LPS plays a critical role in the onset and progression of NAFLD (Carpino et al., 2020; Ji et al., 2020). Following intestinal barrier damage, LPS translocates into the portal circulation. By binding to Toll-like receptor 4 (TLR4) on HSCs and KCs, it activates the NF-κB signaling pathway, promoting the expression of inflammatory factors and fibrogenic factors, thereby exacerbating hepatic inflammation and fibrosis (Reid et al., 2016). Beyond TLR4, LPS can also bind to lipopolysaccharide-binding protein (LBP), facilitating the formation of the CD14-TLR4 complex and further enhancing inflammatory responses (Csak et al., 2011). Studies demonstrate that blocking the LPS-TLR4 signaling pathway or reducing plasma LPS levels with polymyxin B significantly alleviates liver injury and steatosis in mice (Pappo et al., 1992; Xu et al., 2023). LPS also accelerates hepatic fibrosis progression by upregulating TGF-β expression, activating the small mother against decapentaplegic (Smad) pathway, and promoting transcription of type I and III collagen (Zhong et al., 2022). For instance, Escherichia coli-derived LPS activates macrophages via the TLR4 pathway, exacerbating liver injury, whereas inhibition of this pathway markedly mitigates hepatic lesions (Carpino et al., 2020). On the other hand, LPS also participates in immunomodulatory processes and can induce endotoxin tolerance. Through the LPS/TLR4 pathway, it promotes the expansion of monocyte-derived myeloid-derived suppressor cells (mMDSCs) in the liver and downregulates T cell populations, thereby modulating local immune responses (Schneider et al., 2022). LPS promotes CD14⁺ CD8⁺ T cells to secrete protective cytokines such as IL-6 and IL-33, and influences immune cell chemotaxis (Pallett et al., 2023). These effects are closely associated with decreased TLR4 and IRAK expression, along with altered p65/p50 ratios in NF-κB (Fan and Cook, 2004).

Peptidoglycan (PG), derived from gut bacteria in the host intestinal tract, constitutes the core structural component of bacterial cell walls (Meroueh et al., 2006). The diversity of GM gives rise to various types of PG (Krueger et al., 1982). As microbe-associated molecular patterns (MAMPs), PG can activate pattern recognition receptors TLR2, NOD1, and NOD2, thereby eliciting immune responses (Wagner and Cresswell, 2012; Juárez-Verdayes et al., 2013). NOD1 recognizes iE-DAP fragments while NOD2 identifies MDP fragments; both receptors activate NF-κB/MAPK signaling pathways, promote hepatic inflammation, and contribute to NAFLD progression (Travassos et al., 2004; Al Nabhani et al., 2017; Keestra-Gounder and Tsolis, 2017). In immune regulation, NOD1 perceives nutritional signals and drives neutrophil migration toward the liver, exacerbating inflammatory reactions (Dharancy et al., 2010; Meli et al., 2014). Notably, during advanced NAFLD stages, NOD1 promotes OX40L expression through metabolic reprogramming, upregulates CD8⁺ T cell activity, and thereby enhances immune responses to combat HCC (Zhang F. et al., 2024). In contrast, NOD2 primarily maintains GM balance and epithelial barrier homeostasis (Balasubramanian and Gao, 2017). Its activation stimulates Paneth cells to produce antimicrobial peptides (e.g., α-defensins) and enhances mucus secretion by goblet cells, thereby restricting bacterial translocation (Tan et al., 2015). Furthermore, NOD2 participates in host defense by modulating the MDP–NF-κB axis while moderately suppressing excessive TLR2 activation, thus alleviating intestinal inflammation (De Bruyn and Vermeire, 2017), this mechanism has been explored for therapeutic application in Crohn’s disease (Al Nabhani et al., 2020). Metabolically, NOD1 activation promotes metabolic inflammation and insulin resistance, whereas NOD2 exhibits anti-inflammatory and metabolic protective effects. This process requires the involvement of Receptor-Interacting Serine/Threonine-Protein Kinase 2 (RIPK2) (Cavallari et al., 2020). Therefore, targeting the PG–NOD1/NOD2 signaling pathways may offer novel therapeutic strategies for NAFLD.

As PAMPs, bacterial DNA enters host endosomes through various endocytic pathways. Within endosomes, TLR9 recognizes bacterial DNA-derived CpG oligonucleotides, initiating the MAPK/NF-κB pathway and triggering inflammatory factor secretion (Gomes et al., 2016; Mridha et al., 2017). Moreover, TLR9 signaling can interfere with IRF7 phosphorylation through the IKKα–LC3 pathway, thereby inducing the production of Type I interferon (Hayashi et al., 2018). Additionally, the cyclic GMP–AMP synthase (cGAS)–stimulator of interferon genes (STING) pathway can also recognize bacterial DNA (Zhang and Zhang, 2025). Bacterial DNA triggers dsDNA formation, which then activates cGAS by forming a complex. This activation generates the second messenger cGAMP, which binds to STING to activate TBK1. TBK1 phosphorylates both STING and the IRF3 transcription factor. Phosphorylated IRF3 induces Type I interferon synthesis, while STING accelerates NF-κB activation through IκBα phosphorylation (Zhang and Zhang, 2025). This collectively indicates that bacterial DNA can activate innate immune responses through multiple signaling pathways, playing a significant driving role in the onset and progression of NAFLD.

GM-derived EVs are bilayer membrane-structured nanoparticles released by bacteria, carrying substantial amounts of toxic microbial molecules. These particles can traverse the compromised intestinal barrier into circulation, target the liver, and participate in NAFLD pathogenesis by activating immune-inflammatory responses (Yáñez-Mó et al., 2015). Components such as LPS carried by EVs can enter the cytoplasm via the TLR4–TRIF–GBP3 pathway, activate Caspase-11, and induce inflammation through receptors including TLR2 and NOD1/2 (Bielig et al., 2011; Gu et al., 2019). Furthermore, EVs can promote hepatic inflammation and fibrosis through the TLR4 and NLRP3–GSDMD signaling pathways (Dorner et al., 2024). EVs derived from feces of NASH patients (NASH-fEVs) disrupt intestinal barrier integrity, increase permeability, and activate HSCs via the TLR/LPS pathway, thereby upregulating fibrosis-related protein expression (Fizanne et al., 2023). Notably, the impact of EVs on the liver is context-dependent: for instance, miRNA (miR-129-2-3p) derived from Fusobacterium nucleatum can exacerbate intestinal inflammation by promoting cellular senescence (Wei et al., 2023). Conversely, remodeling GM using the PPARα inhibitor GW6471—which increases the abundance of probiotics (e.g., Bacteroides) while reducing harmful bacterial populations—alleviates hepatic lipid accumulation, ferroptosis, and oxidative stress, thereby improving NAFLD (Yang X. et al., 2025). In summary, EVs exhibit dual roles in NAFLD, where their specific effects are contingent upon both their microbial origin and the host microenvironment. Further investigation into the immune-regulatory mechanisms of active components within EVs will help elucidate their pathological significance and therapeutic potential in NAFLD.

Intestinal tract commensal bacteria metabolize tryptophan (Trp) into various indole derivatives, including indole-3-acetic acid (IAA), indole-3-propionic acid (IPA), indole-3-aldehyde (IAld), indole-3-lactic acid (ILA), and tryptamine (Su et al., 2022). Different bacteria possess distinct tryptophan enzymes that produce specific indole derivatives (Dodd et al., 2017). Indole derivatives accumulate in the intestinal tract and activate the Aryl Hydrocarbon Receptor (AhR) on innate lymphoid cells, thereby promoting goblet cell differentiation and mucus secretion (Powell et al., 2020), and induce tight junction protein expression (Shimada et al., 2013), enhancing the integrity and functionality of the intestinal barrier. On the other hand, AhR is widely expressed in various immune cells, such as DCs, T cells, and lymphocytes (Nguyen et al., 2010; Rothhammer and Quintana, 2019), mediating the regulation of the immune system by indole derivatives, including promoting Treg differentiation (Goettel et al., 2016), inducing T cell apoptosis (Landfried et al., 2011), and suppressing the inflammatory activity of Th17 cells (Rothhammer and Quintana, 2019), thereby alleviating hepatic inflammation. Furthermore, indole derivatives (e.g., IAA and IPA) produced by specific strains (e.g., probiotics) inhibit the NF-κB pathway, reduce levels of pro-inflammatory factors (IL-8), and promote the release of anti-inflammatory factors (IL-10) (Bansal et al., 2010). Clinical studies have revealed decreased levels of IPA and IAA in the feces of NAFLD patients. Increasing the abundance of Bifidobacterium bifidum—the primary source of these metabolites—significantly ameliorates hepatic steatosis and inflammation in mice (Min et al., 2024). Furthermore, indole derivatives promote the proliferation of intestinal crypt epithelial-tubular cells in mice, which plays a critical role in maintaining intestinal immune homeostasis (Powell et al., 2020).

BAs are important signaling molecules generated through enzymatic conversion of cholesterol in the liver. By activating specific receptors, they regulate hepatic lipid metabolism and suppress the transcription of inflammatory factors, thereby influencing NAFLD progression. Among these, Farnesoid X Receptor (FXR) and Takeda G-protein Receptor 5 (TGR5) represent two critical BAs receptors (Chávez-Talavera et al., 2017). FXR plays a pivotal role in anti-inflammatory and immunomodulatory processes, BAs activate FXR to suppress NF-κB signaling, thereby reducing its induction of inflammatory mediators such as IFNγ and COX-2 (Wang et al., 2008). This downregulates monocyte chemoattractant protein-1 (MCP-1) expression, diminishing macrophage infiltration into the liver (Li et al., 2015). Simultaneously, FXR activation restores the intestinal vascular barrier by triggering the endothelial Wnt/β-catenin pathway, which blocks bacterial translocation and alleviates hepatic inflammation (Mouries et al., 2019). FXR signaling also acts on macrophages, NK cells, and DCs, restricting the production of pro-inflammatory factors and suppressing inflammasome activation (Sun et al., 2021; Fiorucci et al., 2022). Since TGR5 is widely distributed in cell types including HSCs, LSECs, and macrophages (Keitel et al., 2007). TGR5 activated by BAs promotes macrophage M2 polarization (Shao et al., 2022), inhibits the TLR4–NF-κB pathway (Biagioli et al., 2017; Hosseinkhani et al., 2021), suppresses NLRP3 inflammasome activation and IL-1β secretion through the cAMP–PKA signaling axis (Pols et al., 2011; Guo C. et al., 2016), and induces endothelial nitric oxide synthase (eNOS) expression to exert anti-inflammatory effects (Keitel et al., 2007). Additionally, TGR5 promotes the release of glucagon-like peptide-1 (GLP-1) in the intestinal tract, thereby improving insulin sensitivity and lipid metabolism (Thomas et al., 2009). Notably, BAs with different structures exhibit distinct effects, for example, 12α-hydroxylated BAs (12α-OH BAs) paradoxically promote HSCs proliferation by binding to TGR5. Simultaneously, they upregulate hepatic fibrosis-related proteins (α-SMA, TGF-ß, COL I, PDGF) and exacerbate fibrosis progression through activation of ERK1/2 and p38 MAPK signaling pathways (Xie et al., 2021).

SCFAs modulate immune and metabolic responses through multiple pathways, thereby influencing the progression of NAFLD. SCFAs promote proliferation of intestinal epithelial cells, enhance expression of tight junction proteins (e.g., ZO-1, occludin, claudin-1, and claudin-2), and activate hypoxia-inducible factor (HIF) to maintain intestinal barrier integrity (Nicolas and Chang, 2019). Butyrate also induces expression of the antimicrobial peptide β-defensin-1, reducing levels of LPS-carrying bacteria and LPS (Beisner et al., 2021). Furthermore, it inhibits the increase in intestinal permeability mediated through the TLR4/myeloid differentiation factor (MyD88) signaling pathway (Nighot et al., 2017). SCFAs deficiency impairs barrier function by causing inadequate energy supply to intestinal epithelium and disrupting mucosal immune homeostasis (Matsumoto et al., 2017).

Secondly, SCFAs regulate immune cell function through G protein-coupled receptors (GPRs) and Toll-like receptors (TLRs) (Canfora et al., 2015). For instance, butyrate promotes anti-inflammatory factor IL-10 secretion and Treg differentiation via GPR109a, while suppressing release of inflammatory factors such as IL-1β, IL-6, and TNF-α through TLR4 (Feingold et al., 2014; Sam et al., 2021). SCFAs also promote Treg differentiation via epigenetic mechanisms including HDAC inhibition and enhanced histone H3 acetylation in the Foxp3 promoter region, thereby ameliorating hepatic inflammation (Furusawa et al., 2013; Park et al., 2015). Supplementation of butyrate-producing Clostridium butyricum B1 (CB) in the NASH mouse model reversed HFD-induced hepatic steatosis, suppressed hepatic MCP-1 and TNF-α expression, reduced pro-inflammatory factors (IFN-γ and IL-17) in both liver and intestinal tract, and increased anti-inflammatory factors (FOXP3⁺, IL-4, and IL-22). These findings were corroborated by in vitro experiments (Zhou et al., 2017).

Additionally, SCFAs intervene in NAFLD through energy metabolism regulation. SCFA supplementation ameliorated hepatic steatosis in mice (Shimizu et al., 2019). Acetate and propionate stimulate peptide YY (PYY) and insulin-like growth factor-1 (IGF-1) release via GPR41/43, thereby suppressing appetite and energy intake. Concurrently activates AMP-activated protein kinase (AMPK) to reduce lipid accumulation (Deng et al., 2020). Sodium butyrate regulates hepatic lipid metabolism by promoting GLP-1 secretion from intestinal L cells (Zhou et al., 2018). Clostridium butyricum capsules combined with rosuvastatin demonstrate superior efficacy over monotherapy in lipid regulation, anti-fibrotic effects, and liver function improvement (Zhu et al., 2022). Notably, acetate promotes liver regeneration by inducing SCD1 expression (Yin et al., 2023), providing novel directions for NAFLD treatment.

Circulating TMAO levels exhibit positive correlations with NAFLD incidence risk, disease severity, and all-cause mortality (Flores-Guerrero et al., 2021). TMAO promotes NAFLD progression through multiple mechanisms. TMAO elevates mitochondrial ROS levels, activates the NF-κB signaling pathway, thereby promoting NLRP3 inflammasome assembly and the release of inflammatory factors such as IL-1β. It also disrupts calcium homeostasis in pancreatic β-cells, leading to dysfunction (Kong et al., 2024). Secondly, TMAO impairs intestinal barrier function by suppressing the Wnt/β-catenin pathway and activating TLR4/MyD88/NF-κB signaling. Simultaneously, it induces LSEC dysfunction and capillarization, while promoting macrophage M1 polarization (Nian et al., 2024). Research reveals that TMAO activates the PERK signaling pathway in zebrafish liver and HepG2 cells, inducing pathological alterations including lipid accumulation, inflammation, and fibrosis (Yang et al., 2024). TMAO triggers endoplasmic reticulum stress (ERS), activates macrophages via the TLR pathway, and exacerbates inflammatory responses (Hakhamaneshi et al., 2021). Concurrently, TMAO suppresses BAs synthesis, disrupts cholesterol metabolism, aggravates intrahepatic lipid accumulation, promotes foam cell formation, and inhibits reverse cholesterol transport (RCT), thereby further compromising hepatic lipid homeostasis (Janeiro et al., 2018). Reduced TMAO synthesis can lower the risk of NAFLD onset and progression (Corbin and Zeisel, 2012).

Berberine (BBR), a natural metabolite derived from Coptis chinensis Franch., alleviates hepatic inflammation by targeting GM. Administration of BBR (40 mg/kg) to NAFLD mouse models increased the relative abundance of Akkermansia and Bacteroides at the genus level, while decreasing the relative abundance of Lactobacillus and Romboutsia (Yang et al., 2022). BBR supplementation elevated intestinal Bifidobacterium abundance and Bacteroidetes/Firmicutes ratio in NASH mouse models, concurrently reducing serum concentrations of inflammatory factors including IL-1, IL-6, TNF-α, and CD14 (Cao et al., 2016). The study also found that BBR supplementation reduced the abundance of F. prausnitzii (Li et al., 2017). Regarding intestinal barrier function, BBR promotes the expression of tight junction proteins (ZO-1 and Occludin), increases the number of colonic glands and mucus secretion by goblet cells, reduces translocation of Gut-Derived LPS to the liver, and alleviates hepatic inflammation (Chen D. et al., 2023; Chen et al., 2023 Y.). Beyond regulating GM, BBR exerts effects through direct anti-inflammatory and anti-fibrotic mechanisms, including inhibition of JNK1 signal transduction (Guo T. et al., 2016) and downregulation of TLR4/MyD88/NF-κB pathway activity (Wang L. et al., 2020), reducing the expression and activity of neutrophil elastase (NE), upregulating α1-antitrypsin (α1-AT), and inhibiting the CXCR4/CXCL12 axis (Yang et al., 2017), as well as inducing apoptosis of HSCs and suppressing their proliferation (Eissa et al., 2018). Animal studies demonstrate that BBR supplementation (200 mg/kg/d) significantly alleviates hepatic inflammation and steatosis in HFD-induced NASH mouse models, with these effects closely linked to GM modulation and intestinal barrier repair. (Cao et al., 2016). A clinical trial involving 184 NAFLD patients further confirmed that oral BBR administration (1.5 g/d for 16 weeks) significantly reduced hepatic fat content, lipid parameters (TG, TC), and liver enzyme levels (ALT, AST), while exhibiting a favorable safety profile (Yan et al., 2015). BBR demonstrates promising therapeutic potential for NAFLD/NASH prevention and treatment through multi-target modulation of GM, enhancement of barrier function, and suppression of inflammatory signaling pathways and fibrotic progression.

Resveratrol (RSV), a natural polyphenolic metabolite primarily extracted from Reynoutria japonica Houtt., exhibits antioxidant, anti-apoptotic, and anti-inflammatory properties (Tian and Liu, 2020). As a natural agonist of silent information regulator 1 (SIRT1), RSV ameliorates hepatic lesions by exerting anti-inflammatory and anti-fibrotic effects through multiple pathways. In hepatocytes, RSV significantly alleviates hepatic inflammation by activating the AMPKα–SIRT1 signaling pathway to inhibit the NF-κB inflammatory pathway (Tian et al., 2016). Simultaneously, RSV induces apoptosis of activated HSCs and suppresses their activation in a dose-dependent manner via the SIRT1 and JNK signaling pathways, thereby reversing hepatic fibrosis (Zhang et al., 2022). On the other hand, RSV also exerts significant regulatory effects on immune cells. It interferes with interferon-gamma (IFN-γ)-mediated macrophage activation by inhibiting the JAK/STAT-1 pathway, consequently reducing the production of inflammatory mediators such as nitric oxide (NO), IP-10, and MIG, while downregulating the expression of inducible nitric oxide synthase (Chung et al., 2011). Additionally, RSV promotes macrophage polarization toward the M2 anti-inflammatory phenotype and upregulates IL-10 synthesis, thereby alleviating fibrosis (Yu et al., 2019; Jin et al., 2025). Furthermore, RSV inhibits NF-κB nuclear translocation and reduces inflammatory factor release by disrupting crosstalk between the TLR2/MyD88/ERK and NF-κB/NLRP3 inflammasome pathways, thereby delaying the progression of hepatic fibrosis (Lei et al., 2025). Regarding intestinal effects, RSV not only remodels GM and enhances microbial diversity but also strengthens intestinal mucosal barrier function by upregulating tight junction proteins (Occludin, ZO-1, and Claudin1). It concurrently suppresses mRNA expression of cannabinoid receptor type 1 (CB1), further consolidating its protective effects along the gut-liver axis (Chen et al., 2020).

Supplementation with RSV (50/75/100 mg/kg/d) significantly reduced hepatic steatosis and fibrosis in HFD-induced NASH rats, with the ameliorative effect demonstrating dose dependency. RSV restructured the GM composition in NASH rats. At the species level, the abundance of Akkermansia muciniphila increased; at the genus level, Bacteroides abundance increased while Desulfovibrio abundance decreased; at the family level, Ruminococcaceae and Lachnospiraceae abundances increased. However, these GM alterations were not observed in the low-dose RSV group (50 mg/kg/d) (Campbell et al., 2019). The study also found that RSV supplementation reduced the abundance of harmful bacteria Desulfovibrio, Lachnospiraceae_NK4A316_group, and Alistipes in the intestinal tract, while increasing the abundance of SCFA-producing bacteria Allobaculum, Bacteroides, and Blautia (Wang P. et al., 2020). An RCT involving 60 NAFLD patients demonstrated that 3 months of RSV supplementation (300 mg/d) significantly reduced serum levels of ALT, AST, TC, and TNF-α (Chen et al., 2015).

Curcumin (Cur), a natural metabolite extracted from Curcuma longa L., exhibits multiple biological activities including antioxidant, anti-inflammatory, and antitumor effects. Cur intervenes in NAFLD progression through multiple mechanisms, including anti-inflammatory effects, regulation of lipid metabolism, improvement of insulin resistance, and modulation of fibrotic processes (Li X. et al., 2024). In recent years, its role in modulating GM has garnered increasing attention. Studies demonstrate that Cur significantly increases Bacteroides abundance and ameliorates hepatic lipid accumulation through microbiota-dependent BAs metabolism (He et al., 2024). In NAFLD models, Cur reverses the elevated Firmicutes/Bacteroidetes ratio and reduced Akkermansia abundance (Hong et al., 2022), while concurrently upregulating expression of tight junction proteins Occludin and ZO-1, suppressing TLR4/NF-κB pathway activation, and reducing LPS exposure, thereby alleviating hepatic inflammation (Hong et al., 2022). Further studies (Li S. et al., 2021; Hong et al., 2022) confirmed that Cur effectively ameliorated hepatic steatosis and reduced serum LPS levels in HFD-fed mice. This protective mechanism correlates with modulation of GM composition, specifically manifested through: decreased Firmicutes/Bacteroidetes ratio and reduced Desulfovibrio abundance, alongside elevated abundance of Akkermansia and multiple SCFA-producing genera including Bacteroides, Parabacteroides, Alistipes, and Alloprevotella. Cur supplementation (200 mg/kg/d for 16 weeks) significantly alleviated hepatic steatosis and oxidative stress in HFD-fed mice, mediated through multiple pathways (Yang J. et al., 2025). Cur enhanced the alpha-diversity of the GM. At the family taxonomic level, a significant increase in the abundance of Coriobacteriaceae was observed. At the genus level, the abundance of Mailhella and Parabacteroides increased, while that of Alistipes decreased. At the species level, the abundance of Phocaeicola vulgatus and Bacteroides intestinalis rose, whereas Acutalibacter muris abundance declined, thereby reducing the synthesis of enterogenic toxins. Simultaneously, Cur inhibits the JNK2/FOXO1/Bcl6 signaling axis to alleviate lipid accumulation (Yang J. et al., 2025). Moreover, Cur suppresses M1 polarization of macrophages and reduces the secretion of IL-1β and TNF-α (Tong et al., 2021). By promoting PPARα mRNA m6A methylation through inhibition of FTO protein, it activates the PPARα/CPT1α pathway to enhance fatty acid β-oxidation (Fan et al., 2025b), regulates AMPK, ChREBP, and SREBP1-c expression to ameliorate lipid metabolism (Guariglia et al., 2023), downregulates CYP2E1 and C/EBPβ, reduces ROS generation, and alleviates oxidative stress (Afrin et al., 2017). A meta-analysis encompassing 1,028 NAFLD patients also demonstrated that curcumin effectively ameliorates hepatic steatosis (Ngu et al., 2022).

Quercetin (QUE), a metabolite isolated from Scutellaria baicalensis Georgi, intervenes in NAFLD through multiple pathways. QUE reverses HFD-induced GM dysbiosis, significantly lowering the Firmicutes/Bacteroidetes ratio and reducing the abundance of Gram-negative bacteria such as Helicobacter. This diminishes endotoxemia occurrence, ultimately suppressing TLR4/NF-κB signaling pathway activation and inflammasome initiation, thereby ameliorating hepatic inflammation (Porras et al., 2017). QUE supplementation also inhibits oxidative stress in hepatocytes by regulating cytochrome P450 2E1 (CYP2E1), thereby conferring hepatoprotective effects against NAFLD (Porras et al., 2017). Conversely, QUE inhibits the NF-κB p65/iNOS signaling pathway in a concentration-dependent manner and reduces serum TNF-α levels (Ying et al., 2013). It blocks phosphorylation of IκBα and NF-κB p65 while upregulating expression of superoxide dismutase (SOD) and glutathione peroxidase 1 (GPX1), thus systematically alleviating hepatic oxidative stress and excessive immune activation (Jiang et al., 2025). Furthermore, QUE can activate the antioxidant transcription factor Nrf2 and alleviate hepatic lipid accumulation, mitochondrial dysfunction, and oxidative stress through the AMPK-dependent autophagy pathway (Panchal et al., 2012; Cao et al., 2023).

The effect of QUE on ameliorating lipid metabolism is closely associated with its promotion of beneficial A. muciniphila proliferation. Indole-3-lactic acid (ILA), produced by this bacterium’s metabolism, upregulates CYP8B1 via the FTO/m6A/YTHDF2 pathway, driving cholesterol conversion into cholic acid (CA). The latter suppresses lipid accumulation through FXR receptor activation (Liu J. et al., 2025). A randomized controlled trial (n = 41) demonstrated the clinical value of QUE. NAFLD patients supplemented with 500 mg QUE daily for 12 weeks exhibited significant reductions in hepatic lipid content, body weight, and body mass index (BMI), with favorable safety profiles (Li N. et al., 2024).

Lycium barbarum polysaccharides (LBPs) constitute a key active metabolite in Lycium chinense Mill. LBPs delay NAFLD progression by modulating GM and enhancing barrier function. In NAFLD mouse models, LBPs reduce the relative abundance of Verrucomicrobia and Enterococcaceae (Gao et al., 2021), and the latter serves as the primary source of gut-derived LPS. This helps reduce the risk of LPS translocation and hepatic inflammation (Hu et al., 2020), while simultaneously increasing the abundance of Deferribacteres and butyrate-producing bacteria (such as Butyricicoccus and Butyricimonas) (Gao et al., 2021). Butyrate enhances the expression of intestinal mucus and tight junction proteins (ZO-1, occludin), thereby improving intestinal barrier function (Peng et al., 2007). The study (Ding et al., 2019) further confirmed that LBPs promote the proliferation of Bacteroides, Bifidobacterium, and SCFA-producing bacteria such as Phascolarctobacterium, Prevotella, and Collinsella. LBPs play a crucial role in inhibiting the progression of NAFLD.

Notably, the effects of LBPs on modulating GM are not solely determined by their metabolites; the structural domains of LBPs also exert influence. This structure-function relationship is particularly evident in Bacteroidetes and Parabacteroides. RG-I and its neutral sugar side chains increase the abundance of beneficial bacterial families such as Comamonadaceae; whereas linear homogalacturonan (HG) promotes the proliferation of potentially harmful bacterial families including Pseudomonadaceae, Xanthomonadaceae, Caulobacteraceae, and Oxalobacteraceae (Wei et al., 2025).

LBPs also stimulate putrescine secretion by murine GM, which subsequently inhibits the JAK2-STAT3 pathway via TRAF6-mediated suppression, thereby reducing Th17 cell differentiation and inflammatory factor release (Wang et al., 2025). Moreover, Th17 differentiation drives the progression from NASH to HCC, rendering the inhibition of this differentiation a crucial intervention strategy for NASH (Huang Y. et al., 2025). Supplementation with LBPs (100 mg/kg, 10 weeks) significantly alleviated liver injury, dyslipidemia, and inflammation in NASH rats. This effect was achieved by activating the AMPK/PPARα/PGC-1α pathway to promote hepatic lipid consumption (Li et al., 2022). LBP inhibited caspase-9/3 activity and TNF-α levels in CCl4-induced hepatic fibrosis mice, thereby mitigating hepatic inflammation and fibrosis (Chiang and Chao, 2018). A pre-post study also demonstrated that LBP supplementation (300 mg/day, 12 weeks) improved both GM diversity and liver function in NAFLD patients (Fan et al., 2025a).

Poria cocos polysaccharide (PCP) is a botanical drug-derived metabolite (Zhao et al., 2023). PCP increases the relative abundance of Faecalibaculum, reduces gut-derived LPS levels, thereby inhibiting the NF-κB/CCL3/CCR1 signaling pathway, alleviates hepatic inflammation, and delays NASH progression (Tan et al., 2022). Furthermore, PCP reduces hepatocyte apoptosis by suppressing the CYP2E1/ROS/MAPKs signaling pathway, and decreases the liver’s exposure risk in inflammatory environments through restoration of intestinal barrier function (Jiang et al., 2022). In both zebrafish and mouse NAFLD models, PCP demonstrated efficacy in counteracting hepatic steatosis (Ye et al., 2022). This beneficial effect stems from reducing translocation of gut-derived LPS to the liver and suppressing PARP-1-mediated pyroptosis in intestinal cells. Furthermore, PCP inhibited disease progression in methionine-choline-deficient (MCD)-induced NASH mice by downregulating expression of F4/80, CD68, IL-1β, CD11b, and CCL5 genes (Gao et al., 2023). Simultaneously, PCP alleviated hepatic steatosis in NAFLD mice by modulating glucose and lipid metabolism through upregulation of lipid transport proteins and suppression of lipid synthesis-associated proteins (Wang et al., 2022). PCP is even considered a prebiotic. Supplementation with PCP (50 mg/kg/d, for 8 weeks) can alleviate insulin resistance, lipid metabolism imbalance, and inflammation in the NASH mouse model. This effect stems from PCP enhancing the intestinal barrier, improving GM diversity, and increasing the relative abundance of probiotics including Lactobacillus, Allobaculum, and Phascolarctobacterium. These probiotics synthesize SCFAs, which subsequently ameliorate insulin resistance through the FGF21-PI3K/AKT signaling pathway (Liu et al., 2025b).

Ginsenoside (Rg) is a metabolite extracted from Panax ginseng C. A. Mey. Rg supplementation ameliorates hepatic steatosis and reduces hepatic inflammation in HFD-induced NAFLD mouse models, with its therapeutic effects on NAFLD being closely related to modulation of the GM-immune axis (Shi et al., 2024). Studies demonstrate that Rg can restructure GM composition, and this alteration proves beneficial to host health. At the phylum level, Bacteroidota abundance increases while the Firmicutes/Bacteroidetes ratio decreases; at the family level, Muribaculaceae abundance elevates; At the genus level, the relative abundances of Akkermansia, Parabacteroides, Lachnospiraceae_NK4A136_group, Oscillospira, Phascolarctobacterium, Bacteroides, and Dehalobacterium increased, while the relative abundances of Allobaculum and Olsenella decreased (Liang et al., 2021; Shi et al., 2024). Concurrently, Rg enhances intestinal barrier integrity by upregulating the expression of tight junction proteins (including ZO-1, Occludin, and Claudin-1), thereby reducing the translocation of Gut-Derived LPS. Furthermore, Rg reduces LPS levels and inhibits the TLR4/NF-κB signaling pathway, consequently decreasing the production of pro-inflammatory factors and suppressing macrophage activation and inflammatory cell infiltration in the liver, ultimately alleviating hepatic inflammation (Liang et al., 2021).

Beyond the intestinal tract, Rg delays NAFLD progression by multi-target regulation of lipid metabolism. Regarding lipid metabolism, Rg reduces lipid uptake through suppression of CD36 expression (Wu et al., 2025) while activating the hepatic LKB1/AMPK/mTOR signaling pathway (Shi et al., 2024). This dual action cooperatively downregulates key lipid synthesis genes (e.g., SREBP-1c, FAS, ACC) and upregulates the fatty acid oxidation gene CPT-1a, thereby significantly ameliorating hepatic lipid accumulation (Liang et al., 2021; Shi et al., 2024). Furthermore, activated AMPK exerts hepatoprotective effects through metabolic and anti-inflammatory mechanisms: it inhibits mTORC1 and SREBP-1c to reduce lipid synthesis, while suppressing NF-κB signaling and oxidative stress via the sirtuin 1/FOXO1 pathway (Wu et al., 2025). Notably, lipid overload can induce ferroptosis, thereby driving the progression of NAFLD (Chen et al., 2022). Rg effectively enhances antioxidant capacity by activating the Keap1/Nrf2 signaling pathway and preserving mitochondrial structural and functional integrity, consequently inhibiting ferroptosis (Liu et al., 2025c). Significantly, the anti-ferroptosis effect of Rg markedly diminished following antibiotic intervention, indicating its dependence on GM involvement. This demonstrates that Rg primarily suppresses NAFLD development through multiple pathways by modulating the “GM–immune inflammation” axis while synergistically improving lipid metabolism and antioxidant pathways.

Pachymic acid (Pac) is a metabolite derived from Wolfiporia cocos (F. A. Wolf) Ryvarden & Gilb. Pac supplementation alleviated hepatic inflammation in HFD-induced NAFLD mouse models (Ren et al., 2025a). Pac reshaped the GM structure in NAFLD mice, reversing HFD-induced intestinal dysbiosis. At the phylum level, the Firmicutes/Bacteroidetes ratio decreased. At the genus level, the abundance of Akkermansia increased, while Desulfovibrio and Streptococcus decreased. Furthermore, Pac reduced the expression of hepatic inflammatory factors by suppressing the LPS/TLR4/MYD88/NFκB pathway, thereby mitigating liver inflammation. Pac inhibits the expression of lipid synthesis-related proteins including FASN, SREBP1c, and SCD1, while promoting the expression of fatty acid oxidation-related proteins such as PPARα and CPT1α, thereby reducing hepatic inflammation induced by lipid accumulation. Studies demonstrate that Pac ameliorates HFD-induced NAFLD through synergistic multi-pathway effects. In animal models, Pac supplementation (20/40 mg/kg for 4 weeks) significantly alleviates hepatic steatosis, reduces serum lipid levels, and improves liver function (Ren et al., 2025b). On one hand, Pac upregulates the expression and activity of PPARα, thereby promoting hepatic fatty acid oxidation to accelerate lipid consumption. Additionally, activated PPARα upregulates GPX4 protein expression, thus inhibiting ferroptosis. On the other hand, Pac downregulates TFR1 protein expression by inhibiting the MAPKs signaling pathway, consequently reducing Fe³⁺ uptake and intracellular Fe²⁺ accumulation in hepatocytes. This suppresses the Fenton reaction and further alleviates hepatocellular ferroptosis. Through multiple mechanisms including promoting lipid metabolism, inhibiting inflammation, and suppressing ferroptosis, Pac collectively delays the progression of NAFLD.