ABSTRACT
The gut microbiota significantly influences hepatobiliary cancer therapeutics. Growing evidence indicates that shifts in the gut microbial ecosystem are hallmarks of hepatocellular carcinoma and cholangiocarcinoma, strongly correlating with tumor development, therapeutic resistance, and patient survival. The composition of gut microbiota has emerged as a biomarker associated with treatment outcomes across various modalities, including chemotherapy, radiotherapy, targeted therapy, and immunotherapy. Beneficial bacterial communities enhance antitumor immunity, while pathogenic taxa are linked to reduced therapeutic efficacy. Multi-omics analyses have identified microbial metabolite signatures, such as short-chain fatty acids and bile acids, as potential targets for boosting antitumor responses. This review highlights the transformative potential of leveraging the gut microbiota to enhance precision oncology in hepatobiliary cancer. Future directions should prioritize personalized microbiota modulation approaches, combinatorial therapies targeting gut-liver axis crosstalk, and large-scale validation of microbial biomarkers across diverse populations.
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Keywords: Gastrointestinal microbiome; Hepatobiliary cancer; Immunosuppression therapy; Therapeutic resistance
BACKGROUND OF HEPATOBILIARY CANCER
Hepatobiliary cancer represents a formidable challenge in oncology. For decades, liver cancer has exhibited the most rapid increase in mortality rates, marked by its aggressive nature, propensity for metastasis, and resistance to conventional treatment modalities [
1-
4]. Two primary forms of hepatobiliary cancer have been identified: hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA). The former is the dominant form of hepatobiliary cancer, accounting for approximately 80–90% of tumors, whereas the latter, due to its highly aggressive nature and drug resistance, contributes significantly to its alarming mortality rate, accounting for approximately 2% of all cancer-related deaths worldwide annually [
5].
The increasing incidence of HCC is attributed to the increasing prevalence of key risk factors such as viral hepatitis, alcohol consumption, and metabolic syndrome. In more than half of HCC patients globally, hepatitis B virus (HBV) infection is detected, and hepatitis C virus (HCV) infection is present in approximately 20% of patients [
6]. Long-term alcohol consumption is a well-established risk factor for alcoholic liver disease (ALD) [
7]. A systematic review involving 148,333 patients from 18 studies revealed that individuals with ALD had a cumulative incidence of HCC ranging from 1% at 1 year to 8% at 10 years [
8]. Metabolic dysfunction associated fatty liver disease (MAFLD), having key factors such as obesity and type 2 diabetes, can progress to nonalcoholic steatohepatitis [
9,
10]. MAFLD increases the risk of HCC through chronic inflammation, oxidative stress, and fibrosis, which promote DNA damage and carcinogenesis, particularly in cirrhotic livers [
11].
Based on the anatomical location, CCA can be classified into two main types—intrahepatic CCA (ICCA) and extrahepatic CCA (ECCA)—where the former is situated proximally to the second-order bile ducts within the liver parenchyma and represents 10% of all CCA cases [
12]. The major risk factor for CCA is liver flukes,
Opisthorchis viverrine, which are commonly observed in Southeast Asia [
13]. Other risk factors, such as primary sclerosing cholangitis (PSC), bile duct stones and choledochal cysts, also contribute to carcinogenesis [
12].
Recent scientific endeavors have revealed the profound impact of the gut microbiota on hepatobiliary cancer progression and therapeutic responses [
14-
16]. The human intestinal microbiome, which comprises trillions of microorganisms, exerts multifaceted influences on host metabolism, immune function, and disease pathogenesis, encompassing not only obesity but also cancer development [
17]. Emerging evidence underscores the pivotal role of the gut microbiome in modulating hepatobiliary diseases through the intricate gut‒liver axis [
18]. Experimental investigations have elucidated how disturbances in the gut microbial composition, known as dysbiosis, can exacerbate hepatic inflammation, steatosis, and fibrosis, thereby creating a favorable milieu for tumorigenesis [
19-
22]. In this review, we explore the dynamic shifts in the gut microbiota composition associated with HCC and CCA arising from liver disease. We also examine the impacts of traditional therapies and immunotherapies on the gut microbiota and its derived metabolites. Furthermore, we discuss the emerging potential of modulating the gut microbiome and its metabolites as a therapeutic strategy to increase treatment efficacy and improve patient outcomes. By highlighting these interactions, we aim to provide new insights into the gut‒liver axis and its role in advancing personalized medicine for hepatobiliary cancer.
GUT MICROBIOTA AND DERIVED METABOLITE CHANGES IN HEPATOBILIARY DISEASE-LINKED HCC AND CCA
HCC
Emerging evidence underscores that gut dysbiosis—characterized by shifts in microbial diversity and abundance—induces correlated alterations in gut-derived metabolites and antigens, which collectively contribute to the pathogenesis of HCC across diverse etiologies including HBV, HCV, ALD, and MAFLD. In virus-related HCC, significant depletion of commensal genera such as
Turicibacter, Fecalibacterium, and
Blautia occurs alongside reductions in immunomodulatory metabolites like 4-hydroxyretinoic acid, which inversely correlates with serum aspartate aminotransferase (AST) levels and fibrosis severity (
Fig. 1) [
23-
27]. Similarly, in ALD,
Streptococcus overgrowth exacerbates liver injury, while MAFLD-HCC patients exhibit marked decreases in short-chain fatty acid (SCFA)-producing
Firmicutes and increased proteobacterial taxa [
28-
31]. These dysbiotic profiles can also be distinguished between viral (HBV/HCV) and non-viral HCC, with NBNC-HCC showing unique enrichment in Bacteroides [
32]. Concomitant metabolic disruptions include reduced indole-3-propionic acid and fecal butyrate, and elevated lipopolysaccharide (LPS) and cytotoxic secondary bile acids, driven by loss of commensal gut bacteria [
32-
34]. Such shifts not only reflect disease progression but also correlate with clinical biomarkers like serum LPS binding protein and intestinal fatty acid binding protein, indicating gut barrier dysfunction [
32].
Mechanistically, gut dysbiosis fuels hepatic tumorigenesis through three interlinked pathways: inflammation, metabolite-mediated oncogenesis and immune modulation. Indole-3-propionic acid depletion compromises intestinal barrier, permits microbial translocation of LPS and other pathogen-associated molecular patterns (PAMPs) [
33]. LPS activates hepatic toll-like receptor 4 (TLR4) signaling, triggering NF-κB-mediated proinflammatory cytokine production, which promotes hepatocyte damage, fibrosis, and oncogenic transformation [
26,
27,
32,
34]. Dysregulated microbial metabolites directly influence hepatic signaling; for instance, increased secondary bile acids such as deoxycholic acid (DCA) activate hepatic stellate cells and induce DNA damage via reactive oxygen species (ROS) [
35,
36]. In MAFLD-HCC, acetate produced by
Bifidobacterium pseudolongum suppresses tumor growth via GPR43-dependent inhibition of interleukin (IL)-6/janus activated kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) signaling, highlighting metabolite-specific protective roles [
37,
38]. Conversely, depletion of 4-hydroxyretinoic acid in HBV cirrhosis compromises retinoid-mediated anti-tumor surveillance [
23,
26,
39]. Dysbiosis skews peripheral and intrahepatic immunity; bacterial extracts from HBV-cirrhotic patients attenuate Th1 responses, and MAFLD-HCC microbiota promotes expansion of immunosuppressive Tregs and reduces cytotoxic CD8
+ T cells, fostering an immune-tolerant microenvironment conducive to tumor evasion [
23,
34,
39]. Thus, these mechanisms—spanning chronic inflammation, metabolic dysregulation, and immune dysfunction—establish the gut-liver axis as a pivotal orchestrator of HCC pathogenesis across etiological spectra.
ICCA originates in the bile ducts within the liver itself and is characterized by the malignant transformation of the cells that line the intrahepatic bile ducts [
40]. These cancerous cells can invade nearby liver tissue and may spread to other parts of the body over time. Liver fluke-induced ICCA is prevalent in regions endemic to
Opisthorchis viverrini and presents a distinct microbial landscape shaped by a chronic parasitic infection [
41-
43]. Notably,
O. viverrini infection increases the fecal genomic DNA content, which is indicative of microbial overgrowth [
44]. Studies in hamsters confirmed that
O. viverrini-infected hosts exhibit increased microbial diversity in colorectal feces, with the enrichment of
Ruminococcaceae, Lachnospiraceae, and
Enterobacteriaceae (
Fig. 1) [
45,
46]. Functionally,
O. viverrini-associated microbiomes exhibit upregulated amino acid catabolism pathways, including arginine and proline, leading to the accumulation of ammonia, which induces oxidative DNA damage and chromosomal instability [
44,
47]. The combined effects of persistent inflammation and oxidative stress create a permissive environment for the malignant transformation of cholangiocytes.
PSC and gallstones represent established precursors to ECCA, characterized by progressive microbial dysbiosis and metabolite imbalances. PSC is a chronic liver disease characterized by inflammation and fibrosis of the bile ducts, increasing the risk of ECCA [
48,
49]. In PSC, enrichment of
Veillonella and
Enterococcus genera in stool drives amine oxidase production, promoting lymphocyte adhesion to hepatic endothelia and perpetuating immune-mediated bile duct injury [
50,
51]. Concurrently, reduced SCFA-producing bacteria, such as
Faecalibacterium and
Coprococcus diminish antiinflammatory signaling, exacerbating Th17-driven inflammation and intestinal barrier integrity [
52,
53]. Gallstones similarly feature pathogenic microbial shifts, showing a significant rise in
Proteobacteria (phylum level) in the gut, indicating dysbiosis favoring opportunistic pathogens [
54]. Similarly, elevated Firmicutes/Bacteroidetes ratio (F/B ratio) can be served as a marker of gut dysbiosis linked to gallstone formation [
55]. These precursor states culminate in ECCA, where dysbiosis evolves toward
Fusobacterium, Prevotella, and
Campylobacter dominance with near-complete loss of SCFA producers correlating with tumor aggressiveness [
56,
57].
The convergence of microbial dysbiosis and metabolite imbalances synergistically drives hepatobiliary carcinogenesis through genotoxic, inflammatory, and metabolic mechanisms. Genotoxicity is directly mediated by bacterial products: gut-translocated
Escherichia coli-derived colibactin induces double-strand DNA breaks and chromosomal instability in biliary epithelial cells, initiating genomic instability characteristic of early tumorigenesis [
58]. PAMPs from translocating gut bacteria further exacerbate inflammation by compromising the gut barrier integrity, creating a self-sustaining loop of immune dysregulation [
59,
60]. Chronic inflammation, perpetuated by persistent dysbiosis, amplifies carcinogenic signaling via TLR4/NF-κB pathway activation [
61]. This upregulates IL-6 production, fostering a pro-tumorigenic niche that promotes cholangiocyte proliferation and survival [
62-
64]. In PSC,
Veillonella-induced lymphocyte adhesion and Th17 polarization sustain inflammatory injury, facilitating metastatic progression [
65]. Bile acid dysmetabolism critically contributes to oncogenesis: elevated LCA generates ROS, causing oxidative DNA damage and mitochondrial dysfunction, while reduced tauroursodeoxycholic acid (TUDCA) diminishes protective anti-apoptotic and anti-inflammatory signaling [
61,
66]. Other secondary bile acids like DCA additionally promote fibrosis and cellular senescence, creating a microenvironment conducive to malignant transformation [
67,
68]. Collectively, these interconnected mechanisms—genomic instability, chronic inflammation, and metabolic dysregulation—establish a permissive landscape for hepatobiliary tumor development and progression.
TRADITIONAL THERAPY
Understanding the influence of the gut microbiota on hepatobiliary cancer therapy is paramount due to its profound impact on therapeutic efficacy and toxicity. Emerging evidence indicates that microbial communities significantly modulate host systemic and local immune responses related to tumorigenesis, critically affecting the effectiveness of cancer therapies (
Fig. 2).
Patients with hepatobiliary cancers exhibit distinct gut microbiota profiles pre-surgery. In resectable ECCA, elevated
Bacteroidetes and depleted
Firmicutes/Actinobacteria correlate with poor prognosis, while metabolites like 4-hydroxyacetophenone and palmidrol independently predict survival [
57]. Antibiotic treatment prior to surgery leads to a dysbiosis status, with a profound population of aerobic bacteria such as
Proteobacteria and decreased
Firmicutes [
69,
70]. Compared to
Proteobacteria, Firmicutes is a typical SCFA producer, which leads to an acute decline in SCFAs in the environment [
71,
72].
Surgical interventions for hepatobiliary cancers, particularly hepatectomy, induce profound perturbations in the gut microbiota that exacerbate preoperative dysbiosis and impair postoperative recovery (
Table 1). The resection process itself disrupts the gut-liver axis, leading to an increase in
Proteobacteria and decrease in
Firmicutes [
69,
73,
74]. Concurrently, proteolytic bacteria such as
Bacteroides and Pantoea become enriched in patients who developed posthepatectomy liver failure (PHLF) postoperatively, driving organic acid metabolism that exacerbates hepatic oxidative stress and delays regeneration. These perturbations are positively correlated with total bilirubin, international normalized ratio, and albumin, suggesting the potential role of these bacteria in preventing and treating PHLF (
Fig. 3) [
26]. Post-surgery, metabolic pathways like the tricarboxylic acid cycle (TCA) cycle and glycolysis are upregulated in both the host and bacteria, suggesting a dynamic metabolite profile crucial for liver recovery [
74]. An alternative activation of macrophages is triggered by increased IL-25 levels in the tumor microenvironment (TME), subsequent to antibiotic treatment. This state is inversely correlated with the survival rate post-hepatectomy [
75].
The validation through a mouse model reinforces the assertion that the microbiota plays a crucial role in liver regeneration. Colonization with SCFA-producing bacteria mitigates the heightened mortality observed in germ-free mice post-hepatectomy. SCFAs are critical for hepatocyte proliferation through their role in hepatic lipogenesis and membrane phospholipid synthesis via upregulation of
FASN and
SCD1 genes [
69]. Additionally, surgery-induced intestinal barrier dysfunction facilitates the translocation of bacterial products like LPS into the portal circulation. Research has shown that LPS enhances the invasive ability of cancer cells through the TLR4/MyD88 signaling pathway (
Fig. 3) [
62-
64]. Although capable of activating the TLR4 pathway and downstream inflammation cascades, an optimal level of LPS can have a beneficial impact on liver regeneration by enhancing DNA replication [
76]. Notably, steroid hormone biosynthesis pathways (e.g., corticosterone synthesis) are upregulated post-hepatectomy, potentially modulating immune responses and compensatory hyperplasia [
74]. Furthermore, fecal microbiota transplantation (FMT) from patients with rapid recovery rescues SCFA production and hepatocyte proliferation in mouse model, highlighting the therapeutic potential of microbiota-targeted strategies to mitigate surgical stress [
77].
For patients with HCC presenting a single tumor less than 3 cm in size, surgical and locoregional therapies should be considered [
78]. As the tumor stage progresses, the utilization of chemotherapy and radiotherapy becomes increasingly important. Chemotherapeutic agents induce distinct shifts in the gut microbial diversity and composition in patients with HCC, with implications for both treatment efficacy and toxicity (
Table 1). Compared with tumor models and healthy controls, transarterial chemoembolization (TACE), a well-established locoregional therapy for HCC patients with contraindications for resection and thermal ablation, restores the levels of
Firmicutes, Bacteroidetes, Tenericutes, and
Synergistetes as time progresses after treatment [
78,
79]. Moreover, the concentrations of the microbial metabolite LPS decreased after TACE, suggesting the recovery of liver function.
Conversely, the administration of 5-fluorouracil (5-FU) and other chemotherapeutic agents, such as cisplatin and doxorubicin, is commonly associated with renal and liver toxicity, and these side effects occur alongside an imbalanced gut microbiota and decreased ecological diversity [
80]. 5-FU interacts with thymidylate synthase, forming a complex that hinders the production of deoxythymidine monophosphate, which is critical for DNA replication and repair [
81]. Owing to its distinctive structure, 5-FU can be mistakenly integrated into RNA and DNA instead of uracil or thymine, culminating in autophagic cell death [
82]. Both cisplatin and 5-FU have been documented to compromise gut permeability by reducing mucus production through the inhibition of goblet cells [
83]. This compromised gut barrier facilitates bacterial translocation and the movement of bacterial metabolites through the gut-liver axis [
84]. Additionally, Jin reported that the Chao 1 index tended to decrease in the 5-FU treatment group, indicating a reduced gut microbiota richness, despite no significant changes in the Simpson and Shannon indices between the HCC control group and 5-FU-treated group [
85]. At the phylum level, 5-FU treatment was associated with increased abundances of
Proteobacteria and
Epsilonbacteraeota. In healthy humans,
Proteobacteria is typically present at low levels, and its expansion is often linked to dysregulated innate immune responses. For example, both TLR-5- and IL-10-deficient mice exhibit a proinflammatory environment that promotes the overgrowth of
Proteobacteria, ultimately leading to spontaneous colitis [
86-
88]. Bile salts, the final products of cholesterol metabolism, acquire specific hydrophilic and hydrophobic functions by binding Na+ and K+ ions through conjugation facilitated by microbiota [
89]. Research has shown that the conjugated bile acid (BA) glycochenodeoxycholic acid promotes the proliferation of HCC cells in vivo while significantly inhibiting the effect of 5-FU [
90].
Concurrently, cisplatin exacerbates HCC dysbiosis by increasing the abundances of
Escherichia, Parabacteroides, and
Ruminococcus, most of which are gram-negative bacteria known for their high production of LPS [
91,
92]. Dysbiosis also leads to a decrease in the bacterial metabolite palmitic acid, which promotes the phosphorylation of protein kinase C (PKCζ) and integrin β1, thereby favoring the phosphoinositide 3-kinases (PI3K)/protein kinase B (AKT) pathway [
92].
The presentation of gut dysbiosis in doxorubicin -treated rat models of HCC is characterized by increases in operational taxonomic unit (OTU) numbers at the phylum level and the F/B ratio in fecal samples [
93]. Compared with no treatment, the administration of doxorubicin significantly reduced the abundances of bacterial species from two genera of
Firmicutes (unclassified
Lachnospiraceae and
Pseudoflavonifractor) and three genera of
Bacteroidetes (unclassified_
Porphyromonadaceae, Paraprevotella, and
Prevotella) and increased the abundances of
Clostridium cluster XIVa and
Oscillibacter. A reduction in the abundance of unclassified
Lachnospiraceae is linked to decreased butyric acid production, thereby promoting cancer growth [
94,
95]. The abundance of
Prevotella sp. is directly linked to the production of IL-9, which plays a crucial role in suppressing tumorigenesis in solid cancers [
96].
Clostridium cluster XIVa can generate secondary BAs via a 7α-dehydroxylation reaction, leading to decreased CXCL16 expression and the depletion of natural killer T cells, consequently facilitating tumor progression and growth [
18,
97,
98]. Such agent-specific microbiota disruptions highlight the delicate interplay between the therapeutic and toxic effects of chemotherapy, necessitating a deeper understanding of microbial ecology in treatment planning.
The administration of broad-spectrum anti-anaerobic antibiotics before and during 5-FU induces dysbiosis predicting poor prognosis in HCC patients independently, with significantly reduced progression-free survival (PFS) and overall survival (OS). This adverse outcome correlates directly with depleted abundance of
Blautia—a genus of anaerobic, SCFA-producing bacteria [
99].
In combination with the antioxidant curcumin, the chemosensitivity of 5-FU can be restored by increasing the abundance of probiotics such as
Bifidobacterium and
Lactobacillus, thereby inhibiting the PI3K/AKT/mTOR pathway in mouse model and in vitro cell model [
100,
101]. Doxorubicin paired with ZnCM-SD (a zinc-curcumin formulation) reverses HCC-associated dysbiosis by restoring
Prevotella sp. and depleting
Oscillibacter, normalizing the F/B ratio to increase intestinal barrier integrity [
93]. Moreover, the coadministration of probiotics (
Lactobacillus reuteri and
Clostridium butyricum) restores alpha diversity (Ace and Shannon indices) and attenuates cisplatin-induced microbial imbalances in rat model [
83]. These changes not only reduce the tumor burden but also mitigate treatment-related adverse events, such as mucosal damage, as evidenced by the upregulation of tight junction proteins (ZO-1 and occludin) [
102].
Radiotherapy is advised for patients who are ineligible for radical resection through surgery [
103]. This therapy is known to induce immunogenic cell death, triggering the activation of antitumor adaptive immunity through the process of tumor-associated antigen cross-priming [
104]. Following the engulfment of tumor antigens by antigen-presenting cells, apoptotic tumor cells stimulate CD8
+ cytotoxic T lymphocytes [
105]. This immune reaction can extend its influence to distant nonirradiated tumor sites, thereby inducing the abscopal effect [
106].
Li conducted experiments to examine the differences in the gut microbiota composition between HCC patients who respond to radiotherapy (R) and those who do not respond to radiotherapy (NR) [
107]. The study revealed that parameters measuring gut microbe diversity, such as the Chao, Shannon, and Simpson indices, were significantly lower in NR patients than in healthy controls and responders. Through principal coordinate analysis (PCoA) of microbiome polymorphisms, the R group presented a similar distribution to that of healthy controls, whereas the NR group presented a distinguishable microbial community. The family
Ruminococcaceae and the genus
Faecalibacterium were significantly enriched in the R group and healthy controls, whereas the NR group presented a notably higher abundance of the genus
Streptococcus. Further analysis of the mechanism by which the gut microbiome regulates radiosensitivity was conducted using a gut microbiome-depleted HCC mouse model [
107]. Following antibiotic treatment, mice experienced a rapid decrease in the number of gut bacteria, which counteracted the apoptosis induced by radiotherapy. FMT conducted before tumor establishment restored the elimination effect of radiotherapy and restored interferon (IFN)-γ levels in tumor tissues, a response that could be reversed by depleting CD8
+ T cells. A clinical immunohistochemistry analysis of tumor tissue also revealed that the R group presented a greater number of infiltrating CD8
+ T cells than the NR group, accompanied by an increased abundance of the genus
Faecalibacterium and decreased abundance of the genus
Streptococcus. Moreover, decreased levels of IFN-α and IFN-β, along with the expression of their corresponding interferon-stimulated genes, were observed in antibiotic-treated mice, suggesting that the impact of gut dysbiosis on radiotherapy may depend on dendritic cells. Consistent with the RNA-seq findings, reduced phosphorylation of STING, p65, IRF3, and TBK1 was evident in antibiotic-treated mice, indicating the suppression of the cGAS‒STING pathway. This modulation was facilitated through the bacterial metabolite c-di-AMP, which was more abundant in the R group than in the NR group, and thereby activated the STING pathway [
104].
However, the potential side effects resulting from radiation exposure to nontumor regions cannot be overlooked. Radiation exposure was found to promote high-fat diet-induced MAFLD in a dose-dependent manner, leading to carcinogenesis [
108]. A high level to low level of radiation leads to the increased accumulation of lipids in liver tissue than a low to high level of radiation in individuals consuming a Western diet, which is associated with worse liver function. These results can be explained by gut microbiota restructuring, with significant increases in the F/B ratio and the abundances of
Butyricococcus, and
Clostridiaceae (
Fig. 3). This shift activates INSR/PI3K/AKT signaling through a decrease in the levels of the anaerobic intestinal bacterial metabolite isocaproic acid during dietary fiber fermentation, alongside an increase in the levels of lithocholic acid [
109]. These findings highlight the possibility of predicting the response and deploying targeted interventions, transforming radiotherapy into a more precise and tolerable modality. Future research must validate these findings in diverse populations and elucidate the complex interplay between the diet, microbiota, and radiation dose optimization. Ultimately, a holistic approach integrating microbiota modulation into HCC treatment paradigms promises to unlock the full potential of radiotherapy, offering hope for patients with this formidable malignancy.
Similar to HCC, complete resection of diseased regions is the only way to achieve a cure in CCA patients, while palliative procedures, such as percutaneous transhepatic cholangial drainage (PTCD), are also commonly required to relieve obstructive jaundice [
110]. However, PTCD reduces the OS rates of CCA patients, accompanied by a marked reduction in
Escherichia-Shigella levels within fecal samples. The effect of
Escherichia-Shigella on cancer progression may either stimulate or impede tumor proliferation across various cancer subtypes [
111-
113]. Moreover, the use of antibiotics has been applied in the clinic, leading to a lower overall response rate (ORR) and shorter PFS in patients with CCA treated with a combination of chemotherapeutic agents and immune checkpoint inhibitors (ICIs) [
114]. While the report did not address the targeted depletion of specific bacterial strains, it focused on the timing of antibiotic administration. These findings highlight the microbiome‒metabolite axis as a critical regulator of the efficacy of standard therapy in patients with CCA.
Systemic chemotherapy and radiotherapy are recommended for patients who suffer from unresectable or metastatic CCA [
115]. Chemosensitivity in patients with CCA is mechanistically linked to intestinal microbial shifts and metabolite alterations. Despite the reduced microbial alpha diversity (Shannon and Simpson indices), the abundance of commensals such as
Actinobacteria is positively related to the chemosensitivity to gemcitabine and cisplatin [
116,
117]. However, the development of resistance during the treatment period remains a significant concern. In an ongoing study (n=17) investigating the combined response to cisplatin and gemcitabine in patients with ICCA, the resistant group presented increased abundances of
Ruminococcaceae, Oribacterium, Oxalobacter, and
Peptostreptococcus, which were associated with a shorter PFS of 6.6 months compared with 11.8 months in the responder group [
118]. Elevated
Oribacterium and
Peptostreptococcus levels can be used as diagnostic biomarkers for HBV-induced cirrhosis patients and patients with colorectal cancer [
119,
120].
Gemcitabine resistance is associated with significantly increased levels of metabolites, including acetylcholine, adenine, carnitine and inosine [
116]. The concentrations of acetylcholine and carnitine were also elevated in the cisplatin-resistant group, as well as heightened levels of alpha-D-glucose. Acetylcholine and carnitine are able to facilitate cancer development by inhibiting apoptosis and promoting cancer stem cell proliferation, respectively [
121,
122]. Adenine is able to promote the proliferation, invasion and migration of CCA cell lines by modulating long noncoding RNA fragments [
123]. Inosine, a metabolic product of adenosine, has a limited inhibitory effect on CCA cells [
124,
125]. These metabolites, as well as the bacterial community, could serve as biomarker panels to predict patient outcomes and suggest potential therapeutic strategies by targeting these metabolites to overcome chemoresistance and enhance therapeutic efficacy.
TARGETED THERAPY
Targeted therapies, such as sorafenib and lenvatinib, which are multitarget tyrosine kinase inhibitors (TKIs), have been used as either first- or second-line treatments to limit HCC progression. However, their benefits are constrained by intrinsic and acquired resistance, with only 30–40% of patients achieving disease control [
126].
The efficacy of sorafenib is influenced by the gut microbiota composition (
Table 2). The intestinal microbiota is able to produce β-glucuronidase (GUS), increasing the blood levels of sorafenib, which prolongs its effective period [
127]. Studies of patients with advanced HCC receiving sorafenib treatment have revealed that the composition of the gut microbiota can be utilized to differentiate therapeutic responsiveness [
128]. Compared with the responder group (R), patients who progressed after the administration of sorafenib had a significantly lower Chao1 index. Another study in 2020 further corroborated the relationship between sorafenib sensitivity and the complexity of the gut bacterial community [
129]. This shift in the microbial community is a particular marker of a greater abundance of probiotic
Lactobacillus species, including
Lactobacillus johnsonii, Lactobacillus murinus, and
L. reuteri, and
Bifidobacterium species [
130]. A study focusing on modulating the microbial composition via stigmasterol, a common unsaturated phytosterol found in plant oil and vegetable fats, reported a significantly higher Simpson index, suggesting that an increased diversity of the microbial community is associated with improved sorafenib performance [
131]. Conversely, dysbiosis characterized by a reduced microbial diversity or antibiotic-induced depletion of commensals diminishes the sorafenib response. For example, antibiotic therapy prior to sorafenib treatment is correlated with shorter PFS and median OS in the clinic [
132].
Lenvatinib has been approved as a first-line HCC treatment in the USA and China [
133,
134]. Its effect compared with that of sorafenib is supported by an open-label, phase 3, multicenter, noninferiority trial in patients with unresectable HCC [
135]. In terms of the primary endpoint of OS, lenvatinib achieved a noninferior but not superior effect to that of sorafenib. In terms of PFS, the time to treatment failure and maximum objective response rate, it was associated with significantly greater improvements than sorafenib. Higher alpha diversity and beta diversity in terms of the Shannon, Simpson and Chao indices were achieved after lenvatinib treatment in patients with primary liver cancer [
130].
Lenvatinib administration also significantly increased the relative abundances of the probiotics
Faecalibacterium and
Bifidobacterium while reducing the abundances of the pathogenic species
Bacteroides, Escherichia-Shigella, Prevotella, and
Eisenbergiella in liver cancer patients (
Fig. 3) [
136].
Eisenbergiella has been shown to be highly abundant in patients with poorly differentiated colorectal cancer and is associated with relatively high mortality rate, but its direct mechanism in cancer remains unclear [
137]. This shift is correlated with improved antitumor immune regulation, suggesting that lenvatinib-induced microbiota remodeling may explain its improved efficacy compared to sorafenib.
Microbial metabolites serve as molecular mediators of the gut‒liver axis, directly influencing drug pharmacokinetics and tumor biology. For example, an increase in the abundance of the probiotic
Faecalibacterium prausnitzii could promote butyrate production, inducing Foxp3 expression and blocking the downstream IL-6/STAT3/IL-17 signaling pathway, suggesting a synergetic effect with TKIs [
138-
140]. In a mouse model, the increased abundance of bacterial species in the R group, such as
Enterococcus faecium, enhanced the antitumor effects of sorafenib by expanding the number of IFN-γ
+CD8
+ T cells in the TME, triggering ferroptosis in cancer cells [
141]. This expansion can be explained by the secretion of the microbial metabolite exopolysaccharide by
E. faecium [
128,
142,
143]. These insights highlight the additional role of bacterial metabolites in modulating the host immune response, suggesting biomarkers for personalized therapy.
Despite the widespread use of first-line TKIs in HCC treatment, a significant number of patients fail to meet the criteria for their effective use in controlling cancer progression or experience progression on sorafenib or lenvatinib [
144]. Second-line options, such as regorafenib, have been introduced in clinical practice, supported by evidence of prolonged OS in a randomized, double-blind, placebo-controlled, phase III trial [
145]. In an HCC mouse model, however, regorafenib administration was associated with increased bacterial translocation, as evidenced by significantly elevated LPS levels [
146]. This finding suggests increased intestinal permeability, which is further supported by increased inducible nitric oxide synthase levels [
147,
148]. Together with elevated IL-6 levels, regorafenib promoted local inflammation via TLR4 pathway activation, inducing downstream tumor necrosis factor (TNF)-α production. Combined therapy with probiotics, including
Lactobacillus rhamnosus, improved gut permeability in the presence of reduced inducible nitric oxide synthase levels in mouse model. The anti-inflammatory effects of
L. rhamnosus were supported by decreased LPS and TNF-α levels, which is consistent with findings from another colitis mouse model [
146,
149]. Additionally, inhibition of the IL-6/STAT3 pathway reduces M2 macrophage polarization in the TME, thereby increasing the effectiveness of regorafenib [
150].
Adverse events during the treatment period could lead to dose reductions or discontinuation, thus compromising therapeutic outcomes. Skeletal muscle loss is a common side effect in patients treated with molecular targeted therapy, namely, either sorafenib or lenvatinib [
151]. This metabolic syndrome is also significantly associated with higher mortality rates and an increased likelihood of tumor recurrence [
152]. Dietary astaxanthin alleviates sorafenib-induced cachexia by regulating the composition of the gut microbiota. This recovery is evidenced by the restored muscle mass in mice that underwent FMT from mice that consumed astaxanthin, as opposed to those that consumed astaxanthin directly [
153].
Blautia, Parabacteroides, Roseburia, and
Enterococcus were enriched in response to astaxanthin, whereas
Tuzzerella, Colidextribacter, Bilophila, Alloprevotella, Lachnoclostridium, and
Lachnospiraceae_NK4A136 groups were depleted.
Blautia, a probiotic, has been identified previously to ameliorate metabolic syndrome, such as type 2 diabetes and obesity [
154,
155].
Parabacteroides, a common commensal bacteria, also influences metabolic dysfunction by secreting succinate [
156,
157].
Roseburia has been identified as a butyrate producer that participates in the antitumor immune response via the activation of cytotoxic CD8
+ T cells [
158].
Enterococcus has been shown to play a controversial role in cancer, exerting either an inhibitory effect through the expression of the NlpC/p60 peptidoglycan hydrolase SagA, which generates immune-active muropeptides, or a stimulatory effect by activating Wnt/β-catenin signaling in epithelial cells, thereby facilitating the epithelial‒mesenchymal transition [
159,
160].
Patients treated with sorafenib or lenvatinib often suffer from diarrhea [
161]. A clinical report investigating the gut microbiota composition in patients with diarrhea compared with those without noticeable side effects after lenvatinib treatment revealed no significant differences in alpha and beta diversities between the groups [
162]. In the diarrhea group, the fecal samples presented increased levels of the family
Tannerellaceae and the genera
Lactonifactor, Parabacteroides, and
Prevotella, whereas the fecal samples from patients without diarrhea presented increased abundances of the genera
Blautia, RuminococcaceaeUCG_005, and
Negativibacillus. Moreover, a KEGG analysis revealed the enrichment of butyrate metabolism in the nondiarrhea group, which was consistent with the increased abundance of the butyrate-producing genus
Blautia [
163]. An increase in the abundance of butyrate-producing bacteria among patients without diarrhea was also observed in another study examining the posttreatment effects of sorafenib [
164]. GUS has also been linked to diarrhea associated with TKIs. GUS reactivates sorafenib-glucuronide into active sorafenib, thereby prolonging its effectiveness in the patient’s body [
165,
166]. By modulating metabolic processes, researchers were able to alleviate diarrhea without compromising the efficacy of regorafenib in a mouse model [
167]. These results may help support the potential application of gut microbiota in alleviating diarrhea without compromising therapeutic efficacy [
168,
169].
Studying the gut microbiota is indispensable for optimizing targeted therapy for hepatobiliary cancers. Limited research on the gut microbiota in CCA patients receiving TKI treatment has been published, although dysbiosis in affected individuals has been previously documented. By elucidating microbial contributions to immune activation, drug metabolism, and toxicity, researchers can develop biomarkers to predict the response and design microbiota-modulating interventions to increase TKI performance and alleviate related adverse symptoms.
IMMUNOTHERAPY
Differences in microbial profiles and related metabolites between ICI responders and nonresponders with HCC
In 2020, the combination of the PD-1 inhibitor atezolizumab and the antiangiogenic agent bevacizumab was first tested in patients with unresectable HCC through a global, open-label, phase III trial [
170]. Compared with patients receiving systemic administration of sorafenib, patients receiving immunotherapy experienced a prolonged OS at 12 months and increased median PFS. A subsequent study utilizing another PD-1 monoclonal antibody, sintilimab, combined with bevacizumab biosimilar reported consistent trends in OS and median PFS compared with the front-line sorafenib group in a randomized, open-label, phase II–III study [
171]. Despite these promising results illustrating the effective application of immunotherapy in limiting HCC, some patients do not fully respond to PD-1 inhibitors [
172].
Studies have consistently shown that responders to ICIs exhibit distinct gut microbiota profiles compared with nonresponders (
Table 3). Shen et al. (2021) [
173] reported transient enrichment of
Bifidobacterium, Coprococcus, and
Acidaminococcus in disease--controlled HCC patients under ICI. However, there is no robust link between gut microbiome dynamics and ICI efficacy, which lacked survival benefit. In a 2022 clinical study by Wu et al. [
174], responders (R) to anti-PD-1 therapy significantly prolonged PFS and OS and were characterized by a separate microbial community with greater baseline alpha diversity (Shannon index) than nonresponders (NRs). Enriched taxa such as the family
Lachnospiraceae, genus
Ruminococcus, and species
Akkermansia muciniphila were detected in the R group. Moreover, Mao et al. [
175] specifically identified a positive correlation between the species
Ruminococcus callidus and OS in an HCC cohort receiving anti-PD-1 treatment in 2021. This enrichment in commensal microbiota taxa has also been supported by clinical data from Zheng and Xin with the addition of hepatoprotective probiotics, including
Bifidobacterium dentium and
Streptococcus thermophilus [
176-
179]. The levels of the enriched species
Ruminococcus in the R group were positively correlated with the serum galactaric acid concentration and negatively correlated with the concentrations of formononetin and oxypurinol [
174,
180]. Increased galactaric acid levels suggest powered galactose metabolism, which can be attributed to the increased abundance of
Ruminococcus bromii [
181]. Oxypurinol, an isostere of xanthine, is considered to have an inhibitory effect on the genus
Ruminococcus [
182]. The correlation between formononetin and
Ruminococcus levels was first identified in Wu’s paper, and this metabolite is associated with tumor inhibitory effects on HCC and multiple myeloma models [
183,
184]. Moreover, the abundance of the
Ruminococcus family is significantly correlated with increased CD8
+ T-cell infiltration in the tumor tissue [
185].
A. muciniphila can suppress HCC by promoting the recovery of hepatic natural killer T cells and increasing the proportion of CD8
+ T cells in the TME (
Fig. 3) [
186,
187]. Conversely, nonresponders were dominated by proinflammatory genera such as
Bacteroides and
Escherichia. The genera
Actinomyces and
Senegalimassilia were first identified in a clinical study to be predominantly enriched in the NR group of patients with HCC treated with PD-1/PD-L1 inhibitors [
188]. The abundance of the genus
Senegalimassilia increases in patients with exacerbated cirrhosis [
189]. Nevertheless, its effect on pancreatic cancer can be protective, although the underlying mechanism remains unclear [
190]. The species
Roseburia inulinivorans was enriched in the NR group and was positively correlated with glutamate metabolism according to the KEGG pathway analysis [
188]. Inhibiting glutamate metabolism by blocking glutaminase activity leads to immunogenic cell death in tumor cells and synergistically increases the efficacy of anti-PD-L1 therapy [
191]. However, complete bacterial depletion via antibiotics in HCC patients receiving anti-PD1 agents significantly decreases the median OS [
192]. Although the initial differences in diversity between the R and NR groups diminish over time, these key taxa remain stable, suggesting that the baseline microbiota may serve as a predictive biomarker characterizing patients who favorably respond to ICI therapy and potential targets for modulating therapeutic efficacy [
174,
179].
The gut microbiota converts primary BAs (e.g., cholic acid) into secondary BAs (e.g., DCA), which can regulate the TME through hepatic natural killer T cells and CXCR6
+ T-cell trafficking [
18,
193]. In patients with HCC, elevated levels of lithocholic acid are correlated with a deteriorated ICI response, impeding type 1 T helper cell differentiation via vitamin D receptor activation [
194]. However, other secondary BAs such as ursodeoxycholic acid, TUDCA, ursocholic acid and murideoxycholic acid are enriched in the fecal samples of responders [
180]. Positive correlations between the fecal concentrations of ursodeoxycholic acid, ursocholic acid and murideoxycholic acid and genus
Lachnoclostridium were observed. Species
Clostridium scindens from genus
Lachnoclostridium can synthesize ursodeoxycholic acid by oxidizing and epimerizing specific hydroxy groups from chenodeoxycholic acid [
195]. Elevated ursodeoxycholic acid levels can also result from metabolism driven by 7β-hydroxysteroid dehydrogenase, which is contributed by the enriched
Ruminococcus gnavus and
R. callidus species in the R group [
175,
196,
197]. In turn, increased ursodeoxycholic acid formation in the human colon can rebalance the intestinal microbiota, improving dysbiosis by increasing the abundance of the beneficial genera
Holdemanella and
Alistipes [
198]. TUDCA itself can suppress HCC initiation and progression by inducing epigenetic changes, positively correlated with
A. muciniphila abundance [
187,
199]. Its ability to increase the efficacy of PD-1 therapy is achieved through an interaction with farnesoid X receptor, which is a nuclear receptor involved in BA metabolism and has an inverse correlation with PD-L1 expression [
187,
200]. Moreover, TUDCA relieves endoplasmic reticulum stress in HCC cells, decreasing PD-L1 expression in macrophages and thus increasing CD8
+ T-cell function [
201,
202]. The function of BAs may vary regardless of their classification, highlighting the need for mechanistic studies to understand how specific BAs regulate the TME and to advance the development of BA-targeted therapeutics.
SCFAs, major metabolites produced by the microbiota, are commonly studied to reveal the profiles of microbial metabolite in patients receiving ICI therapy. In both the R and NR groups, acetic acid was the dominant SCFA in fecal samples from HCC patients, followed by propionic acid and butyric acid [
180]. The enrichment of the butyric acid-producing family
Lachnospiraceae, genus
Collinsella, and
Erysipelotrichaceae bacterium GAM147 in HCC patients who respond to anti-PD-1 treatment is supported by various clinical data [
174,
175,
178]. The ability of butyrate to boost anti-PD-1 therapy has been studied intensively. PD-L1 and IL-10 expression are downregulated in tumor-associated macrophages and correlated with elevated butyrate levels [
203]. Butyrate can block STAT1 nuclear translocation in cancer cells via lysine acetylation, thus reducing the binding of STAT1 to the PD-L1 promotor and suppressing PD-L1 expression [
204]. Moreover, butyrate promotes PD-1/CD28 expression on human CD8
+ T cells to modulate the T-cell receptor signaling pathway [
205]. The effects of butyrate and other SCFAs on antitumor immunity can be used in sensitizing different ICIs in limiting hepatobiliary malignancy.
Immunotherapy has produced modest clinical benefits in patients with CCA, although its efficacy remains constrained by biological and microenvironmental barriers. While ICIs such as pembrolizumab achieve a 40.8% objective response rate in microsatellite instability-high CCA subgroups, the objective response rate for unselected patients rarely exceeds 25% due to the low tumor mutational burden and immunosuppressive stromal interactions [
206,
207]. Similarly, the TOPAZ-1 trial, which established durvalumab combined with gemcitabine and cisplatin as the first-line standard treatment, documented a modest survival benefit (median OS improvement of 1.3 months) and a 26.7% objective response rate [
208]. Combination strategies, such as dual PD-1/cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) blockade with durvalumab+tremelimumab, produce incremental improvements (median OS: 10.1 months) but are accompanied by serious immune-related adverse events (grade 3 or higher in 23.1% of patients) [
209]. These challenges underscore the urgent need for strategies that not only increase ICI efficacy but also mitigate toxicity, ensuring that therapeutic gains are not offset by compromised safety.
The immunosuppressive TME of CCA is a key barrier to ICI success. Characterized by sparse CD8
+ T-cell infiltration, abundant myeloid-derived suppressor cells, and elevated levels of immunosuppressive cytokines (e.g., IL-10 and TGF-β), the TME renders CCA inherently resistant to ICIs [
210-
212]. Clinical confounders such as biliary obstruction and its management further complicate the outcomes. Over 50% of CCA patients present with biliary obstruction, necessitating interventions such as PTCD. In the study by Huang in 2023, PTCD-treated patients showed no OS benefit from ICIs+chemotherapy (hazard ratio [HR] 0.98,
P=0.92), unlike non-PTCD patients (HR 0.21,
P<0.0001) (
Fig. 3) [
213]. This impairment has been further validated in a mouse model, suggesting that biliary drainage alters BA levels, thereby influencing long-term survival [
214]. Similarly, antibiotic use—which is common in patients with CCA due to cholangitis or sepsis—depletes immunostimulatory taxa such as
Alistipes and
Clostridia while increasing the levels of immunosuppressive metabolites such as kynurenine, a tryptophan derivative linked to myeloid-derived suppressor cell (MDSC) expansion [
215]. These factors collectively contribute to the low durability of responses and highlight the interplay between clinical interventions, microbiome dysbiosis, and immunotherapy resistance.
As a method to address these challenges, microbiome modulation has emerged as a promising strategy to increase ICI efficacy while reducing ICI toxicity. The gut microbiota influences both antitumor immunity and irAE development through mechanisms such as metabolite production, immune cell recruitment, and antigen cross-reactivity. For example,
Alistipes, a genus enriched in ICI responders, produces SCFAs such as acetate and propionate, which suppress proinflammatory type 17 T helper cells in the liver and enhance dendritic cell antigen presentation [
193]. Conversely, disease-induced dysbiosis enriches
Bacilli and
Enterobacterales, which generate immunosuppressive metabolites such as pyrrolidine and kynurenine [
215]. The dual goals of enhancing immunotherapy efficacy and alleviating adverse events in patients with CCA as well as HCC rely on exploiting the microbiome‒immune axis. By restoring microbial symbiosis, targeting metabolite-driven immunosuppression, and personalizing therapy through biomarker-guided approaches, clinicians can amplify antitumor immunity without exacerbating toxicity.
CLINICAL TRANSLATION OF MICROBIOMEBASED THERAPIES IN HEPATOBILIARY CANCER
Microbiome-based interventions—including FMT, probiotics, prebiotics, and postbiotics—show promising clinical translation in recent years (
Table 4). These approaches leverage intestinal microbial communities to improve treatment responses and promote post-operative recovery (
Fig. 4).
FMT demonstrates potential in augmenting hepatobiliary cancer therapy responses. The prospective single-arm clinical trial (NCT04264975) has examined the potential effectiveness of FMT in individuals with advanced solid tumors, notably including HCC under anti-PD1 therapy. Although the patient cohort was limited in size, initial findings revealed a partial response in one individual with HCC among 13 total patients. As for mechanism, this response was linked to heightened levels of cytotoxic T cells in both blood and tumors, showing a positive association with
Prevotella sp. Marseille_P4119 [
216]. Concurrently, two additional clinical trials are underway to evaluate the safety and efficacy of FMT in combination with anti-PDL1 and anti-VEGFA therapies in advanced HCC patients (NCT05690048, NCT05750030). There is also an upcoming prospective single-arm multicenter clinical trial that evaluates the safety and efficacy of FMT in addressing drug resistance within the context of the triple therapy regimen for patients with unresectable HCC at mid-to-late stages (NCT06643533). FMT capsules, tailored to match the gut microbiome profiles of healthy donors and patients who achieved complete response with the triple therapy, are administered to participants with HCC that has progressed despite the standard treatment, comprising TACE, lenvatinib, and Sintilimab.
Probiotics (e.g.,
Bifidobacterium strains) reduce postoperative complications and synergize with systemic therapies. Perioperative probiotic administration in HCC patients undergoing liver resection significantly decreased infections, sepsis, and hospital stays by reinforcing gut barrier integrity and suppressing pro-inflammatory cytokines [
217]. In 2015, Liu et al. [
218] demonstrated that patients undergoing treatment for colorectal liver metastasis experienced reduced endotoxin levels (
P<0.001) and a decreased infection rate (
P=0.008) following a regimen of three probiotics administered six days prior to surgery and continued for ten days postoperatively. In a randomized clinical trial that targeted individuals with HCC, the administration of probiotics led to a noteworthy enhancement of intestinal barrier function. This improvement was achieved by fostering the growth of advantageous bacterial communities while concurrently inhibiting the proliferation of harmful bacteria. Despite these beneficial effects on intestinal health, the trial did not yield a statistically significant clinical outcome (NCT02021253) [
219]. Specific interventions such as
Bifidobacterium longum supplementation enhance postoperative recovery in hepatobiliary cancer patients. Clinical experiments demonstrate that
B. longum restores microbial balance by promoting
Lachnospiraceae, resulting in enriched fecal butyrate level.
B. longum increases intestinal tryptophan bioavailability, elevating 5-hydroxy-tryptophan and 5-tryptophan-serotonin synthesis, which directly promotes hepatocyte proliferation by upregulating cyclin D1 and other cell-cycle proteins. Survival analysis showed significantly higher OS at both 1-year and 2-year follow-ups in the probiotic group compared to the control group [
77]. Nevertheless, there is limited clinical data investigating the impact of probiotics on treatments for HCC beyond surgical interventions. In 2024, Liu et al. [
220] conducted a clinical experiment on HCC patients treated with radiotherapy, along with probiotic supplementation that included
Bifidobacterium and
Lactobacillus. This clinical intervention decreased
Enterobacter and
Enterococcus levels, leading to improved liver function, as supported by lower AST, ALT and total bilirubin levels, thus resulting in a higher ORR. Currently, multiple clinical trials are underway to evaluate the effects of supplementing with
L. rhamnosus Probio-M9,
Bifidobacterium, and
Faecalibacterium on the efficacy of anti-PD1 therapy with antiangiogenesis targeted agents (NCT05032014, NCT05178524, NCT06551272). There is also one clinical trial (NCT06563934) aiming to investigate the impact of oral enterobacterial capsules on the combined treatment regimen involving lenvatinib and anti-PD1 therapy.
Prebiotics and postbiotics offer non-viable alternatives with enhanced safety profiles. Prebiotics are non-digestible fibers that promote the growth and activity of beneficial bacteria in the colon. They serve as food for probiotics and help maintain a healthy balance of gut microbiota, supporting digestive health and overall well-being [
221]. A meta-analysis involving 3,912 patients with HCC revealed that a daily increment of 100 grams in vegetable intake was linked to an 8% decrease in the likelihood of developing HCC [
222]. There is an ongoing clinical trial (NCT04552418) aimed at evaluating the efficacy of potato starch in conjunction with dual ICI treatments in individuals with solid tumors regarding gut microbial profiles. However, no clinical trial has been identified to directly investigate the potential efficacy of prebiotics in augmenting therapeutic outcomes for hepatobiliary cancer. Postbiotics—microbial metabolites such as SCFAs and cyclic di-AMP—directly activate antitumor immunity. Elevated fecal c-di-AMP levels in radiotherapy-responsive HCC patients enhanced IFN-γ secretion and CD8+ T-cell infiltration, synergizing with radiation to suppress tumor growth [
107]. Similarly, the coadministration of TKIs with BA sequestrants might mitigate microbial-driven drug resistance [
156,
180]. Therapies targeting microbial enzymes (e.g., GUS inhibitors) could reduce chemotherapy toxicity by preventing the reactivation of prodrugs in the gut.102 These findings underscore metabolites as druggable targets for adjuvant therapies.
Microbiome-based therapies represent a paradigm shift in HCC management. Despite there not being a lot of description related to CCA management, restoring the symbiotic microbiota through FMT from ICI responders has achieved preclinical success in promoting CD8+ T-cell infiltration and reducing the number of myeloid-derived suppressor cells in patients with melanoma [
223]. Early-phase trials in patients with melanoma suggest that FMT may also mitigate immune-related adverse events by rebalancing gut immune homeostasis, a concept that could be adapted to treat CCA [
224]. Dietary interventions, such as high-fiber diets to enrich SCFA-producing bacteria or probiotics targeting
Lactobacillus and
Bifidobacterium strains, represent additional avenues to amplify ICI responses while dampening inflammation in melanoma patients [
225]. By harnessing gut bacteria and their metabolites, these strategies potentiate conventional treatments and pave the way for microbiome-guided precision oncology.
CURRENT LIMITATIONS AND FUTURE DIRECTIONS
The hypothesis that the gut microbiota influences the TME to enhance therapeutic efficacy in patients with HCC and CCA represents a compelling frontier in oncology. While preclinical and clinical studies underscore the potential of microbial modulation to reshape antitumor immunity and improve treatment related adverse effects without compromising its efficacy, significant limitations impede translation.
Variability in the microbiota composition and related metabolites
The composition of the human gut microbiota varies widely across individuals due to genetic, environmental, and lifestyle factors. This heterogeneity poses challenges in identifying universal microbial signatures predictive of therapeutic efficacy or toxicity. While certain taxa (e.g.,
A. muciniphila and
F. prausnitzii) are consistently associated with improved therapy responses in patients with hepatobiliary cancer, other taxa remain underexplored [
108,
138,
140,
174,
179,
226]. For example, Family
Ruminococcaceae is enriched in nonresponders in CCA patients under radiotherapy associating with vascular invasion, while it is also reported to show high abundance in responders in HCC patients under the same therapy [
66,
107,
118]. In non-small cell lung cancer patients treated with immunotherapy, the enriched family
Tannerellaceae was found to prolong PFS [
227]. However, secretomes from
Tannerellaceae were correlated with stimulatory effects on colorectal cancer cell lines in vivo [
228].
Lactonifactor has been associated with toxic effect such as diarrhea after lenvatinib treatment in HCC patients, while it is also negatively correlated with the acetate concentration in fecal water from breast cancer patients, suggesting its potential role in impairing antitumor immunity by interfering with T-cell function [
162,
229,
230]. Similarly,
Negativibacillus has been identified as a biomarker for identifying responders among patients with relapsed/refractory diffuse large B-cell lymphoma treated with anti-CD19 CAR-T-cell therapy, suggesting its ability to mediate the T-cell antitumor response [
231]. However, its presence in patients who experience diarrhea cannot be ignored [
162]. The presence of variations in the bacterial compositions remains across different cohorts of same type of cancer. Genus
Bifidobacterium has been widely identified as a probiotic that strengthens the immune system to limit the growth of HCC [
37,
77,
232], while its enrichment in patients who fail to respond to anti-PD-1 treatment also highlights a potential risk [
174,
179]. This discrepancy persists even across different cohorts comprising patients with the same disease and treated with the same therapy. The species
Bacteroides stercoris has been identified as an enriched species in PD-1 responders in one HCC cohort (n=37), while it significantly increases in abundance in PD-1 nonresponders in another HCC cohort (n=22) [
233,
234]. Moreover, microbial metabolites such as SCFAs and BAs exert different effects, with the outcomes dependent on the concentration, tissue context, and host genetics. For example, while SCFAs such as butyrate can induce immunosuppressive pathways, they may also promote regulatory T-cell differentiation and suppress inflammation under specific conditions, highlighting the dual roles of microbial products [
235,
236]. However, increased butyrate and propionate levels have been correlated with the inhibitory effect of anti-CTLA-4 therapy in patients with metastatic melanoma, which is associated with an increased proportion of Treg cells [
237]. Thus, interventions such as FMT, probiotics and antibiotics may yield divergent outcomes depending on the baseline microbial ecology, necessitating personalized approaches.
Current mechanistic insights into microbiota‒TME interactions are largely derived from preclinical models, which inadequately recapitulate human hepatobiliary cancer heterogeneity. Although researchers have started to focus on the role of the gut microbiota in regulating key TME components—such as myeloid-derived suppressor cells, tumor-associated macrophages, and cytotoxic T lymphocytes—additional investigations are needed to explore microbiota-related immunological mechanisms. For example, while microbial dysbiosis is linked to MDSC accumulation in murine CCA models, the underlying pathways (e.g., TLR4/NF-κB signaling or metabolite-driven epigenetic changes) require validation in human cohorts [
238].
A systematic biology approach is needed to elucidate the microbiota–TME interactions. The integration of metagenomics, metabolomics, and single-cell transcriptomics can be used to map microbial taxa and metabolites to specific immune and stromal cell populations within the TME. For example, spatial transcriptomics could elucidate how microbial-derived molecules such as polyamines or tryptophan metabolites localize to tumor niches and influence PD-1/PD-L1 expression or T-cell exhaustion [
239]. Emerging technologies, such as organoid–microbiome cocultures and gnotobiotic models, will enable the precise dissection of causal relationships [
240-
242].
Translating microbiota-based strategies into clinical practice faces hurdles, including the lack of standardized protocols for microbial modulation and the risk of unintended consequences. Probiotics or dietary interventions risk inducing dysbiosis or systemic inflammation in immunocompromised patients [
243,
244]. Safety concerns are particularly salient for FMT, the mechanism of which remains unclear and involves risks of pathogen transmission and immune activation [
245-
247]. Furthermore, the long-term effects of microbiota-targeted therapies on cancer recurrence and secondary malignancies remain unknown.
Thus, early-phase trials should evaluate the safety and feasibility of interventions such as FMT from ICI responders, next-generation probiotics, or microbiota-directed diets. While clinical trials have investigated the efficacy and safety of FMT and probiotics in hepatobiliary patients (
Table 4), research on prebiotics and postbiotics, including microbial metabolites, necessitates more robust clinical substantiation. Standardized protocols for stool collection, processing, and microbial analysis are critical to ensure reproducibility. Regulatory agencies must also establish frameworks for microbiota-based therapies, addressing challenges such as batch variability in FMT and quality control for live biotherapeutics. Concurrently, longitudinal studies should monitor long-term outcomes, including microbiome stability, immune reconstitution, and survival benefits.
The spatial dynamics of microbial communities within the TME of HCC and biliary system of CCA are increasingly recognized as critical modulators of hepatobiliary malignancy progression and therapeutic efficacy. Bednarsch et al. (2021) [
248] demonstrated that preoperative endoscopic biliary drainage in perihilar CCA induces near-ubiquitous bacterial colonization of the bile ducts, predominantly by
E. faecium, which exhibits significant predictive value for postoperative infectious complications (odds ratio 5.21,
P=0.018). It is necessary to examine how compartment-specific bacterial shifts—notably intratumoral enrichment and biliary dysbiosis—influence neoplastic behavior and treatment responsiveness through immune and metabolic reprogramming.
Intratumoral bacterial shifts, such as
E. faecium enrichment in HCC patients, directly potentiate sorafenib efficacy by expanding IFN-γ+ CD8+ T-cell populations and inducing ferroptosis via JAK-STAT1-mediated suppression of the cystine transporter SLC7A11 [
128]. Similarly, chemosensitivity in patients with CCA is mechanistically linked to intratumoral microbial shifts and metabolite alterations. Despite the reduced microbial alpha diversity (Shannon and Simpson indices), the abundance of commensals such as
Actinobacteria is positively related to the chemosensitivity to gemcitabine and cisplatin [
116,
117]. However,
Gammaproteobacteria were enriched in gemcitabine- and cisplatin-resistant patients. By expressing the long form of the enzyme cytidine deaminase (CDD
L),
Gammaproteobacteria can convert the active form of gemcitabine into its inactive form through metabolism [
249]. The inactivation of the chemotherapeutic drug leads to decreased efficacy, thus explaining the resistance of gemcitabine in the
Gammaproteobacteria-enriched population. Clinically, bile-based biomarkers such as
Enterobacteriaceae (increase in patients with ECCA) and
Nesterenkonia (decrease in patient with ECCA) show diagnostic potential [
61,
65].
The origin and functional significance of the intratumoral microbiota in HCC and CCA are debated, with competing hypotheses implicating gut translocation versus local proliferation [
61,
174,
234]. In Zhu et al.’s [
188] paper published in 2024, his group identified
Actinomyces within HCC tumors that were distinct from those in matched gut samples, supporting local proliferation hypothesis. Similarly,
O. viverrini induced CCA is specifically marked with enriched
Deinococcus and
Cyanobacteria in the biliary system compared to fecal sample, emphasizing the impact of locally proliferating environmental bacteria on cancer progression [
250,
251]. Confounding factors—such as biliary obstruction altering the microbial load and duodenal contamination during endoscopic retrograde cholangiopancreatography—necessitate a cautious interpretation [
252]. Collectively, spatial shifts in intratumoral and biliary bacteria critically modulate therapeutic efficacy in hepatobiliary cancers by rewiring immune and metabolic pathways; however, causal validation of bacterial effector molecules and their direct mechanistic impact on tumor cell death pathways remains underexplored. Future studies must employ spatially resolved multiomics (single-cell metatranscriptomics, spatial metabolomics) and targeted bacterial manipulation (e.g., CRISPR-engineered probiotics, niche-specific antibiotics) to elucidate how localized microbial dynamics can be leveraged to overcome therapy resistance and enable personalized microbiota modulation.
CONCLUSIONS
The gut microbiota critically influences therapeutic efficacy by modulating immune responses and drug metabolism while mitigating adverse effects through anti-inflammatory and antioxidant mechanisms in individuals with hepatobiliary cancer. The strategic manipulation of microbiota composition—via probiotics, FMT, or dietary changes—provides a dual benefit: increasing treatment efficacy and reducing toxicity without compromising therapeutic goals. Further clinical validation is needed to translate these insights into standardized protocols.
FOOTNOTES
-
Authors’ contributions
MYSL was responsible for drafting the manuscript, XQW and TKWL was responsible for revision of the manuscript.
-
Acknowledgements
This work was supported by the RGC TRS T12-705-24-R and RGC Collaborative Research Fund (C5017-24G).
-
Conflicts of Interest
The authors declare that this review article was written in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.
Figure 1.Gut microbial changes in patients with liver diseases and associated tumorigenic mechanisms. (A) Microbial dysbiosis includes increased abundance of pathogenic bacteria while reducing abundance of commensals. (B) Reduced levels of IPA lead to compromised intestinal barrier function, enabling the translocation of endotoxins. (C) Increased cytotoxic bile acids activate HSC thus enhancing HCC progression. (D) Translocated endotoxins, such as LPS, activate toll-like receptor, execrating local inflammation. (E) Decreased levels of SCFA-generating bacteria, such as Faecalibacterium and Coprococcus, contribute to diminished anti-inflammatory signaling, exacerbating Th17-mediated inflammation and compromising intestinal barrier integrity. (F) Bacterial extracts from HBV patients attenuate Th1 responses, while the microbiota associated with MAFLD-HCC promotes expansion of immunosuppressive Tregs and reduces cytotoxic CD8+ T cells, fostering an immune-tolerant microenvironment conducive to tumor evasion. DCA, deoxycholic acid; HBV, hepatitis B virus; HCC, hepatocellular carcinoma; HSC, hepatic stellate cell; IFN, interferon; IL, interleukin; IPA, indole-3-propionic acid; LCA, lithocholic acid; LPS, lipopolysaccharides; MAFLD, metabolic dysfunction associated fatty liver disease; SCFA, short-chain fatty acid; TCA, taurocholic acid; TLR, toll-like receptor; TNF, tumor necrosis factor.
Figure 2.Beneficial and pathological bacteria strains and their metabolites in relation to tumorigenesis. AKT, protein kinase B; GCA, glycocholic acid; GCDCA, glycochenodeoxycholic acid; IκB, inhibitor of nuclear factor κB; IFN, interferon; LCA, lithocholic acid; LCFAs, longchain fatty acids; LPS, lipopolysaccharides; MDCA, murideoxycholic acid; mTOR, mammalian target of rapamycin; MyD88, myeloid differentiation primary response 88; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells; PI3K, phosphatidylinositol 3-kinase; PKCζ, protein kinase C; SCFAs, short-chain fatty acids; TAM, tumor associated macrophage; TCA, taurocholic acid; TLR4, tolllike receptor 4; TUDCA, tauroursodeoxycholic acid; UCA, ursocholic acid; UDCA, ursodeoxycholic acid.
Figure 3.The effect of gut microbiota-related mechanisms on hepatobiliary malignancy treatments. (1) Post-operative albumin level is positively related to proteolytic bacteria Bacteroides and Pentoea. (2) CCA patients under PTCD showed no clinical benefit from combination therapy including chemotherapy and ICIs. (3) High radiation induced dysbiosis in patients with high-fat diet, leading to fat accumulation in liver, thus promoting cancer growth through AKT pathway. (4) Lenvatinib administration improves gut permeability by increasing probiotic abundance such as Faecalibacterium and Bifidobacterium, thus restoring gut microbiota balance. (5) Patients who respond to immunotherapy showed an increased abundance of Akkermansia. muciniphila, enhancing therapy efficacy by promoting CD8+ T cell expansion. AKT, protein kinase B; CCA, cholangiocarcinoma; GPCRs, G-protein-coupled receptors; ICI, immune checkpoint inhibitor; IFN, interferon; OS, overall survival; PIP, phosphatidylinositol phosphates; PTCD, percutaneous transhepatic cholangial drainage; PTEN, phosphatase and tensin homolog ; TKIs, tyrosine kinase inhibitors; TNF, tumor necrosis factor; TSC1/2, tuberous sclerosis complex1/2.
Figure 4.Integrating microbiome-based therapies such as FMT, probiotic, and prebiotic to enhance hepatobiliary treatments. (1) FMT from responders helps non-responder patients regain their anti-tumor ability. (2) Probiotic supplementation such as Bifidobacterium longum restores gut permeability and promotes liver regeneration by facilitating cell cycle progression. (3) Prebiotic-rich diet promotes growth and activity of probiotics. FMT, fecal microbiota transplantation; SCFA, short-chain fatty acid.
Table 1.Clinical studies of microbes in hepatobiliary malignancy patients receiving traditional therapy including surgical treatment, chemotherapy and radiotherapy
Table 1.
|
Study |
Cancer type |
Therapeutic agent |
Gut microbiota |
Metabolites |
|
Iida et al., 2019 [99] |
HCC |
5-FU, IFN injections, and cisplatin |
1. Blautia: Associated with a good prognosis for chemotherapy-treated patients with HCC. A higher abundance of Blautia in fecal microbiota correlates positively with PFS and OS. |
SCFAs such as acetate and propionate were positively correlated with OS but not with PFS. |
|
2. Acidaminococcus: Negatively correlated with OS, suggesting a potential negative impact on the prognosis. |
|
Peng et al., 2022 [26] |
HCC |
Extended hepatectomy |
The α-diversity of gut microbiota was significantly higher in patients with extended hepatectomy liver failure compared to those without postoperatively. Key genera enrichment including Bacteroides, Pantoea, and Faecalibacterium, and declined abundance of Turicibacter. |
Metabolism pathways related to amino acid, organic acid, pyrimidine, palmitate biosynthesis, and stearate biosynthesis are associated with liver failure after extended hepatectomy. |
|
Ketpueak et al., 2023 [118] |
ICCA |
Gemcitabine and cisplatin |
Ruminococcaceae, Oribacterium, Oxalobacter, Peptostreptococcus, and Aggregatibacter levels were significantly increased in the chemotherapy nonresponder group. |
N/A |
|
Huang et al., 2023 [213] |
Advanced CCA |
Gemcitabine+oxaliplatin or cisplatin with or without anti PD-1 therapy |
1. The abundance of Escherichia-Shigella in feces was significantly reduced after PTCD and was associated with shorter OS. |
N/A |
|
2. ICI plus chemotherapy significantly improved OS and PFS in patients who did not undergo PTCD, but this benefit was not observed in patients who received PTCD. |
|
Sun et al., 2024 [74] |
HCC |
Hepatectomy |
High levels of Akkermansia and Methylobacterium are associated with favorable OS and recurrence-free survival. |
N/A |
|
Yu et al., 2024 [77] |
HCC |
Hepatectomy |
1. Bifidobacterium longum is significantly enriched in patients with normal postoperative liver function recovery. |
Post-surgery, there was a significant increase in the levels of 5-hydroxytryptamine, secondary bile acid, and SCFAs in the intervention group compared to the control group. |
|
2. Administering a probiotic bacteria cocktail containing B. longum reduced the rates of delayed recovery, shortened hospital stays, and improved overall 1-year survival. |
|
Lin et al., 2025 [141] |
HCC |
TACE or HAIC with lenvatinib and PD-1 inhibitors |
A significant increase in the abundance of Actinobacteriota and a decrease in the abundance of Escherichia-Shigella were observed in the treated group. |
Actinobacteriota can produce SCFAs, which help maintain intestinal barrier homeostasis and exert anti-inflammatory effects, potentially inhibiting cancer growth. |
|
Ye et al., 2025 [57] |
ECCA |
Surgery |
N/A |
Preoperative total bilirubin, indirect bilirubin, and specific metabolites such as 4-hydroxyacetophenone and palmidrol were closely associated with OS post-surgery. |
|
Li et al., 2022 [107] |
HCC |
Radiotherapy |
Patients with responsive tumors had a higher abundance of Faecalibacterium and a lower abundance of Streptococcus. |
Cyclic-di-AMP, a bacterial second messenger, was present at higher levels in responsive patients and may act as a STING agonist. |
Table 2.Clinical studies on microbes in liver cancer patients receiving targeted therapy
Table 2.
|
Study |
Therapeutic agent |
Cancer type |
Gut microbiota |
Metabolites |
|
Lian et al., 2020 [129] |
Sorafenib |
HCC |
1. The sorafenib-sensitive group had higher abundances of Faecalibacterium, Enterococcus, and Veillonella. |
Salbutamol and glyclopyramide correlated positively with Anaerostipes. |
|
2. The sorafenib-resistant group had higher levels of Lactobacillus and Prevotellaceae. |
|
Yamamoto et al., 2020 [164] |
Sorafenib |
HCC |
1. The nondiarrhea group had a higher abundance of Butyricimonas. |
The microbiome may influence sorafenib metabolism through enterohepatic recycling. |
|
2. The diarrhea group had higher abundances of Citrobacter, Peptostreptococcus, and Staphylococcus. |
|
Inukai et al., 2023 [162] |
Lenvatinib |
HCC |
1. The order Bacteroidales (including Parabacteroides and Prevotella) and genus Lactonifactor were more abundant in the diarrhea group after lenvatinib treatment. |
The diarrhea group was enriched in pathways related to pentose and glucuronate interconversions and vitamin B6 metabolism. |
|
2. The genera Blautia, RuminococcaceaeUCG_005, and Negativibacillus were more abundant in the nondiarrhea group. |
|
Chai et al., 2024 [130] |
Lenvatinib |
Primary liver cancer |
1. The relative abundance of probiotics (Bifidobacterium, Coprococcus) was significantly increased after lenvatinib treatment. |
Increased gene expression related to primary and secondary bile acid biosynthesis pathway post-treatment. |
|
2. Potential microbial markers for predicting lenvatinib efficacy were identified, including Clostridia, Bifidobacteriaceae, Bifidobacteriales, Faecalibacterium, Butyricicoccus, Butyricicoccaceae, Ruminococcaceae-uncultured, Ruminococcaceae-Incertae_Sedis, Lachnospiraceae_NK4A136_group, Ruminococcaceae, and Lachnospiraceae_UCG_010. |
|
Yu et al., 2024 [128] |
Sorafenib |
Advanced HCC |
Enterococcus faecium was enriched after treatment. |
Exopolysaccharides from E. faecium stimulate IFN-γ+CD8+ T cells to secrete IFN-γ, which enhances the antitumor activity of sorafenib by promoting ferroptosis. |
Table 3.Studies describing the associations between the gut microbiome and the efficacy of ICI immunotherapy against hepatobiliary malignancy
Table 3.
|
Study |
Cancer origin |
Therapeutic agent |
R |
NR |
Sequencing methods |
Gut microbiota in responders (R) |
Gut microbiota in non-responders (NR) |
|
Zheng et al., 2019 [179] |
Advanced-stage HCC |
PD-1 inhibitors |
3 |
5 |
Metagenomic sequencing |
Lactobacillus spp. (L. oris, L. mucosae, L. gasseri, L. vaginalis), Bifidobacterium dentium, Streptococcus thermophilus, Akkermansia muciniphila, Ruminococcus spp. (R. obeum, R. bromii), Coprococcus comes, Bacteroides cellulosilyticus, Subdoligranulum spp. |
Escherichia coli, Proteobacteria
|
|
Mao et al., 2021 [175] |
Advanced-stage HCC and CCA |
PD-1 inhibitors |
32 |
33 |
Metagenomic sequencing |
Lachnospiraceae bacterium-GAM79, Alistipes sp. Marseille-P5997, Ruminococcus calidus, Erysipelotrichaceae bacterium-GAM147
|
Veillonellaceae
|
|
Chung et al., 2021 [253] |
HCC: chronic HBV |
PD-1 inhibitors |
10 |
19 |
16S rRNA gene sequencing |
Citrobacter freundii, Azospirillum sp., Enterococcus durans
|
Dialister pneumosintes, E. coli, Lactobacillus reuteri, Streptococcus mutans, Enterococcus faecium, Streptococcus gordonii, Veillonella atypica, Granulicatella sp., Trichuris trichiura
|
|
Shen et al., 2021 [173] |
HCC: chronic HBV (69.4%), HCV, and ALD |
PD-1 inhibitors |
10 |
26 |
16S rRNA sequencing and shotgun whole-genome sequencing |
Bifidobacterium, Coprococcus sub-group 3, Acidaminococcus |
N/A |
|
Ponziani et al., 2022 [226] |
HCC: HBV/HCV, MAFLD, and ALD |
CTLA-4 PD-1 inhibitors |
6 |
5 |
16S rRNA sequencing |
Akkermansia, Bifidobacterium
|
Enterobacteriaceae
|
|
Lee et al., 2022 [180] |
HCC: HBV (63.4%) |
PD-1 inhibitors |
20 |
21 |
16S rRNA sequencing |
Lachnoclostridium, Lachnospiraceae, Veillonella
|
Prevotella 9
|
|
Wu et al., 2022 [174] |
HCC: HBV (88.57%), ALD |
PD-1 inhibitors |
16 |
19 |
16S rRNA sequencing |
Ruminococcus, Blautia, Lachnospiracea incertae Sedis, Megamonas, Coprococcus, Dorea, Haemophilus,
|
Atopobium, Leptotrichia, Campylobacter, Allisonella, Methanobrevibacter, Parabacteroides, Bifidobacterium, Lactobacillus,
|
|
Zhu et al., 2024 [188] |
HCC: chronic HBV/HCV |
PD-1 inhibitors |
25 |
24 |
Metagenomic sequencing |
Phascolarctobacterium_faecium, Candidatus_ Avimonas_narfia, E. coli, Faecalibacterium_prausnitzii
|
Actinomyces_sp_ICM47, Senegalimassilia_anaerobia, Faecalibacillus_faecis
|
|
Inukai et al., 2024 [233] |
HCC: HBV, HCV, ALD, NBNC liver disease |
PD-1 inhibitors VEGF/VEGFR inhibitors |
28 |
9 |
16S rRNA sequencing |
Bacteroides stercoris, Parabacteroides merdae
|
Phylum Synergistota, Leuconostocaceae, Morganellaceae, Synergistaceae, Weisella, Lachnospiraceae UCG 008
|
|
Xin et al., 2024 [178] |
HCC: HBV (95.6%) |
PD-1 inhibitors |
30 |
15 |
Shotgun whole-genome sequencing |
Collinsella genus
|
Bacteroides_AF20_13LB
|
|
Ruminococcus_ AM42_11
|
Veillonella_atypica
|
|
Ruminococcus_ AF25_28AC
|
Veillonella_AF13_2
|
|
Fujii et al., 2024 [234] |
HCC: HCV (22.7%), others with nonviral causes |
PD-1 inhibitors VEGF/VEGFR inhibitors |
11 |
11 |
16S rRNA sequencing |
Bacteroides coprocola
|
B. stercoris
|
|
PAC002364_s
|
Prevotella_uc
|
|
Sutterella wadsworthensis
|
|
Zhu et al., 2024 [215] |
CCA |
PD-1/PD-L1 inhibitors |
47 |
41 |
Metagenomic sequencing |
Alistipes
|
Bacillus, Lactobacillales
|
Table 4.Clinical applications of gut microbiome-based modulation in hepatobiliary cancer therapy
Table 4.
|
Therapy type |
Study |
Cancer therapy |
Key bacteria species |
Mechanism of action |
Outcome measure/clinical benefit |
|
FMT |
NCT04264975 [216] |
HCC patients treated with PD-1 inhibitor |
Beneficial bacteria: Prevotella merdae and Prevotella stercorea. |
Boost CD8+ T cell proliferation and activity, increase secretion of the immune cytokine IFN-γ |
Overcoming anti-PD1 resistance |
|
Detrimental bacteria: Bacteroides plebeius and Lactobacillus salivarius. |
|
NCT05690048 |
Liver cancer patients treated with PDL1 inhibitor and VEGF/R inhibitor |
Not yet completed |
Not yet completed |
CD8+ T cell infiltration, AEs, PFS, OS, change of hepatic function |
|
NCT05750030 [132] |
Liver cancer patients treated with PDL1 inhibitor and VEGF/R inhibitor |
Not yet completed |
Not yet completed |
AEs, best radiological response, ORR, DCR, PFS, OS |
|
NCT06643533 |
Improve sensitivity of patients with unresectable HCC to transarterial chemoembolization, lenvatinib, and Sintilimab |
Not yet started |
Not yet started |
Primary: ORR, AEs, OS, PFS, and DCR; Secondary: gut microbiome composition, metabolomic profiles, and immune cell subsets before and after FMT |
|
Probiotics |
NCT02021253 |
Preoperative treatment in HCC patients under hepatectomy |
Lactobacillus strains |
Reduce bacterial translocation of LPS thus decreasing systemic inflammation |
Did not demonstrate significant clinical benefits |
|
Liu et al., 2015 [218] |
Perioperative treatment for patients with colorectal liver metastases under hepatectomy |
Did not explicitly name the specific bacterial strains |
Reinforce gut barrier by decreased measurement of plasma LPS levels and liver protection |
Reduced postoperative infections and faster recovery |
|
Liu et al., 2024 [220] |
Radiotherapy with probiotics |
Bifidobacterium and Lactobacillus
|
Decrease in harmful Enterobacter and Enterococcus levels |
Higher overall response rate in treatment group |
|
Yu et al., 2024 [77] |
Intervention on HCC patients post-hepatectomy |
Bifidobacterium longum
|
Reduce inflammation and fibrosis and enhance hepatocyte proliferation |
Reduced complications, faster recovery and improved 1-year and 2-year OS |
|
NCT05032014 |
Synergetic treatment with PD-1 inhibitor in HCC patients |
Lactobacillus rhamnosus Probio-M9 |
Increase tumor infiltration of dendritic cells and T cells |
Primary: OR; secondary: PFS and OS |
|
NCT05178524 |
Postoperative liver function recovery in HCC patients |
Bifidobacterium-based product |
Not available |
Not available |
|
NCT05620004 |
Synergetic treatment with PD-1 inhibitor and VEGF/R inhibitor in advanced HCC patients |
Bifidobacterium bifidum
|
Not yet completed |
Not yet completed |
|
NCT06551272 |
Microbiota modification in patients treated with PD-L1 inhibitor and VEGF/R inhibitor for advanced HCC |
Faecalibacterium prausnitzii based product |
IL10 stimulator |
Not yet completed |
|
NCT06563934 |
Oral enterobacterial capsules in liver cancer patients treated with lenvatinib and PD-1 inhibitor |
Did not explicitly name the specific bacterial strains |
Not yet completed |
Primary: PFS; Secondary: OS, ORR, DOR, DCR |
|
NCT06563947 |
Oral enterobacterial capsules combined with immune checkpoint inhibitors and antiangiogenesis targeted agents |
Did not explicitly name the specific bacterial strains |
Not yet completed |
Primary: PFS; Secondary: OS, ORR, DOR, DCR |
Abbreviations
cytotoxic T lymphocyte-associated antigen 4
Firmicutes/Bacteroidetes ratio
fecal microbiota transplantation
immune checkpoint inhibitor
intrahepatic cholangiocarcinoma
interferon regulatory factor 3
metabolic dysfunction associated fatty liver disease
mammalian target of rapamycin
mammalian target of rapamycin complex 1
myeloid differentiation primary response 88
nonalcoholic steatohepatitis
operational taxonomic units
pathogen-associated molecular patterns
principal coordinate analysis
progression-free survival
post-hepatectomy liver failure
phosphoinositide 3-kinases
percutaneous transhepatic cholangial drainage
primary sclerosing cholangitis
signal transducer and activator of transcription 3
transarterial chemoembolization
tyrosine kinase inhibitors
tauroursodeoxycholic acid
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