influence of microbial metabolism on host nutrient homeostasis (64).

Regulation of host metabolic functions

Beyond substrate competition, bacterial activity directly regulates expression or biological function of host enzymes involved in AAA metabolism. For instance, recent studies have demonstrated that gut microbial metabolites, including butyrate, propionate, tryptamine, deoxycholate, and p-aminobenzoate, can upregulate Tph1 expression, thereby influencing systemic serotonin levels (65). Similarly, certain commensal bacteria, including Clostridium, Lachnoclostridium, Ruminoclostridium, and Roseburia species, repress Ido1 expression through butyrate-mediated STAT1 inhibition via its effect on histone deacetylase activity (66). A recent study demonstrated a developmental stage-specific regulation of host serotonin metabolism: neonatal gut bacteria such as Rodentibacter heylii and Enterococcus gallinarum maximize serotonin availability by inducing higher TPH1 expression and maintaining lower monoamine oxidase A levels in the small intestine, effects not observed in adult intestine (57). In addition, the gut microbiota also influences AAA metabolism indirectly through effects on GI motility (67,68). Studies in GF or antibiotic-treated mice have shown slower GI motility and prolonged intestinal transit time, accompanied by the loss of enteric neurons (69,70). These changes in gut physiology can significantly impact the absorption and metabolism of AAAs.

Integration of metabolic networks

The metabolic sharing of AAAs and their derivatives represents a sophisticated form of microbial cooperation that fundamentally shapes gut microbial community structure and function. This metabolic interdependence appears to be an evolutionary adaptation, as many gut bacteria lack complete AAA biosynthetic pathways in their genome, likely due to the high energetic costs and local availability of these compounds from host and other microbial sources (71).

The metabolism of Phe and Tyr exemplifies these complex networks. Certain Firmicutes, particularly Clostridium sporogenes, initiate reductive metabolism of these amino acids through the phenyllactate dehydratase (FldABC) complex, generating phenylpropanoate and 4-hydroxyphenylpropionic acid. These products support auxotrophic bacteria including Clostridioides difficile, Streptococcus pneumoniae, and various Lactobacillus species. The metabolic web extends further through an alternative oxidative pathway, mediated by pyruvate ferredoxin oxidoreductase alpha subunit (PorA), which produces phenylpropanoate and 4-hydroxyphenylacetate. Notably, these pathways respond to glucose availability – when glucose is limited, bacteria primarily use AAAs for energy, and when glucose is abundant, they focus on producing bioactive metabolites that influence community behavior (9).

Trp metabolism provides another compelling example of microbial cooperation. Lactobacillus species initiate the process by converting Trp into indole-3-lactate, which Clostridium species subsequently transform into other bioactive compounds such as indole-3-propionate and indole-3-acetate. This cross-feeding pathway shows enhanced activity under inflammatory conditions, suggesting its potential role in maintaining gut homeostasis during dysbiosis (8). These intricate metabolic relationships ultimately determine the profile of immunomodulatory metabolites available to the host, highlighting how community-level microbial interactions influence host physiology. Understanding these networks is crucial for developing targeted therapeutic approaches that consider the complex web of microbial interactions rather than focusing on individual species or pathways.

MOLECULAR MECHANISMS TARGETED BY AAA METABOLITES FOR IMMUNE REGULATION

AAA metabolites orchestrate immune responses through several distinct but interconnected signaling mechanisms: rapid non-genomic signaling via membrane receptors, sustained genomic regulation through nuclear receptors, unique post-translational modifications, and metabolic signaling pathways (Fig. 3). While our understanding of how these distinct signaling pathways converge in immune cells remains limited, this multi-layered control system enables precise modulation of immune responses across different temporal and spatial scales (4).

Figure 3. Molecular mechanisms of AAA metabolite signaling and receptor distribution across immune cells. Schematic diagrams illustrating signaling pathways and cellular distribution of receptors and transporters. (A) Left panel: Non-genomic signaling mechanisms showing membrane receptor-mediated pathways. AAA metabolites activate various membrane receptors, leading to diverse signaling cascades including cAMP, MAPK, PI3K, and mTOR pathways, ultimately affecting transcription factors (NF-κB, CREB, eIF-4B). Right panel: Genomic regulation mechanisms depicting transporters facilitating cellular uptake of metabolites. Inside the cell, metabolites activate nuclear receptors (AHR, PXR, NRF2), while TGM2 catalyzes histone monoaminylation. Colored boxes indicate predominant metabolite origins: microbe-derived (tan), host-derived (blue), or co-produced (purple). Colored dots denote ligand specificity for different nuclear receptors. (B) Distribution of key receptors and transporters across immune cells and intestinal epithelial cells, highlighting cell type-specific expression patterns.

Ras, rat sarcoma virus; Akt, protein-kinase B; 4E-BP1, eukaryotic initiation factor 4E-binding protein 1; eIF-4B, eukaryotic translation initiation factor 4B.

Non-genomic signaling mechanisms (membrane receptor-mediated pathway)

While nuclear receptor pathways have traditionally dominated our understanding of metabolite sensing, recent evidence highlights the critical importance of rapid non-genomic signaling (72). Through membrane receptors, AAA metabolites can trigger immediate cellular responses within seconds to minutes, far faster than the hours required for genomic regulation. In addition, through second messenger cascades and signal amplification, activation of membrane receptors often allows precise control of immune cell function without requiring new protein synthesis (73,74). The distribution and expression patterns of these receptors across different immune cell populations allow for sophisticated functional regulation. This rapid and sophisticated response system is particularly crucial in dynamic immune environments where quick adaptations can be essential for proper immune function (Fig. 3).

G protein-coupled receptors (GPCRs)

GPCRs constitute the largest family of cell membrane receptors, serving as fundamental mediators of signal transduction. Upon ligand binding, these receptors undergo conformational changes that activate specific G protein subtypes (Gαs, Gαi, Gαq), which in turn trigger distinct intracellular signaling cascades (75). In immune regulation, GPCRs serve as key molecular targets for AAA metabolites, with multiple receptor families orchestrating diverse aspects of immune cell function.

Trace amine-associated receptors (TAARs) represent important targets for bacterial and host-derived AAA metabolites in the immune system. Bacterial metabolites, β-phenethylamine, tyramine, and tryptamine are known ligands for TAARs. These receptors are expressed in various immune cells including B cells, T cells, neutrophils, monocytes, and mononuclear cells, where they mediate distinct immunological responses. Phenethylamine is a potent agonist that activates both TAAR1 and TAAR2, leading to IgE synthesis in B cells and chemosensory migration in polymorphonuclear leukocytes. Tyramine similarly acts through TAAR1, although with lower affinity, and has been shown to induce pro-inflammatory cytokine production in macrophages (76). The clinical significance of these interactions is highlighted by elevated phenethylamine levels serving as potential biomarkers for Crohn’s disease, while tyramine modulates bacterial adhesion to the intestinal epithelium and modulate TNF-α production (76).

Hydroxycarboxylic acid receptor 3 (HCA3) represents another crucial GPCR target in immune regulation. This receptor responds to bacterial phenyllactate produced by Lactobacillus species and host-derived β-hydroxylated fatty acids. Phenyllactate activation of HCA3 promotes monocyte migration through specific signaling cascades (77). Additionally, G-protein coupled receptor 35 (GPR35) responds to Trp metabolites including kynurenic acid and 5-hydroxyindoleacetate, inducing leukocyte adhesion and migration (78,79).

The serotonergic signaling system exemplifies precise immune regulation through cell-type specific receptor expression patterns, with serotonin acting through multiple serotonin receptors (HTRs) subtypes expressed differentially across immune cell populations (10). T cells predominantly express HTR1, HTR2, and HTR7, which coordinate their activation status and cytokine production profiles. In contrast, DCs express a different complement of receptors, including HTR4 and HTR7, enabling distinct responses to serotonin signals (80). Bacterial tryptamine exhibits a unique dual targeting capability, activating both HTR4 and TAAR1. Tryptamine has been shown to induce mucus secretion in colon goblet cells through HTR4 activation (Fig. 3B) (81).

Non-GPCRs

TLR4 expands the repertoire of AAA metabolite signaling through distinct mechanisms. Cinnamic acid, a bacterial Phe derivative, may interact with TLR4 and regulate subsequent NF-κB signaling to regulate inflammatory responses. Cinnamic acid treatment has shown inhibition effect to cytokine production by blocking TLR4 in monocyte (82). Indole-3-acetate, in conjunction with LPS, stimulates the formation of IL-35-producing B cells, which is mediated by NF-κB pathway activation via TLR4 (83). This mechanism highlights the complex interplay between gut microbiota metabolites, bacterial components, and the host immune systems.

Receptor Tyr kinases represent a distinct class of high-affinity cell surface receptors that respond to various polypeptide growth factors, cytokines, and hormones. Within this family, the epidermal growth factor receptor (EGFR) pathway demonstrates particular significance in AAA metabolite signaling. p-Cresol, generated through bacterial Tyr metabolism, interferes with EGFR and TLR4 crosstalk. This blocks synergistic signal transduction and decreases epithelial CCL20 production (84).

HTR3 represents a unique member of serotonin receptor family, functioning as a ligand-gated ion channel rather than a GPCR. When serotonin binds to the receptor, it triggers a rapid cation influx that leads to membrane depolarization and subsequent cellular activation (85).

Genomic regulation mechanisms (nuclear receptor-mediated and epigenetic regulation)

In contrast to membrane receptor-mediated mechanisms, several AAA metabolites, particularly Trp metabolites, also exert effects through nuclear receptor activation following cellular uptake. While Phe and Tyr metabolites enter cells via specific transporters, their roles in nuclear receptor-mediated pathways have not yet been identified. Additionally, emerging evidence has uncovered that some AAA metabolites can modulate gene expression through histone modifications, broadening their regulatory mechanisms (Fig. 3).

Cellular transport mechanisms

Despite the diverse physiological effects of AAA metabolites, their intracellular transport mechanisms remain incompletely understood. These mechanisms vary depending on the molecular structure of the precursor compounds. For instance, hydrophobic molecules like indole are believed to passively diffuse across cell membranes, whereas others require specific transport proteins for cellular uptake (86). Monoamine transporters (MATs)—including the serotonin transporter (SERT), dopamine transporter (DAT), and norepinephrine transporter (NET)— along with organic cation transporters (OCTs) from the SLC22 family (OCT1, OCT2, OCT3) have been identified as key mediators in the transport of AAA metabolites (87,88). All 3 OCTs (OCT1, OCT2, and OCT3) are predominantly expressed in neuronal cells, whereas OCT1 and OCT3 are also expressed in IECs. Experimental evidence demonstrates that OCT1 facilitates the transport of dopamine, tyramine, phenethylamine, and tryptamine. OCT2 exhibits similar substrate specificity, mediating the transport of dopamine, tyramine, phenethylamine, and serotonin, while OCT3 functions in the transport of dopamine, tyramine, and phenethylamine. SERT, expressed in neurons, intestinal enterocytes, and various immune cells such as monocytes, macrophages, DCs, mast cells, and lymphocytes, is capable of transporting dopamine, tyramine, phenethylamine, serotonin, and tryptamine (40). DAT, predominantly expressed in brain neurons and some immune cells such as monocytes, macrophages, and lymphocytes, shares substantial substrate overlap with NET, a brain-specific transporter (89). Both DAT and NET facilitate the movement of dopamine, tyramine, phenethylamine, serotonin, and tryptamine.

Additionally, L-amino acid transporters, expressed in lymphocytes, macrophages, DCs, and NK cells, mediate transport of phenethylamine and kynurenine (90). The plasma membrane MAT, broadly distributed across various tissues, including intestinal enterocytes, is specifically involved in the transport of tryptamine (91). This diverse array of transport mechanisms highlights the complexity of bacterial metabolite absorption and distribution in mammalian systems (Fig. 3B).

Aryl hydrocarbon receptor (AHR) pathway

Indole metabolites, such as indole-3-acetate, indolelactate, indole-3-propionate, and indolealdehyde, predominantly act through AHR after cellular uptake. As a ligand-dependent transcription factor, AHR responds to both endogenous and exogenous ligands. In its inactive state, AHR exists in the cytoplasm as part of a multi-protein complex, associated with heat shock protein 90, co-chaperone p23, and protein Tyr kinase c-Src (92). Upon ligand binding, AHR undergoes a conformational change that triggers its release from the protein complex and subsequent nuclear translocation and heterodimerization with AHR nuclear translocator (92). This complex recognizes and binds to specific DNA sequences known as xenobiotic response elements (XREs) in target gene promoters, activating transcription of target genes involved in immune regulation, including Il22 and Cyp1a1 (15).

Pregnane X receptor (PXR) pathway

PXR, a member of the nuclear receptor superfamily, provides an additional layer of regulation for certain metabolites, particularly for indole metabolites such as indole, indole-3-acetate, and indole-3-propionate. When ligands bind to PXR, it undergoes a conformational change that promotes coactivator recruitment while displacing corepressors (93,94). The activated PXR functions as a master regulator of xenobiotic metabolism by controlling the transcription of drug-metabolizing enzymes and transport proteins. Additionally, PXR orchestrates diverse immunoregulatory responses in innate and adaptive immune cells—suppressing pro-inflammatory cytokine production in macrophages, modulating T cell differentiation, and regulating B cell responses (95). Notably, many PXR ligands overlap with AHR ligands, suggesting that Trp metabolites coordinate these two pathways to fine-tune immune responses, though the exact mechanisms of their potential crosstalk or cooperation remain to be fully elucidated (8).

Epigenetic modification

A unique aspect of AAA metabolite signaling is exemplified by their involvement in epigenetic modification. Serotonylation, the covalent attachment of serotonin to glutamine residues of target proteins by tissue transglutaminases (TGMs), occurs on histone H3 (H3Q5ser), resulting in long-lasting changes to cellular function and gene expression (96). This modification has emerged as a novel epigenetic regulatory mechanism (97), as demonstrated in neuronal cells where serotonylation of H3Q5 promotes the binding of the transcription factor IID-containing transcription initiation complex to H3K4me3-enriched promoters (98). While histone serotonylation has not been directly demonstrated in immune cells, the presence of serotonin and other monoamines that can serve as TGM2 substrate in immune cells, along with the expression of various serotonin transporters, suggests the potential occurrence of this modification in immune cells (99). The functional significance of protein serotonylation has been demonstrated in CD8⁺ T cells, where serotonylation of GAPDH at position Q262 promotes its cytoplasmic localization and enhances glycolytic metabolism, supporting T cell activation and antitumor immune responses. The therapeutic potential of this pathway can be enhanced through engineering CAR-T cells to increase serotonin production (100).

Bacterially produced indole-3-propionate provides another example of epigenetic regulation, enhancing H3K27 acetylation at the super-enhancer region of the Tcf7 gene, although the underlying molecular mechanism is not clear. This epigenetic modification increases expression of TCF-1, a master regulator of T cell stemness, promoting the differentiation of progenitor exhausted CD8⁺ T cells (T_pex) in the tumor microenvironment. The pathway’s essential role was confirmed in Tcf7-knockout mice, where indole-3-propionate failed to enhance immunotherapy efficacy. Therefore, indole-3-propionate represents a molecular connection between microbial metabolites and T cell stemness programming and enhanced antitumor immunity through the maintenance of stem-like CD8⁺ T cells (101).

Intracellular signaling pathways

cyclic AMP (cAMP)-dependent pathway

The cAMP-dependent signaling serves as a central mechanism through which AAA metabolite modulate immune responses after GPCR activation. The HTR1, HCA3 and GPR35 couple to inhibitory G-proteins (Gαi/o), suppressing adenylyl cyclase activity and reducing intracellular cAMP levels (102,103,104). In contrast, the HTR4, HTR6, and HTR7 couple to the stimulatory G-proteins (Gαs), enhancing adenylyl cyclase activity and elevating cAMP levels. These changes in cAMP levels trigger protein kinase A (PKA) activation, leading to phosphorylation of downstream targets including cAMP response element-binding protein (CREB) and subsequent modulation of gene expression (105). In mature DCs, serotonin-mediated activation of HTR4 and HTR7 modulates cytokine production through cAMP-dependent mechanisms, selectively enhancing IL-1β and IL-8 secretion while suppressing IL-12 and TNF-α production (105).

MAPK signaling pathway

Activation of HTR2 by serotonin promotes cell proliferation through the MAPK signaling pathway (105). Macrophages express HTR2B, which plays a key role in serotonin-mediated regulation of immune function. Activation of HTR2B triggers ERK1/2 phosphorylation via the MAPK signaling pathway, leading to transcriptional regulation of genes such as AP1, c/EBP, and SRF, which drive macrophage activation and polarization. Notably, HTR2B stimulation promotes M2 macrophage polarization while inhibiting M1 polarization and also suppresses the secretion of pro-inflammatory cytokines such as IL-12 in monocyte-derived M2 macrophages through NF-κB signaling upon LPS stimulation (106).

mTOR signaling pathway

The mTOR is a highly conserved serine/threonine protein kinase that functions as a central regulator of cell metabolism, growth, proliferation, and survival in response to nutrients, growth factors, and cellular energy status. Multiple mechanisms have been identified through which AAA metabolites can regulate mTOR activity. Kynurenine, kynurenic acid, and indole-3-lactate have been shown to modulate the mTOR-mediated autophagy pathway, regulating intracellular protein turnover and the intestinal barrier functions (107). IDO, the primary enzyme responsible for host-mediated Trp catabolism, depletes Trp through kynurenine pathway activation and leads to mTOR inhibition, subsequently triggering autophagy (108).

A recent study identified that Trp, Phe, and Try function as direct agonists of mTOR through interaction with Sestrin3, disrupting its association with GATOR2, distinct from the mechanism of previously known mTOR-activating amino acids (glutamine, leucine, and arginine). This activation influences proteasomal localization; under amino acid starvation, mTOR inhibition allows proteasome translocation from nucleus to cytosol for protein breakdown and survival, while AAA-mediated mTOR activation causes nuclear proteasome sequestration, potentially leading to cell death under stress (109). This newly discovered pathway thus emerges as a crucial mechanism for coping with cellular stress, but the ability of other structurally similar metabolites to activate mTOR in the same way remains unexplored.

IMMUNE CELL RESPONSES TO AAA METABOLITES

AAA metabolites exhibit diverse regulatory effects on immune cell populations through multiple signaling pathways, orchestrating both innate and adaptive immune responses. These metabolites fine-tune immune cell function through complex mechanisms that can be broadly categorized by their effects on specific immune cell populations. Table 1 presents a detailed compilation of AAA metabolites and their immunomodulatory effects, highlighting specific target cells, functional changes, and the molecular mechanisms through which they exert their influence (7,40,76,77,78,80,81,82,83,84,100,101,102,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143).

Table 1. Immunomodulatory effects and mechanisms of AAA metabolites.

Amino acid	Metabolites	Target cells	Function	Mechanism	Reference
Trp	Indole*	Treg, Th17	Maintaining balance	AHR signaling pathway	(115)
		HCT-8 cells (colon epithelial cell model)	NF-κB activation ↓	TNF-α	(124)
			IL-8 ↓	-	(124)
			IL-10 ↑	-	(124)
	Indole-3-pyruvate*,† (IPyA)	Treg1	Treg1 differentiation ↑	AHR signaling pathway	(125)
		Th17			(125)
		DCs	Th1 ↓		(125)
		NK cells	Formation ↑	H3K27 acetylation	(101)
		ILCs			(101)
	Indole-3-acetate* (IAA)	DCs	IL-22 expression and secretion ↑	AHR signaling pathway	(110)
		B cells	IL-35+ B cells ↑	PXR and TLR4 activation	(83)
		Macrophages	IL-1β ↓, TNF-α and MCP-1 expression and secretion ↓	AHR signaling pathway	(126)
	Indole-3-lactate* (ILA)	Intraepithelial CD4+ T cells	Reprogram into immunoregulatory T cells	AHR signaling pathway	(127)
	Indole-3-propionate* (IPA)	Macrophages	IL-10 ↑, TNF ↓, IL-6 ↓	PXR activation	(115,128)
		CD8+ T cells	Differentiation into Tpex cells	H3K27 acetylation	(101)
	Indole-3-acrylic acid* (IA)	Goblet cells	Muc2 expression ↑	AHR signaling pathway	(115)
		Macrophages	IL-10 ↑, IL-6 ↓		(115)
			ARE pathway ↑, pro-inflammatory signaling pathway ↓	NRF2-ARE pathway	(115)
		PBMC	IL-6 ↓, IL-1 β ↓	NRF2-ARE pathway	(115)
	Tryptamine*,†	Goblet cell	Mucus release ↑	HTR4	(81)
		Macrophages	IL-1β ↓, TNF-α and MCP-1 secretion ↓	AHR signaling pathway	(126)
		Treg cells	P4EBP1 expression in Tem cells ↑	mTOR activation	(120)
		NK cells	Cytotoxicity toward tumor cells ↑	AHR signaling pathway	(120)
	Indole-3-aldehyde* (IAld)	ILC3	IL-22 ↑	AHR signaling pathway	(118,119)
	Kynurenine*,† (Kyn)	DCs	IDO1 ↑	TGF-β signaling pathway	(111,112)
			TGF-β ↑	AHR signaling pathway	(129)
		CD8+ T cells	PD-1 ↑		(130)
		CD4+ T cells	Foxp3, TGF-β ↑		(131,132)
		Th17	Differentiation to IL-10 producing Treg1	TGF-β signaling pathway	(133)
				AHR signaling pathway	(134,135)
	Kynurenic acid*,† (KYNA)	Monocytes	TNF, IL-4, IL-23 ↓	-	(134)
		CD4+ T cells	Differentiation to Treg cells ↑	AHR signaling pathway	(134)
			Differentiation to Th17 cells ↓		(102)
		DCs	IL-23 ↓	GPR35	(102)
		CD4+ T cells	IL-17 ↓		(136)
		iNKT	IL-4 ↓		(137)
	3-Hydroxyanthranilic acid*,† (3-HAA)	Glial cells, astrocytes	TNF-α ↓, IP-10 ↓	-	(117)
		Macrophages	Immunophenotyping remodeling	CCL2/CCR2 inhibition	(122)
		CD4+ T cells	Apoptosis	NF-kB inhibition	(138)
		DCs	TGF-β ↑	AHR signaling pathway	(139)
	3-Hydroxykynurenine*,† (3-HK)	T cells	Suppression	-	(123)
	5-Hydroxytryptophan*,† (5-HTP)	CD8+ T cells	CD8+ T cell exhaustion	AHR signaling pathway	(140)
	5-Hydroxytryptamine*,† (5-HT, Serotonin)	Smooth muscle cells	IL-6 ↑	HTR2	(80)
		Platelets	T cell activation	IgE receptor	(40)
		Monocytes	TNF-α ↓	HTR4, HTR7	(40)
			IL-6, IL-1β ↑	HTR3, HTR4, HTR7	(40)
		Macrophages	CCL2 ↑	HTR2C	(40)
			Phagocytosis	HTR1A, NFkB	(40,113)
		DCs	IL-1β, IL-6, IL-8, IL-10 ↑	HTR3, HTR4, HTR7	(114)
			IL-12, TNFα ↓	HTR7	(40)
		Eosinophils	Asthmatic response	HTR2	(40)
		Mast cells	Cell adhesion and migration	HTR1A	(121)
		Lymphocytes	IL-2, IL-16 ↑, T cell proliferation	HTR1A	(100)
		CD8+ T cells	IFN-γ, IL-17 ↓	Serotonylation	(121)
		CD4+ T cells	IL-10 ↑	HTR1A, HTR2	(121)
		Th17 cells	IL-17 ↑	HTR2A, HTR2B	(141)
		B cells	B-cells proliferation	HTR1A	(78)
	5-Hydroxyindoleacetate*,†	Neutrophils	Transmigration ↑	GPR35	(142)
Phe	Phenylalanine*	Macrophages	Pyroptosis ↑	NLRP3 inflammasome	(7)
			M1 macrophage inflammation ↓	OXPHOS ↑	(116)
	Phenylpyruvate*,†	Macrophages	IL-1β ↑	NLRP3 inflammasome	(76)
	Phenethylamine*,†	T cells	IL-4 secretion ↑	TAAR1 signaling	(76)
	(PEA)	B cells	IgE expression ↑	TAAR1 signaling	(143)
	Phenylacetate*,†	Neutrophils	Recruitment	-	(82)
	Phenylacrylic acid (Cinnamic acid)*	Monocytes	TLR-4 ↑, TLP-2 ↓, HLA-DR ↓, CD80 ↓	TLR4 blocking	(82)
			TNF-α ↓, IL-10 ↓		(77)
	Phenyllactate*	Monocytes	Migration ↑	HCA3 activation	(84)
Tyr	p-Cresol*	Airway epithelial cells	CCL20 production ↓	EGFR and TLR4 signaling	(76)
	Tyramine*,†	T cells	IL-4 secretion ↑	TAAR1 signaling

^*Metabolic compound that can be synthesized by bacteria.

^†Metabolic compound that can be synthesized by host.

Regulation of innate immune cells

DCs integrate multiple AAA metabolite signals through diverse molecular pathways to modulate their function and subsequent T cell responses. Trp metabolites particularly demonstrate potent regulatory effects on DCs through both AHR-dependent and independent mechanisms: Indole-3-acetate enhances IL-22 expression and secretion through AHR signaling pathway activation (110). Kynurenine exhibits dual regulatory mechanisms—inducing IDO1 expression through TGF-β signaling and increasing TGF-β production via AHR signaling pathway, creating a potential feedback loop (111,112). The serotonin signaling system in DCs involves multiple receptor subtypes, including HTR3, HTR4, and HTR7, leading to complex cytokine responses. This signaling network results in increased IL-1β, IL-6, IL-8, and IL-10 production (40,113), while specifically reducing IL-12 and TNF-α through HTR7 activation (114), demonstrating how a single metabolite can orchestrate diverse immune responses through distinct receptor-mediated pathways.

Macrophages respond to AAA metabolites through an intricate network of signaling cascades. Indole-3-propionate and indole-3-acrylic acid reduce pro-inflammatory cytokine production through distinct mechanisms; indole-3-propionate operates through PXR activation to increase IL-10 while decreasing TNF and IL-6, whereas indole-3-acrylic acid employs the NF erythroid 2-related factor 2 (NRF2)-antioxidant response element (ARE) pathway to achieve similar anti-inflammatory effects (115). Tryptamine suppresses inflammatory mediators via AHR signaling, while Phe metabolites like phenethylamine uniquely influences M1 macrophage inflammation through OXPHOS regulation, demonstrating metabolic reprogramming as an additional regulatory mechanism (7). The nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome pathway adds another layer of complexity, mediating phenylpyruvate-induced IL-1β production (116). Furthermore, 3-hydroxyanthranilic acid modulates macrophage function through CCL2/CCR2 inhibition, highlighting the diversity of signaling pathways involved in metabolite-mediated regulation (117).

NK cells and innate lymphoid cells (ILCs) demonstrate specific responses to Trp metabolites through both transcriptional and epigenetic mechanisms. Indole-3-propionate enhances NK cell formation through H3K27 acetylation (101), while indole-3-aldehyde specifically targets ILC3s to promote IL-22 production and intestinal stem cell regeneration through AHR signaling (118,119). Tryptamine increases NK cell cytotoxicity toward tumor cells through AHR pathway activation (120).

Regulation of adaptive immune cells

T cell populations show remarkable sensitivity to AAA metabolites through multiple signaling pathways that influence their differentiation, function, and cytokine production patterns. The regulation of CD4⁺ T cell differentiation involves complex interplay between different signaling cascades. Multiple Trp metabolites, including indole and indole-3-propionate, regulate the balance between Treg and Th17 cells through both AHR-dependent and independent mechanisms (144). Interestingly, AHR activation has ligand-specific effects for T cell regulation; for example, while 6-formylindolo(3,2-b)carbazole (FICZ) promotes Th17 cell differentiation, 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) preferentially induces Foxp3⁺ Tregs (145,146). However, the underlying molecular mechanisms of this distinction remain poorly understood.

Serotonin signaling adds another layer of complexity through various receptor subtypes, particularly HTR1A and HTR2, which modulate cytokine production with specific effects on IL-10 and IL-17 production in different T cell subsets (121). Additionally, 3-hydroxyanthranilic acid induces apoptosis through NF-κB inhibition, demonstrating how metabolites can control T cell populations through both functional modification and cell survival pathways (122).

In CD8⁺ T cells, indole-3-propionate promotes the differentiation of progenitor exhausted CD8⁺ T cells through epigenetic modification via H3K27 acetylation (101), while 5-hydroxytryptophan influences CD8⁺ T cell exhaustion through AHR signaling (123). Serotonylation of GAPDH provides an additional regulatory mechanism in CD8⁺ T cells by enhancing glycolytic metabolism, which in turn promotes T cell proliferation and IFN-γ production for effective antitumor immunity (100).

B cells demonstrate diverse responses to AAA metabolites. Indole-3-acetate coordinates the development of IL-35-producing B cells in the presence of LPS (83), through a coordinated activation of PXR and TLR4 pathways, demonstrating pathway convergence in immune regulation. Phenethylamine increases IgE expression through TAAR1 signaling, while serotonin promotes B cell proliferation via HTR1A activation (76). These diverse effects underscore how different receptor systems can be engaged to modulate various aspects of B cell function.

The complexity of AAA metabolite-mediated immune regulation extends to the tissue microenvironment. For instance, p-Cresol modulates immune responses through EGFR and TLR4 crosstalk in epithelial cells, affecting CCL20 production and subsequent immune cell recruitment (84). This highlights how metabolites can influence immune function through both direct and indirect mechanisms.

Pathway crosstalk for context-dependent regulation

The regulation of immune responses by AAA metabolites involves sophisticated networks of interacting signaling pathways that create context-dependent outcomes. While individual pathways demonstrate distinct regulatory functions, their crosstalk enables more nuanced control of immune responses based on specific tissue environments and physiological conditions.

AHR pathway demonstrates extensive crosstalk with other major signaling networks in response to Trp metabolites. The interaction between AHR and NF-κB pathways represents a crucial regulatory axis, with bidirectional control mechanisms. NF-κB RelA directly controls AHR expression through promoter binding, while AHR activation induces CYP1A1 expression, generating reactive oxygen species that can activate NF-κB signaling (147,148). This reciprocal regulation enables coordinated control of inflammatory responses and oxidative stress. Additionally, indole derivatives like indole-3-acetate inhibit NLRP3 inflammasome, through which suppress inflammation in macrophages and promote tolerogenic phenotypes in DCs (18,51).

AHR signaling also converges with the NRF2 pathway to orchestrate antioxidant responses. NRF2 protein is a transcription factor binding on the ARE. Key target genes such as Nqo1 and Sod1 contain both XRE and ARE sequences in their promoters, enabling integrated regulation by both pathways. Furthermore, AHR activation can directly induce NRF2 expression through XRE elements, establishing a feed-forward loop that amplifies antioxidant responses (149). In addition to this transcriptional crosstalk, indole acrylic acid has been shown to activate both AHR and NRF2-ARE pathways, promoting antioxidant and anti-inflammatory immune responses (115). These mechanisms of pathway convergence demonstrate the multiple levels at which AHR and NRF2 signaling can coordinate cellular responses.

Despite this evidence for pathway crosstalk, our understanding of how these networks integrate signals in different physiological and disease contexts remains limited. Further investigation is needed to fully map these regulatory networks and their context-dependent effects.

DISEASE IMPLICATIONS AND THERAPEUTIC APPLICATIONS

The intricate networks of AAA metabolite signaling pathways play crucial roles in various pathological conditions, offering potential therapeutic opportunities while presenting complex challenges. Understanding these disease-specific mechanisms is essential for developing targeted interventions that can modulate immune responses effectively.

Disease implications

Autoimmune diseases

AHR functions as a central immunological regulator in autoimmune conditions through its modulation of inflammatory and immune pathways. In rheumatoid arthritis (RA), AHR activation exhibits distinct context-dependent effects. AHR activation by TCDD or FICZ promotes disease progression through enhanced osteoclast formation and increased IL-17-expressing cell population within joint tissues. Supporting this pro-inflammatory role, AHR-deficient mice show reduced levels of inflammatory mediators (matrix metalloproteinase 3, IL-1β, and IL-6) and decreased disease severity, primarily through T cell-dependent rather than macrophage-dependent mechanisms (150). Conversely, intestinal AHR activation by oral administration of Norisoboldine promotes Treg differentiation in gut-associated lymphoid tissues, leading to anti-arthritic effects through Th17/Treg balance (151). Mechanistically, TCDD-activated AHR directly bind to the Foxp3 promoter, thereby inducing Foxp3 expression and promoting T cell differentiation (145,146). Similarly, AHR activation by kynurenine also triggers Foxp3 expression in T cells, leading to their differentiation into Foxp3⁺ Tregs (152). Additionally, microbiota-derived Trp metabolites, particularly indole-3-acrylic acid, indole-3-propionate, and indole-3-acetate, activate AHR signaling in the intestine to regulate Th17/Treg balance and attenuate RA-associated inflammation (Fig. 4A) (153). In psoriasis, AHR’s multifaceted effects manifest through regulation of inflammatory responses, where its antagonism leads to excessive inflammation, while activation by FICZ reduces disease severity through modulation of stromal-immune system interactions. Of clinical relevance, elevated AHR expression in RA patients indicates its role as an environmental response mediator, while in psoriasis, the therapeutic efficacy of the AHR agonist Tapinarof demonstrates its potential as a treatment target (5).

Figure 4. AAA metabolite signaling in inflammatory diseases. (A) In rheumatoid arthritis, dysbiosis leads to disrupted AHR activation, resulting in Th17/Treg imbalance and increased pro-inflammatory cytokine production. (B) During inflammatory bowel disease, deficient AHR activation in the intestinal epithelium causes impaired barrier function through decreased tight junction proteins and mucus production, promoting inflammation. (C) In diabetic foot ulcers, phenylpyruvate triggers M1 macrophage polarization via NLRP3 pathways, leading to increased inflammation and compromised wound healing.

IBD

AHR emerges as a critical mediator in IBD through its pleiotropic effects on intestinal homeostasis, where decreased intestinal AHR expression has been consistently observed in IBD patients, particularly in Crohn’s disease (154). AHR signaling maintains mucosal barrier integrity through multiple mechanisms: regulation of tight junction proteins, promotion of goblet cell differentiation, and enhancement of mucus production, collectively establishing a robust defense against pathogenic invasion (154,155). Within the immune compartment, AHR activation modulates both innate and adaptive immune responses by regulating the differentiation of Th17 cell and Treg, while also inducing the production of anti-inflammatory cytokines such as IL-10 and IL-22 (Fig. 4B) (156).

Notably, AHR plays a crucial role in maintaining vascular homeostasis in the intestine, affecting angiogenesis and vascular repair mechanisms that are often dysregulated in IBD (16). As a sensor for microbiota-derived metabolites, AHR establishes a critical link between microbial metabolism and host immune responses. The integrated effects of AHR signaling on barrier function, immune regulation, and microbial interactions create a complex regulatory network that, when disrupted, contributes to IBD pathogenesis (157).

Diabetic foot ulcer (DFU)

Recent metabolomic profiling of DFUs has revealed a critical pathological feature: the significant accumulation of phenylpyruvate. Initial analyses demonstrated that elevated phenylpyruvate levels positively correlate with NLRP3 inflammasome activation and chronic inflammation, suggesting its potential role in impaired wound healing. This correlation manifests clinically through the persistent activation of proinflammatory M1 macrophages and compromised transition to healing-associated M2 phenotypes, establishing a pathological inflammatory cycle that impedes proper wound resolution (158).

The molecular basis for this pathology has been precisely delineated: phenylpyruvate enters macrophages through the CD36 scavenger receptor and specifically binds to palmitoyl-protein thioesterase 1 (PPT1) protein at residues Lys229 and Gly245. This binding effectively inhibits PPT1’s depalmitoylase activity, resulting in increased palmitoylation of NLRP3 protein, particularly at cysteine residue 6 within its pyrin domain. The enhanced NLRP3 palmitoylation not only augments protein stability and reduces lysosomal degradation but also promotes interaction with the apoptosis-associated speck-like protein containing a caspase recruitment domain adaptor protein, facilitating inflammasome assembly. This stabilized complex trigger sustained release of inflammatory mediators, including IL-1β, IL-18, and TNF-α, perpetuating a self-reinforcing inflammatory state characterized by reduced epidermal thickness, decreased collagen deposition, and compromised angiogenesis (Fig. 4C). Notably, therapeutic intervention through dietary Phe restriction can attenuate phenylpyruvate accumulation and associated inflammation, suggesting a promising treatment strategy for these otherwise refractory wounds (116).

Therapeutic considerations and future directions

The therapeutic application of AAA metabolite pathway modulation represents a complex landscape filled with both promising opportunities and significant challenges. Our growing understanding of these pathways has revealed their potential as therapeutic targets, yet several critical considerations must be carefully weighed as we move forward in this field (159,160).

The context-dependent nature of AAA metabolite signaling presents perhaps the most significant challenge for therapeutic development. The same metabolite or pathway can exhibit opposing effects depending on the disease state or tissue environment. For example, AHR activation in RA can either exacerbate disease progression through enhanced osteoclast differentiation or ameliorate symptoms through suppression of inflammatory responses (161). This dual nature of signaling necessitates more comprehensive research on understanding the underlying molecular mechanisms by which diverse signals are integrated in disease states. Based on that, the development of highly targeted therapeutic approaches that can achieve tissue-specific and context-appropriate modulation.

Furthermore, the redundancy and interconnectedness of metabolic pathways adds another layer of complexity to therapeutic targeting. Multiple pathways often regulate similar immune functions, creating potential compensatory mechanisms that could limit the effectiveness of single-pathway interventions. Our understanding of these compensatory networks remains incomplete, highlighting the need for comprehensive pathway mapping before developing targeted therapies.

Looking ahead, several critical knowledge gaps in host-microbe metabolic interactions must be addressed. Understanding how different bacterial species contribute to the metabolite pool, how dietary factors influence microbial metabolite production, and how host-microbe interactions regulate metabolite availability will be essential. Additionally, investigating the temporal dynamics of microbiota-dependent metabolite production and their influence on immune responses across different developmental stages and disease states will provide crucial insights for therapeutic development. The development of more sophisticated tools for monitoring metabolite concentrations and pathway activity in real-time will be vital for progressing these research directions (160).

The path forward requires a balanced approach that acknowledges both the potential and limitations of targeting AAA metabolite pathways. Success will likely come from therapeutic strategies that can achieve precise, context-specific pathway modulation while maintaining overall metabolic homeostasis. As our understanding of these complex networks continues to evolve, we may uncover new opportunities for therapeutic intervention in inflammatory conditions.

CONCLUDING REMARKS

Recent advances in understanding AAA metabolite-mediated immune regulation have revealed sophisticated molecular mechanisms through which these compounds influence immune cell function and homeostasis. The convergence of multiple signaling pathways—including membrane receptor-mediated rapid responses, nuclear receptor-dependent transcriptional regulation, and post-translational modifications— are considered to enable precise temporal and spatial control of immune responses. However, several critical questions remain unexplored. First, while individual pathways are well-characterized, how multiple signals in response to the same metabolites as well as how signals by multiple distinct metabolites are integrated under physiological conditions remains poorly understood. Second, the tissue microenvironment-specific concentrations and temporal dynamics of many metabolites await precise determination. Third, the mechanisms governing metabolite availability through host-microbe metabolic networks require further investigation, particularly in different disease states. Finally, the therapeutic potential of targeting AAA metabolite pathways, while promising, faces challenges due to their context-dependent effects and pathway redundancy. Future research addressing these knowledge gaps, supported by advanced technologies such as single-cell metabolomics and spatial metabolomics that enable simultaneous analysis of metabolites at the single-cell resolution from the tissue microenvironment (162,163), will be crucial for developing targeted therapeutic strategies that can effectively modulate immune responses while maintaining metabolic homeostasis.

Abbreviations

AAA

aromatic amino acid

ABC

ATP-binding cassette

AHR

aryl hydrocarbon receptor

ARE

antioxidant response element

cAMP

cyclic AMP

CREB

cAMP response element-binding protein

DAT

dopamine transporter

DC

dendritic cell

DDC

DOPA decarboxylase

DFU

diabetic foot ulcer

EGFR

epidermal growth factor receptor

ENS

enteric nervous system

FICZ

6-formylindolo(3,2-b)carbazole

GF

germ-free

GI

gastrointestinal

GPCR

G protein-coupled receptor

GPR35

G-protein coupled receptor 35

HCA3

hydroxycarboxylic acid receptor 3

IBD

inflammatory bowel disease

IDO

indoleamine 2,3-dioxygenase

IEC

intestinal epithelial cell

ILC

innate lymphoid cell

MAT

monoamine transporter

NET

norepinephrine transporter

NLRP3

nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3

Nrf2

NF erythroid 2-related factor 2

OCT

organic cation transporter

PAH

phenylalanine hydroxylase

Phe

phenylalanine

PKA

protein kinase A

PPT1

palmitoyl-protein thioesterase 1

PXR

pregnane X receptor

RA

rheumatoid arthritis

SERT

serotonin transporter

TAAR

trace amine-associated receptor

TCDD

2,3,7,8-Tetrachlorodibenzo-p-dioxin

TGM

transglutaminase

TPH

tryptophan hydroxylase

Trp

tryptophan

Tyr

tyrosine

XRE

xenobiotic response element