Clin Mol Hepatol > Volume 31(2); 2025 > Article |
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Class | Metabolite | Effect | Mechanism | Pathway | Reference |
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Bile acids | Unconjugated bile acids | Impair gut epithelial barrier | Occludin dephosphorylation and tight junction rearrangement | Activation of EGFR/Src kinase pathway in intestinal epithelial cells | [40] |
Disrupt hepatic lipid metabolism | Suppress intestinal FXR activity | Inhibition of FXR-FGF15 signaling in enterocytes | [48] | ||
Conjugated bile acids | Protect gut epithelial barrier | Form micelles to sequester unconjugated bile acids | A signaling-independent and physicochemical way | [41] | |
Secondary bile acids | Impair enterohepatic circulation and inhibit hepatic FXR activation by inducing ileitis | CD8+T cell-mediated ileitis | Activation of TGR5/mTOR/oxidative phosphorylation signaling pathway in CD8+T cells | [49] | |
SCFAs | Propionate | Protect gut mucus layer and epithelial barrier | - | - | [42] |
Alleviate alcohol-induced liver injury | Alleviate endoplasmic reticulum stress | Activation of major urinary protein 1 in hepatocytes | [47] | ||
Butyrate | Protect gut epithelial barrier | Enhance O2 consumption and stabilize HIF-1 by uncompetitively inhibiting HIF prolyl hydroxylases | - | [43,44] | |
Tryptophan derivatives | Indole | Alleviate hepatic steatosis and inflammation | Upregulate PFKFB3 expression and suppress pro-inflammatory activation in macrophage | Activation of AhR signaling pathway in macrophages | [50] |
Indole-3-acetatic acid | Protect gut immune barrier | Upregulate intestinal IL-22 and REG3G expression | Activation of AhR signaling pathway in ILC3s | [45,51] | |
Alleviate hepatic inflammation and cytokine-mediated lipogenesis | Reduce pro-inflammatory cytokines expression and migration of macrophages; downregulate FASN and SREBP-1c expression in hepatocytes | Activation of AhR signaling pathway in hepatocytes | [52] | ||
Indole-3-propionic acid | Protect gut epithelial barrier and alleviate hepatic inflammation | Upregulate expression of tight junction proteins and reduce production of pro-inflammatory cytokines in macrophages | - | [46] | |
Indole-3-aldehyde | Trigger Tet2 deficiency-associated AIH | Induce IFNγ-producing CD8+T cell differentiation | Activation of AhR signaling pathway in CD8+ T cells | [53] | |
Tryptamine | Alleviate hepatic inflammation | Reduce pro-inflammatory cytokines expression and migration of macrophages | - | [52] | |
Others | N,N,N-trimethyl-5-aminovaleric acid | Promote hepatic steatosis | Reduce carnitine synthesis by competitively inhibiting γ-butyrobetaine hydroxylase, and decrease fatty acid oxidation | - | [54] |
AhR, aryl hydrocarbon receptor; AIH, autoimmune hepatitis; CLDs, chronic liver diseases; EGFR, epithelial growth factor receptor; FASN, fatty acid synthase; FGF15, fibroblast growth factor 15; FXR, farnesoid X receptor; HIF-1, hypoxia-inducible factor; IFNγ, interferon-γ; IL-22, interleukin-22; ILC3s, type 3 innate lymphoid cells; mTOR, mammalian target of rapamycin; PFKFB3, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3; REG3G, regenerating islet-derived 3 gamma; SCFAs, short-chain fatty acids; SREBP1, sterol regulatory element-binding transcription factor 1; TGR5, Takeda G-protein-coupled receptor 5.
Etiologies | Study design and participants detail |
Microbial alterations and summary of results |
Reference | ||
---|---|---|---|---|---|
Diversity | Taxonomic changes | Functional shifts | |||
MASLD-related HCC | |||||
MASLD-cirrhosis | • Cohort study of fecal microbiota and microbial metabolites in patients with MASLD | • HCC vs. controls | • HCC vs. cirrhosis | The abundance of many bacterial genes involved in SCFA synthesis (pycA, pta, ptb, frd, sucC) was increased in MASLD-HCC patients, as well as elevated levels of SCFAs (acetate, butyrate and formate) in the faeces and serum. | [7] |
• Decreased | • Family: Enterobacteriaceae ↑ | ||||
• Patients with MASLD-HCC (n=32) | • HCC vs. cirrhosis | • Species: Bacteroides caecimuris ↑, Veillonella parvula ↑ | |||
• Patients with MASLD-cirrhosis (n=28) | • Not significant | • HCC vs. controls | |||
• Non-MASLD controls (n=30) | • Family: Oscillospiraceae ↓, Erysipelotrichaceae ↓ | ||||
• Species: Bacteroides xylanisolvens ↑, Ruminococcus gnavus ↑, Clostridium bolteae ↑ | |||||
MASLD-cirrhosis | • Cohort study of fecal microbiota in patients with MASLD-related cirrhosis | • HCC vs. cirrhosis | • HCC vs. cirrhosis | Akkermansia was positively correlated with fecal calprotectin. Bacteroides was associated with IL-8 and IL-13, activated circulating monocytes and MDSC. | [88] |
• MASLD patients with cirrhosis and HCC (n=21) | • Not significant | • Family: Bacteroides ↑, Ruminococcaceae ↑ | |||
• MASLD patients with cirrhosis without HCC (n=20) | • Genus: Enterococcus ↑, Phascolarctobacterium ↑, Oscillospira ↑, Bifidobacterium ↓, Blautia ↓ | ||||
• Healthy controls (n=20) | |||||
MASLD | • Cohort study of fecal microbiota and serum bile acids in patients with MASH | • Non-cirrhotic HCC vs. HCC-cirrhosis | • Controls → MASH →HCC | Lactobacillus was associated with serum bile acid levels. | [89] |
• Patients with MASH without cirrhosis (n=23) | • Increased | • Genus: Bifidobacterium ↑, Lactobacillus ↓ | |||
• Patients with MASH and cirrhosis (n=11) | • MASH-HCC without cirrhosis vs. MASH-HCC with cirrhosis | ||||
• Patients with MASH-HCC without cirrhosis (n=14) | • Genus: Ruminococcus ↑ | ||||
• Patients with MASH-HCC with cirrhosis (n=19) | |||||
Hepatitis virus-related HCC | |||||
HBV | • Cohort study of fecal microbiota in patients with HBV infection and healthy controls | • Not mentioned | • HCC vs. controls | HCC vs. controls | [90] |
• Patients with HBV-HCC (n=124) | • Phylum: Proteobacteria ↑ | Increased amino acid metabolism | |||
• Healthy controls (n=91) | • Genus: Streptococcus ↑ | ||||
• Patients with HBV without cirrhosis (n=48) | • Between all groups | ||||
• Patients with HBV and cirrhosis (n=39) | • Streptococcus and Escherichia-Shigella display an ascending trend as the disease progresses from HBV to HCC. | ||||
HBV | • Cohort study of fecal microbiota and host transcriptome in patients with HBV-related HCC | • HCC vs. controls | • HCC vs. controls | The gut microbiota characterizing HBV-HCC was associated with tumor immune environment and bile acid metabolism. | [83] |
• Not significant | • Genus: Bacteroides ↑ | ||||
• Patients with HBV-HCC (n=113) | • Small HCC vs. non-small HCC | • Species: Lachnospiracea incertae sedis ↑, Clostridium XIVa ↑ | |||
• Subgroup: Small HCC (n=36) vs. non-small HCC (n=77), non-cirrhotic HCC (n=22) vs. cirrhotic HCC (n=91) | • Decreased | • Non-small HCC vs. small HCC | |||
• Genus: Bacteroides ↑, Parabacteroides ↑ | |||||
• Healthy controls (n=100) | • Species: Lachnospiracea incertae sedis ↑, Clostridium XIVa ↑ | ||||
HBV | • Meta-analysis of public gut microbiome datasets for HBV-related liver diseases and a cohort study for validation | • HCC vs. others | • HCC vs. controls | - | [91] |
• Decreased | • Genus: Lachnospiraceae_ND300 ↓, Eubacterium_ventriosum ↓ | ||||
• Meta-analysis: 139 controls, 133 chronic hepatitis B (CHB), 74 cirrhosis, 140 HCC | • HCC vs. CHB | ||||
• Validation cohort: 15 controls, 23 CHB, 20 cirrhosis, 22 HCC | • Genus: Lachnospiraceae ↓, Dorea ↓ | ||||
HCV | • Analysis of fecal microbiota in patients with HCV-related chronic liver disease (HCV-CLD) | • HCC vs. controls | • HCC vs. controls | HCC vs. HCV-CLD | [6] |
• Patients with HCV without HCC (n=21) | • Increased | • Species: 9 Streptococcus spp. ↑, 4 Lactobacillus spp. ↑, Bifidobacterium dentium ↑, Enterococcus faecalis ↑ | Increased amino acids metabolism and xenobiotics biodegradation | ||
• Patients with HCV and HCC (n=23) | • HCC vs. HCV-CLD | • HCC vs. HCV-CLD | |||
• Healthy controls (n=24) | • Increased | • Species: 4 Streptococcus spp. ↑, Lactobacillus salivarius ↑, Bifidobacterium pseudocatenulatum ↑ | |||
HCC developing from cirrhosis | |||||
Cirrhosis | • Cohort study of fecal microbiota in cirrhotic patients with early HCC | • HCC vs. cirrhosis | • HCC vs. cirrhosis | Butyrate-producing bacterial genera were decreased, while LPS-producing genera were increased. | [92] |
• Increased | • Phylum: Actinobacteria ↑ | ||||
• Patients with HCC (n=150) | • Genus: Gemmiger ↑, Parabacteroides ↑, Paraprevotella ↑ | ||||
• Patients with cirrhosis (n=40) | • HCC vs. controls | ||||
• Healthy controls (n=131) | • Genus: Verrucomicrobia ↓, Alistipes↓, Ruminococcus ↓, Phascolarctobacterium ↓, Klebsiella ↑, Haemophilus↑ | ||||
Cirrhosis | • 2 Cohorts of fecal microbiota in male patients with cirrhosis: a prior HCC cohort and a future HCC cohort | • Not significant | • HCC vs. cirrhosis | Increased amino acid metabolism and toluene metabolism as well as decreased metabolism of urea cycle intermediates | [93] |
• Cirrhotic patients with prior HCC (n=38)/ without prior HCC (n=38) | • Genus: Clostridium sensu stricto ↓, Anaerotruncus ↓, Raoultella ↑, Haemophilus ↑ | ||||
• Cirrhotic patients with future HCC (n=33)/ without future HCC (n=33) | |||||
Cirrhosis | • Cohort study of fecal fungi in cirrhotic patients | • HCC vs. controls | • HCC vs. others | - | [86] |
• Patients with HCC and cirrhosis (n=34) | • Decreased | • Malassezia ↑, Malassezia sp. ↑, Candida ↑, Candida albicans ↑ | |||
• Patients with cirrhosis | • HCC-cirrhosis vs. cirrhosis | ||||
• Healthy controls (n=18) | • Not significant | ||||
Cirrhosis | • Prospective cohort study of duodenal microbiota in patients with cirrhosis | • Not significant | • HCC vs. cirrhosis | - | [87] |
• Patients with cirrhosis (n=227) | • Family: Bacillacea ↓, Christensenellaceae ↓, Lactobacillaceae ↓ | ||||
• Patients developing HCC during the follow-up period (n=14) | • Genus: Listeria ↑, Gemella ↑, Alloprevotella ↑, Anaerostipes ↑ | ||||
Cirrhosis | • Cohort study of fecal microbiota and diet in HCC patients | • HCC-cirrhosis vs. cirrhosis | • HCC vs. controls | Consumption of artificial sweeteners was correlated with presence of A. muciniphila. | [94] |
• Patients with HCC and cirrhosis (n=30) | • Not significant | • Butyrate-producing bacteria ↓ | |||
• Patients with HCC without cirrhosis (n=38) | • HCC vs. controls | • HCC-cirrhosis vs. cirrhosis | |||
• Healthy controls (n=27) | • Decreased | • Genus: Clostridium ↑ | |||
• Species: Paraprevotella_CF321 ↑, Akkermansia muciniphila ↓ | |||||
Cirrhosis | • Cohort study of fecal microbiota | • HCC-cirrhosis vs. cirrhosis | • Non-cirrhotic HCC vs. others | - | [95] |
• Patients with HCC (n=75, 52 with cirrhosis and 23 without cirrhosis) | • Increased | • Genus: Intestinibacter ↑, Intestinimonas ↑ | |||
• Patients with cirrhosis (n=24) | • Non-cirrhotic HCC vs. HCC-cirrhosis | • HCC-cirrhosis vs. others | |||
• Healthy controls (n=20) | • Increased | • Genus: Blautia ↑ | |||
Cirrhosis | • Cohort study of fecal microbiota in patients with cirrhosis | • HCC vs. non-HCC | • Family: Bacteroidaceae ↑, Erysipelotrichaceae ↑, Prevotellaceae ↓, Leuconostocaceae ↓ | Enrichment of NOD-like receptor pathways | [96] |
• Cirrhotic patients with HCC (n=25) | • Increased | ||||
• Matched cirrhotic patients without HCC (n=25) | • Genus: Fusobacterium ↑, Odoribacter ↑, Butyricimonas ↑, Lachnospiraceae ↓ | ||||
Heterogenous HCC | |||||
Mixed | • Comparison of fecal microbiota between virus and non-virus-related HCC | • Higher in HBV-HCC | • Non-viral HCC vs. HBV-HCC | Non-viral HCC vs. HBV-HCC | [84] |
• Patients with HBV-HCC (n=35) | • Genus: Escherichia-Shigella ↑, Enterococcus ↑, Faecalibacterium ↓, Ruminococcus ↓, Ruminoclostridium ↓ | Reduced amino acid and glucose metabolism, high level of transport and secretion activity | |||
• Patients with non-hepatitis virus related HCC (n=22) | |||||
• Healthy controls (n=33) | |||||
Mixed | • Comparison of fecal microbiota between virus and non-virus-related HCC | • Higher in hepatitis virusrelated HCC | • Viral HCC vs. others | Non-viral HCC vs. viral HCC | [85] |
• Patients with virus-related HCC (n=33) | • Genus: Faecalibacterium ↑, Agathobacter ↑, Coprococcus ↑ | Reduced short-chain fatty acid-producing bacteria and declined fecal butyrate level | |||
• Patients with non-virus-related HCC (n=18) | • Non-viral HCC vs. others | ||||
• Healthy controls (n=16) | • Genus: Bacteroides ↑, Streptococcus ↑ Ruminococcus gnavus group ↑, Parabacteroides ↑, Erysipelatoclostridium ↑ | ||||
General characterization of gut microbiome in HCC | |||||
Mixed | • Cohort study of fecal microbiota and liver transcriptome | • HCC vs. cirrhosis | • HCC vs. MASLD | Several host genes, such as MT1B, were associated with specific microbial genera when comparing HCC to cirrhosis and MASLD. | [97] |
• Patients with MASLD (n=21) | • Not significant | • SCFAs-producing genera (Blautia and Agathobacter) ↓ | |||
• Patients with cirrhosis (n=27) | • HCC vs. MASLD | ||||
• Patients with HCC (n=111) | • Decreased | ||||
Mixed | • Cohort study of fecal microbiota in patients with primary liver cancer | • Decreased | • Phylum: Actinobacteria ↓, Firmicutes ↓, Bacteroidetes ↑ | - | [98] |
• Patients with HCC (n=143) | • Genus: Faecalibacterium ↓, Lachnospiraceae ↓, Streptococcus ↑, Collinsella ↑, Akkermansia ↑ | ||||
• Healthy controls (n=40) | |||||
Mixed | • Analysis of fecal microbiota | • Not mentioned | • HCC/CLD vs. controls | - | [99] |
• Patients with HCC (n=21) | • Phylum: Firmicutes ↓, Proteobacteria ↑ | ||||
• Patients with CLD (n=11) | • Genus: Blautia ↓ | ||||
• Healthy controls (n=9) | |||||
Not mentioned | • Analysis of fecal microbiota in elderly patients with HCC | • Decreased | • Genus: Blautia ↓, Anaerostipes ↓, Fusicatenibacter ↓, Escherichia-Shigella ↑, Fusobacterium ↑, Megasphaera ↑, Veillonella ↑ | Reduced enrichment in metabolic process, such as amino acid metabolism | [100] |
• Patients with HCC (n=25) | |||||
• Healthy controls (n=21) | |||||
Not mentioned | • Analysis of fecal microbiota | • Not significant | • Genus: Veillonella ↑, Lachnospiraceae ↑, Ruminococcaceae UCG-014 ↑, Peptostreptococcaceae ↓, Citrobacter ↓, Romboutsia ↓ | - | [101] |
• Patients with HCC (n=21) | |||||
• Healthy first-degree relatives (n=21) | |||||
Intrahepatic CCA | |||||
Not mentioned | • Cohort study of fecal microbiota in patients with ICC | • ICC vs. others | • ICC vs. others | Lactobacillus and Alloscardovia were positively correlated with the plasma-stool ratio of tauroursodeoxycholic acid in ICC patients. | [102] |
• Patients with ICC (n=28) | • Increased | • Genus: Lactobacillus ↑, Actinomyces ↑, Peptostreptococcaceae ↑, Alloscardovia ↑ | |||
• Patients with HCC (n=28) | |||||
• Patients with cirrhosis (n=16) | |||||
• Healthy controls (n=12) | |||||
Not mentioned | • Cohort study of fecal microbiota in patients with primary liver cancer | • Not significant | • ICC vs. others | The gut microbiota of patients with ICC displayed increased amino acid metabolism, nucleotide metabolism and glycolysis pathways. | [103] |
• Patients with ICC (n=19) | • Species: Veillonella atypica ↑, V. parvula ↑, Streptococcus parasanguinis ↑, Ruminococcus gnavus ↓ | ||||
• Patients with HCC (n=25) | |||||
• Healthy controls (n=76) | |||||
Not mentioned | • Cohort study of fecal microbiota in patients with primary liver cancer | • ICC vs. controls | • ICC vs. others | - | [98] |
• Patients with ICC (n=46) | • Not significant | • Phylum: Firmicutes ↓, Bacteroidetes ↑ | |||
• Patients with HCC (n=143) | • Genus: Muribaculaceae ↑, Escherichia Shigella ↑, Klebsiella ↑, Megamonas ↓ | ||||
• Healthy controls (n=40) | |||||
General characterization of gut microbiome in CCA | |||||
Not mentioned | • Cohort study of fecal microbiota in patients with CCA | • Not significant | • Phylum | - | [104] |
• Patients with CCA (n=22) | • Firmicutes ↓, Actinobacteriota ↓, Proteobacteria ↑, Bacteroidetes↑ | ||||
• Healthy controls (n=16) | • Genus | ||||
• Bifidobacterium ↓, Klebsiella ↑ | |||||
Not mentioned | • Cohort study of fecal microbiota in patients with CCA | • CCA vs. controls | • CCA vs. cholelithiasis | - | [105] |
• Patients with CCA (n=53) | • Not significant | • Bacteroides ↑, Muribaculaceae↑, Muribaculum ↑, Alistipes ↑ | |||
• Patients with cholelithiasis (n=47) | • CCA vs. cholelithiasis | • CCA vs. controls | |||
• Healthy controls (n=40) | • Increased | • Faecalibacterium ↓, Burkholderia-Caballeronia-Paraburkholderia ↓, Ruminococcus ↓ |
CCA, cholangiocarcinoma; CLDs, chronic liver diseases; HBV, hepatitis B virus; HCC, hepatocellular carcinoma; ICC, intrahepatic cholangiocarcinoma; IL-8, interleukin-8; MASH, metabolic dysfunction-associated steatohepatitis; MASLD, metabolic dysfunction-associated steatotic liver disease; MDSCs, myeloid-derived suppressor cells; SCFAs, short-chain fatty acids; -, not available.
Models | Description | Liver disease | HCC/CCA development | Microbial alterations | Reference |
---|---|---|---|---|---|
HFHC diet | High fat and high cholesterol diet (HFHC, 43.7% fat, 36.6% carbohydrate, 19.7% protein, 0.203% cholesterol) | MASLD-HCC | 14 mo | Gut dysbiosis and altered gut bacterial metabolites such as increased taurocholic acid and decreased 3-indolepropionic acid. | [15] |
DEN | i.p. injection of DEN (40 mg/kg) weekly | Chemical carcinogens-induced HCC | 14 wk | Gut dysbiosis characterized by decreased probiotics such as Lactobacillus and Bifidobacterium. | [59] |
DEN+CCL4 | i.p. injection of DEN (100 mg/kg) at ages 6-14 weeks followed by 6-12 biweekly i.p. injections of CCL4 0.5 mL/kg in C3H mice | Chemical carcinogens-induced HCC | 54 wk | Gut microbiota contributed hepatocarcinogenesis through LPS-induced TLR4 activation. | [57] |
DEN+HFHC diet | Single injection i.p. DEN (25 mg/kg)+HFHC diet | MASLD-HCC | 26 wk | Gut dysbiosis characterized by depletion of Bifidobacterium pseudolongum. | [109] |
DEN+CDHF diet | Single injection i.p. DEN (25 mg/kg)+choline deficient and high fat diet (CDHF, 60 kcal% fat, no choline) | MASLD-HCC | 28 wk | - | |
STAM | Single subcutaneous injection of 200 μg streptozotocin (STZ) at 4 days after birth+high fat diet at 4 weeks of age | MASH-HCC | 16 wk | Gut dysbiosis characterized by reduction in A. muciniphila. | [110] |
DSS+CDHF diet | Intermittent administration of 1% dextran sodium sulfate (DSS) in the drinking water+CDHF diet | MASH-HCC | 12 wk | Gut dysbiosis | [58] |
DMBA+HFD | Single application of 50 μl 0.5% DMBA (7,12-dimethylbenz [a]anthracene) in acetone+high fat diet (HFD, 60% fat, 20% protein, 20% carbohydrates) | Obesity-HCC | 30 wk | Gut dysbiosis characterized by increased gram-positive bacteria such as Clostridium, which may result in an increase of DCA. | [111] |
MUP-uPA mice+HFD | Overexpression of major urinary protein-urokinase plasminogen activator (MUP-uPA)+high fat diet | MASH-HCC | 32 wk | Gut dysbiosis | [112] |
Tlr5 KO+ICD | TLR5 deficient mice are fed with inulin-containing-diet (ICD, 7.5% inulin and 2.5% cellulose) | Cholestatic HCC | 6 mo | Gut dysbiosis characterized by increased fiber-fermenting bacteria and proteobacteria. | [106] |
NEMOΔhepa/Nlrp6−/− mice | Deletion of NF-kB essential modulator (NEMO) and NOD-like receptor family pyrin domain containing 6 (NLRP6) | MASH-HCC | 52 wk | Gut dysbiosis characterized by reduction in A. muciniphila. | [113] |
Hydrodynamic transfection+BDL | Hydrodynamic injection of plasmids encoding activated AKT and YAP+bile duct ligation (BDL) | PSC-CCA | 3 wk | Gut dysbiosis | [114] |
Hydrodynamic transfection+Mdr2 KO | Hydrodynamic injection of plasmids encoding activated AKT and YAP+deletion of multidrug resistance protein 2 (Mdr2) | PSC-CCA | 3 wk | Gut dysbiosis | [114] |
CCA, cholangiocarcinoma; CCl4, carbon tetrachloride; CDHF, choline-deficient high-fat; DCA, deoxycholic acid; DEN, diethylnitrosamine; HCC, hepatocellular carcinoma; HFHC, high fat and high cholesterol; MASH, metabolic dysfunction-associated steatohepatitis; MASLD, metabolic dysfunction-associated steatotic liver disease; PSC, primary sclerosing cholangitis; -, not available.
Bixiang Zhang
https://orcid.org/0000-0002-1609-7260
Zhao Huang
https://orcid.org/0000-0002-1151-4942