The gut microbiota can use dietary components, host secretions, and intrinsic microbial metabolic pathways to generate diverse classes of small-molecule compounds. These metabolites regulate the intestinal epithelial barrier, energy metabolism, immune-cell differentiation, and signaling in distant organs and therefore serve as important mediators of interactions between the gut microbiome and the host.

Keywords: gut microbiota; microbial metabolites; short-chain fatty acids; tryptophan metabolism; bile acids; TMAO; intestinal barrier; tumor immunity; immunotherapy

1 Sources and Classification of Gut Microbiota-Derived Metabolites

1.1 Metabolites Generated From Dietary Components by the Gut Microbiota

Carbohydrates, proteins, choline, and carnitine that are not completely digested and absorbed in the small intestine can enter the colon and undergo further microbial degradation. Dietary fiber and resistant starch mainly generate short-chain fatty acids such as acetate, propionate, and butyrate. Tryptophan can be converted into indole, indole-3-propionic acid, indole-3-acetic acid, indole-3-lactic acid, tryptamine, skatole, and other metabolites. Choline and carnitine can be converted into trimethylamine, which is subsequently oxidized in the liver to trimethylamine N-oxide.

1.2 Metabolites Formed Through Microbial Modification of Host-Derived Substances

Bile acids, amino acid derivatives, and other endogenous compounds synthesized by the host and secreted into the intestinal lumen can undergo microbial deconjugation, dehydroxylation, oxidation-reduction, and epimerization. Bile acids are representative of this category. After primary bile acids synthesized by the liver enter the intestine, microbial enzymes can convert them into deoxycholic acid, lithocholic acid, and other secondary bile acids, thereby expanding the structural and functional diversity of the host bile acid pool.

1.3 Metabolites Synthesized Directly by the Gut Microbiota

Certain intestinal bacteria can use nitrogen sources, carbon sources, and other precursors to synthesize branched-chain amino acids, polyamines, and vitamins de novo. These metabolites participate in microbial energy metabolism and community competition and may also be absorbed by the host to influence protein synthesis, cell proliferation, redox homeostasis, and immune function.

Figure 1 Formation pathways of gut microbiota-derived and microbiota-modified metabolites

Table 1 Major Sources of Gut Microbiota-Derived Metabolites

2 Gut Microbiota-Derived Metabolites Originating From Dietary Substrates

2.1 Production and Host Utilization of Short-Chain Fatty Acids

(1) Formation of Short-Chain Fatty Acids

Short-chain fatty acids are mainly produced by colonic anaerobic bacteria through fermentation of dietary fiber, resistant starch, and certain oligosaccharides. Acetate is generally the most abundant, followed by propionate and butyrate. Different microbial groups possess distinct substrate-utilization and metabolic cross-feeding capacities. For example, some bacteria first degrade complex polysaccharides and release lactate or acetate, which are subsequently converted into butyrate by other microbial populations.

(2) Local and Systemic Energy Metabolism

Butyrate is an important energy substrate for colonic epithelial cells and supports epithelial metabolism and the low-oxygen environment of the intestinal lumen through mitochondrial oxidation. Acetate and propionate can enter the portal circulation and participate respectively in peripheral-tissue metabolism and hepatic gluconeogenesis, lipid metabolism, and related processes.

(3) Receptor and Epigenetic Regulation

Short-chain fatty acids can act on G protein-coupled receptors including FFAR2, FFAR3, and HCAR2 and can alter chromatin accessibility by inhibiting histone deacetylases. These mechanisms jointly influence epithelial-cell differentiation, hormone secretion, immune-cell activation, and inflammatory mediator expression.

2.2 Effects of Short-Chain Fatty Acids on the Intestinal Barrier and Immune Responses

Butyrate can promote tight-junction protein expression, mucus production, and epithelial-cell differentiation, thereby reducing intestinal permeability. Short-chain fatty acids can also regulate macrophages, dendritic cells, neutrophils, innate lymphoid cells, and T cells. Under homeostatic conditions, butyrate and propionate generally support regulatory T-cell differentiation and restrict excessive inflammation, although their effects vary according to the tissue environment, metabolite concentration, and type of immune stimulus.

2.3 Formation of Tryptophan Metabolites

Tryptophan released during dietary protein degradation can be converted by different microbial populations into diverse indole derivatives. Common metabolites include indole, indole-3-propionic acid, indole-3-acetic acid, indole-3-lactic acid, indoleacrylic acid, tryptamine, and skatole. The metabolite profile is determined by microbial tryptophanases, aminotransferases, decarboxylases, reductases, and related enzymes.

2.4 Regulation of Host Physiology by Tryptophan Metabolites

(1) Regulation of the Intestinal Epithelial Barrier

Indole, indole-3-propionic acid, and indoleacrylic acid can influence tight junctions, mucus secretion, and epithelial stress responses and thereby help maintain the intestinal mucosal barrier. Their protective effects are generally associated with epithelial receptor activation, antioxidant responses, and suppression of inflammatory signaling.

(2) AhR-Mediated Immune Regulation

Indole-3-lactic acid, indole-3-acetic acid, and other aromatic metabolites can act as aryl hydrocarbon receptor ligands and regulate innate lymphoid cells, dendritic cells, macrophages, and different T-cell subsets. AhR signaling can promote IL-22 production and epithelial repair, although different ligands vary in affinity, stability, and cell-type selectivity.

(3) Intestinal Neuroendocrine Regulation

Tryptamine can affect enterochromaffin cells and enteric nervous system activity, promote serotonin-associated signaling, and regulate gastrointestinal motility. Indole can also influence intestinal endocrine L-cell function and glucagon-like peptide-1 release, although the specific effect depends on metabolite concentration and exposure duration.

(4) Systemic Metabolic Effects

Some tryptophan metabolites are absorbed through the intestinal epithelium and enter the circulation. Indole-3-propionic acid has antioxidant and barrier-protective effects, whereas indoxyl sulfate formed from hepatic metabolism of indole can accumulate markedly during renal impairment and exert oxidative, endothelial-damaging, and proinflammatory effects.

2.5 The Choline- and Carnitine-Derived TMA-TMAO Metabolic Axis

Choline, phosphatidylcholine, and L-carnitine can be metabolized by certain gut microorganisms into trimethylamine. Trimethylamine enters the liver through the portal vein and is mainly oxidized by flavin-containing monooxygenases to trimethylamine N-oxide. Circulating TMAO levels are jointly influenced by dietary composition, gut microbial composition, hepatic enzyme activity, and renal clearance.

Elevated TMAO is associated with cardiovascular, renal, and metabolic disease risk, but its biological significance cannot be determined from a single plasma measurement. Renal function, age, medication use, and dietary sources can all affect TMAO levels. Relevant studies should therefore interpret TMAO in the context of host metabolic status and microbial function.

3 Gut Microbiota-Mediated Bile Acid Transformation

3.1 Primary Bile Acid Synthesis and Enterohepatic Circulation

Bile acids are synthesized from cholesterol in hepatocytes and are generally conjugated with glycine or taurine before secretion into bile. After food intake, bile acids enter the small intestine and participate in the emulsification and absorption of lipids and fat-soluble vitamins. Most bile acids are reabsorbed in the terminal ileum through the apical sodium-dependent bile acid transporter and return to the liver through the portal circulation, forming the enterohepatic cycle.

3.2 Microbial Bile Acid-Transforming Enzymes

(1) Bile Salt Hydrolases

Bile salt hydrolases remove glycine or taurine from conjugated primary bile acids and generate unconjugated bile acids. Deconjugation alters bile acid solubility, absorption efficiency, and subsequent microbial conversion pathways.

(2) Hydroxysteroid Dehydrogenases

Hydroxysteroid dehydrogenases catalyze oxidation, reduction, and epimerization of bile acid hydroxyl groups, generating bile acid isomers with different hydroxyl configurations.

(3) 7α-Dehydroxylation Enzyme Systems

Certain anaerobic bacteria carrying bile acid-inducible gene clusters can convert cholic acid and chenodeoxycholic acid into deoxycholic acid and lithocholic acid, respectively. This process is an important source of secondary bile acids.

3.3 Bile Acid Receptor Signaling

Bile acids are not only involved in lipid absorption but also function as important signaling molecules. Farnesoid X receptor mainly regulates bile acid synthesis, transport, and hepatic-intestinal metabolism, whereas TGR5 participates in energy expenditure, incretin secretion, and immune responses. Different primary and secondary bile acids have distinct receptor-activating capacities. Consequently, microbiota-induced changes in the bile acid profile can alter host metabolic and immune status.

3.4 Bidirectional Biological Effects of Secondary Bile Acids

Appropriate levels of secondary bile acids can participate in receptor signaling, colonization resistance, and immune-homeostasis regulation. However, excessive accumulation of hydrophobic bile acids such as deoxycholic acid and lithocholic acid may cause membrane injury, oxidative stress, and inflammation. Their final biological effects depend on molecular species, concentration, conjugation status, tissue localization, and host clearance capacity.

4 Metabolites Synthesized by the Gut Microbiota

4.1 Branched-Chain Amino Acids

Certain gut microorganisms can synthesize leucine, isoleucine, and valine. Branched-chain amino acids are important substrates for protein synthesis and energy metabolism and can influence cell growth through pathways such as mTOR. Elevated circulating branched-chain amino acid levels are associated with metabolic abnormalities including insulin resistance, but their sources include dietary intake, host protein breakdown, and microbial synthesis. Changes in blood levels therefore cannot be attributed directly to the gut microbiota alone.

4.2 Polyamines

Putrescine, spermidine, and spermine can be produced by both host cells and the gut microbiota. Polyamines carry multiple positive charges and can interact with nucleic acids, proteins, and phospholipids, participating in cell proliferation, translational regulation, oxidative stress, and mucosal repair. Polyamine deficiency may impair barrier regeneration, whereas excessive production may support abnormal cell proliferation.

4.3 Microbially Derived Vitamins

The gut microbiota can synthesize certain forms of vitamin K and B vitamins, including folate, biotin, riboflavin, and cobalamin-related compounds. These vitamins primarily support microbial metabolism, although a proportion may be used by the host. Their actual contribution depends on the site of synthesis, site of absorption, microbial-community structure, and dietary intake.

Table 2 Representative Gut Microbiota-Derived Metabolites and Their Major Host Effects

5 Regulation of the Immune System by Gut Microbiota-Derived Metabolites

The intestinal mucosa contains abundant immune cells and lymphoid tissues and is an important interface through which the host recognizes food antigens, commensal microorganisms, and pathogens. Gut microbiota-derived metabolites regulate epithelial cells, macrophages, dendritic cells, innate lymphoid cells, B cells, and T cells and thereby control immune tolerance, inflammatory responses, and tissue repair.

5.2 Short-Chain Fatty Acids and Immune-Cell Differentiation

Butyrate and propionate influence regulatory T cells, helper T cells, and myeloid cells through receptor signaling and histone deacetylase inhibition. Short-chain fatty acids can also promote IL-22 production by certain innate lymphoid cells and CD4+ T cells, thereby strengthening the mucus layer, antimicrobial peptide production, and epithelial repair.

Short-chain fatty acids do not exert exclusively anti-inflammatory effects under all conditions. Infection status, tumor type, local oxygen tension, and metabolite concentration can alter their effects on T-cell differentiation and cytokine production.

5.3 Tryptophan Metabolites and AhR Signaling

Microbially derived indole derivatives can activate AhR in immune and epithelial cells and regulate IL-22, IL-17, and genes involved in barrier repair. Some metabolites suppress NF-κB-associated inflammatory responses, whereas others may become toxic at high concentrations or when host clearance is impaired. Tryptophan-metabolism studies should therefore measure metabolite identity, tissue concentration, and host-derived downstream metabolites.

5.4 Bile Acids and Immune-Cell Function

Different bile acids and their derivatives can affect dendritic cells, macrophages, natural killer T cells, and different CD4+ T-cell subsets. Some bile acid metabolites restrict inflammatory T-cell differentiation or promote regulatory T-cell formation, whereas excessive hydrophobic bile acids can damage epithelial cells and induce inflammation. The bile acid profile is more informative for immune regulation than total bile acid concentration alone.

6 Gut Microbiota-Derived Metabolites and Tumor Immunity

6.1 Effects of Intestinal Metabolites on Antitumor Immunity

Gut microbiota-derived metabolites can influence antitumor immunity by altering dendritic-cell maturation, CD8+ T-cell activation, natural killer-cell function, and the state of tumor-associated myeloid cells. These metabolites can also reach tumor tissues through the circulation and alter nutrient competition, epigenetic states, and immune-cell effector functions within the tumor microenvironment.

6.2 Butyrate and CD8+ T-Cell Antitumor Responses

Butyrate can alter the transcriptional program of CD8+ T cells through metabolic and epigenetic regulation. In certain tumor models, butyrate increases expression of effector-associated factors such as ID2, promotes cytotoxic molecule production, and enhances the antitumor activity of CD8+ T cells.

The effects of butyrate on tumor immunity are context-dependent. Excessively high concentrations, different administration routes, and the local metabolic environment of the tumor may produce different outcomes. Intestinal-lumen concentrations, peripheral-blood concentrations, and tumor-tissue exposure should therefore be distinguished.

6.3 Cytotoxic T-Cell Reprogramming Mediated by Butyrate and Valerate

Butyrate and valerate can enter activated T cells and influence acetyl-CoA metabolism, histone acetylation, and transcription of effector genes. In certain experimental models, both metabolites enhance cytokine release and cytotoxicity of cytotoxic T lymphocytes and chimeric antigen receptor T cells, providing a basis for investigating the use of microbial metabolites to improve cellular therapy.

6.4 Tryptophan Metabolites and Chemotherapy Responses

Certain indole metabolites can alter chemotherapy responses by regulating neutrophils, macrophages, oxidative stress, and drug-response pathways. Under specific microbial and chemotherapy conditions, indole-3-acetic acid can enhance treatment responses in pancreatic ductal adenocarcinoma models. However, this effect depends on the specific drug combination, microbiota composition, and host metabolic environment and cannot be directly generalized to all tumors.

6.5 Bile Acids and the Tumor Immune Microenvironment

Secondary bile acids can influence the immune microenvironment of hepatic and intestinal tumors through nuclear receptors, membrane receptors, and cellular stress pathways. Some bile acids suppress inflammatory mediators or alter natural killer T-cell recruitment, whereas other hydrophobic bile acids may promote tissue injury and tumor-associated inflammation. Specific bile acid molecules should therefore be analyzed rather than comparing total bile acid levels alone.

6.6 Boundaries of Interpretation in Cancer-Treatment Research

The effects of gut microbiota-derived metabolites on cancer therapy are jointly regulated by diet, antibiotics, host genetic background, tumor type, and treatment regimen. Metabolite concentrations in feces do not fully represent actual exposure in the intestinal epithelium, blood, or tumor tissue. Studies should combine microbial functional genes, targeted metabolomics, receptor expression, and immune-cell phenotyping and should avoid inferring causality from a single microbial genus or metabolite.

Table 3 Major Effects of Gut Microbiota-Derived Metabolites on Tumor Immunity

7 Products for Research on Gut Microbial Metabolism and Host Effects

Gut microbiota-derived metabolites connect intestinal microorganisms with host organs through the intestinal epithelium, immune cells, and the circulation. Short-chain fatty acids, tryptophan derivatives, and secondary bile acids are major molecular classes in current research on microbial metabolism and tumor immunity. Their effects are jointly determined by metabolite concentration, host status, and the local tissue environment.

References

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[2] Yang W, et al. Intestinal Microbiota-Derived Short-Chain Fatty Acids Regulate Immune Cell IL-22 Production and Gut Immunity. Nat Commun. 2020;11(1):4457.

[3] Scott SA, et al. Microbial Tryptophan Metabolites Regulate Gut Barrier Function via the Aryl Hydrocarbon Receptor. Proc Natl Acad Sci U S A. 2020;117(32):19376–19387.

[4] Shao J, et al. Synergistic Anti-Inflammatory Effect of Gut Microbiota and Lithocholic Acid on Liver Fibrosis. Inflamm Res. 2022;71(10–11):1389–1401.

[5] He Y, et al. Gut Microbial Metabolites Facilitate Anticancer Therapy Efficacy by Modulating Cytotoxic CD8+ T Cell Immunity. Cell Metab. 2021;33(5):988–1000.e7.

[6] Luu M, et al. Microbial Short-Chain Fatty Acids Modulate CD8+ T Cell Responses and Improve Adoptive Immunotherapy for Cancer. Nat Commun. 2021;12(1):4077.

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