The gut bacterial composition of colon tissue in healthy individuals is dominated by Firmicutes and Bacteroidetes, with a lower proportion of Proteobacteria, Fusobacteria and Acinetobacter (21,22). Dysbiosis in CRC is marked by the abundance of pathogenic species in the colon tissue, including Bacteroides fragilis, Fusobacterium nucleatum (F. nucleatum) and some strains of Escherichia coli. (E. coli), such as phylogroups B2 and A (23-26). These bacteria contribute to tumorigenesis by inducing chronic inflammation, promoting DNA damage and suppressing the antitumor immune responses in cancerous tissues. Additionally, the overrepresentation of species, such as Peptostreptococcus and Parvimonas, is frequently reported in the advanced stages of CRC (18,27,28). Furthermore, depletion of beneficial commensals, such as Faecalibacterium prausnitzii (F. prausnitzii), Lachnospiraceae and Akkermansia muciniphila (A. muciniphila), serving as the key regulators of intestinal barrier function, was associated with decreased production of anti-inflammatory SCFAs (26,29,30). Decreased production of SCFAs, such as butyrate, impedes the inhibitory effects of histone deacetylase (HDAC), thereby improving survival and increasing the proliferation of CRC cells through the Warburg effect (31-33). In addition, carcinogenic metabolites, such as secondary bile acids, N-nitroso compounds and hydrogen sulfide, induce genotoxic stress (caused by production of colibactin by pathogenic strains of E. coli that results in DNA double-strand breakage and somatic mutations) and epithelial transformation (34-37).

Compared with the intestine, the gastric microbiota has less diversity, owing to the acidic environment of the gastric tissue (38). Nevertheless, distinct microbial shifts have been reported in terms of gastric complications. Helicobacter pylori (H. pylori) induces chronic gastritis, epithelial damage and carcinogenesis in the gastric tissues (4,39). The bacterial load of H. pylori is markedly increased in >70% of patients with gastric adenocarcinoma (40). Beyond H. pylori, the other changes in the gastric microbiota, including increased Lactobacillus reuteri (25) and Streptococcus, have been identified in gastric atrophy and intestinal metaplasia (41).

In gastric cancer, H. pylori induces oncogenic signaling pathways through its virulence factors, including cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A gene. CagA activates nuclear factor κB (NF-κB) and STAT3, resulting in the overexpression of IL-8/cyclooxygenase-2 and gastric epithelial apoptosis (35,42,43). H. pylori also increases the production of reactive oxygen species, causes mutations in the tumor protein p53 gene and chromosomal instability (44). By contrast, decreased proportions of beneficial bacteria such as Lactobacillus gasseri and Bifidobacterium have been observed in patients with gastric cancer (45,46). Lactobacillus gasseri is needed for lactic acid production, gastric mucosa protection and maintenance of gastric acidity. Gastric bacteria dysbiosis results in overgrowth of opportunistic bacteria such as Streptococcus, which contributes to alteration in arginine metabolism and increased mucosal inflammation, activation of oncogenic signaling pathways, and increase in the production of N-nitroso compounds in the gastric tissue, thereby promoting DNA damage and mutagenesis in gastric epithelial cells (4,47,48).

Contrary to traditional beliefs, the pancreas is not a completely sterile organ (49). Previous studies have demonstrated that pancreatic ductal adenocarcinoma is influenced by microbial translocation from the oval cavity or gut, indicating a notable link between dysbiosis and pancreatic tumors (50-52). Genomic studies have demonstrated the presence of Proteobacteria, Acinetobacter and Enterobacteriaceae within the pancreatic tumor environment, where they may contribute to immune responses modulation and chemoresistance (20,53-55). In addition, the decreased abundance of beneficial bacteria, particularly Bacteroides and Clostridium in the gut reduces the production of SCFAs which may support cancer progression by disturbing mucosal defense and providing an inflammatory microbial environment (20). Periodontal pathogens, such as Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, have also been identified as risk factors for pancreatic cancer, possibly through the oral-gut axis, systemic inflammation and immune modulation (50). Pancreatic dysbiosis may contribute to the regulation of bile acid metabolism, tumorigenic microenvironment development and tumor progression (20).

The development of HCC is notably associated with chronic liver diseases, such as viral hepatitis and non-alcoholic steatohepatitis (1); both conditions are affected by disturbances in the gut microbiota-liver axis. Dysbiosis in HCC is characterized by increased abundance of pathogenic bacteria (Enterococcus faecalis, Clostridium scindens and Escherichia species) and depletion of beneficial bacteria (Lactobacillus and Bifidobacterium adolescentis), thus reducing the production of SCFAs and impairing epithelial repair and anti-inflammatory signaling (19). Pathogenic bacteria in HCC produce endotoxins, such as lipopolysaccharides (LPS) and other microbial products, that infiltrate the gut, activate hepatic Kupffer cells and promote chronic inflammation and fibrosis in the liver. For instance, Clostridium scindens exerts bile acid toxicity by converting primary bile acids to deoxycholic acid and activating hepatic stellate cells through farnesoid X receptor (FXR)/G protein-coupled bile acid receptor (TGR5) signaling (56,57).

The esophageal microbiota is markedly influenced by diet, reflux and oral hygiene. Dysbiotic alterations in esophageal adenocarcinoma include an increase in the abundance of Veillonella, Campylobacter and Proteobacteria (1). These bacteria can produce proinflammatory molecules and LPS in the esophageal tissue (24). Continuous exposure of esophageal cells to LPS results in the activation of NF-κB and STAT3 signaling pathways and increasing the production of TNF-α and IL-6, which pro-tumorigenesis events, supporting cell survival, proliferation, migration and invasion associated with malignant phenotypes (58,59).

Beneficial commensals, such as F. prausnitzii and Lachnospiraceae, are gut microbiota that produce SCFAs (acetate, butyrate and propionate) through bacterial fermentation of dietary fibers in the colon tissue (31,60). Butyrate serves a bifunctional role in digestive tumors, acting as an epigenetic regulator (inhibition of HDAC) and modulating cell cycle checkpoints, NF-κB and Wnt/β-catenin pathways, which are context-dependent (33,61). This means that in healthy colonocytes, butyrate helps improve differentiation, increases apoptosis and promotes anti-inflammatory signaling primarily by inhibiting HDAC and binding to G-protein-coupled receptors (such as free fatty acid receptor 2/3 and hydroxycarboxylic acid receptor 2) (62-64). However, in advanced colorectal tumors, particularly under hypoxia which results in increased glycolytic effects (Warburg phenotype), the uptake and oxidation of butyrate are altered as its intracellular accumulation suppresses HDAC and arrests cellular growth and differentiation. In addition, butyrate interacts with immune and stromal components within the TME, thereby promoting the differentiation of T lymphocytes and enhancing the epithelial barrier integrity (32). Acetate and propionate affect lipid metabolism and glucose hemostasis in CRC cell lines and exhibit anti-inflammatory properties by activating G-protein-coupled receptors (GPR41 and GPR43) that regulate cytokine production and immune cell function (64-66). In addition, propionate inhibits the activation of the NLR family pyrin domain containing 3 inflammasome and exerts protective effects by reducing colitis-associated CRC (67).

Within the gut, bile acids originate from two distinct sources as follows: Primary bile acids are naturally synthesized in the liver and secreted in conjugated form to the intestine, whereas secondary bile acids, such as deoxycholic acid (DCA) and lithocholic acid (LCA) are produced through transformation by gut microbiota, such as Clostridium species (37). DCA and LCA subsequently contribute to tumor biology and metabolic reprogramming by activating cell-surface receptors (such as FXR and TGR5) in epithelial, immune and hepatic cells, inducing pro-inflammatory cytokines, as well as oxidative and nitrosative stress, thereby modulating DNA damage through the activation of NADPH oxidase. In addition, they can activate oncogenic signaling pathways by affecting the expression of gene involved in the Wnt/β-catenin, NF-κB and EGFR/MAPK pathways (36). Although LCA can induce apoptosis in some types of cancer (such as nephroblastoma, acute myeloid leukemia, and breast cancer), it exhibits inflammatory properties and induces epithelial injury under dysbiotic conditions (68-72). Furthermore, LCA promotes metastasis in gastric cancer cells by activating TGR5, modulating the EGFR/MAPK signaling pathway and inducing cell migration (11,37,61,73,74).

The gut microbiota can metabolize amino acids into different compounds, such as polyamines, hydrogen sulfide (H₂S), kynurenine, indole-3-propionic acid (IPA) and indole-3-acetic acid (IAA), which influence tumor biology (75). Kynurenine, produced by Lactobacillus, serves as a biomarker of poor prognosis in digestive tumors (76); it suppresses the activation of T-lymphocytes, facilitates immune evasion and mediates tryptophan catabolism in the gut (77). Tryptophan can be metabolized in the gut by both kynurenine-dependent pathways and the gut microbiota-host metabolism axis. IPA, a byproduct of tryptophan catabolism, can impair T-cytotoxic immune function, improve epithelial barrier function and modulate the immune response in pancreatic cancer (78,79). In a CRC model, IPA demonstrated anti-inflammatory effects and inhibited tumor growth (80). Bifidobacterium produces IAA, which binding to and activating aryl hydrocarbon receptors on immune cell surface, therefore, contributes to downregulating the expression of interleukin-22 binding protein (IL-22BP), This results in decreasing the intercellular IL-22, a potent oncogenic cytokine, levels that indicates its protective effects in HCC (81-83).

Polyamines (putrescine, spermine and spermidine) are the other amino acid-derived metabolites, which can be produced by Bacteroides species and are derived from ornithine and arginine metabolism (84,85). Aberrant production of polyamines promote tumor proliferation, angiogenesis and metastasis (85). In gastric cancer, elevated polyamine levels are associated with angiogenesis through increased production of hypoxia inducible factor 1-α and VEGF (86). Increased polyamine levels have also been associated with the proliferation of CRC cell lines (87). Sulfate-reducing bacteria, such as Desulfovibrio and Bilophila, metabolize dietary cysteine and produce H₂S, which has dual functions under different conditions. At low, physiological concentrations, H₂S exerts a protective role by supporting mucosal barrier integrity, redox hemostasis and mitigating excessive inflammation in the gut (88,89), thereby contributing to epithelial defense and immune balance. In addition. H₂S serves as a signaling molecule that supports intestinal homeostasis, prevents chronic injury development and preserves epithelial cell survival and repair. By contrast, increasing the abundance of sulfidogenic bacteria during dysbiosis results in locally increased levels of H₂S; therefore, a disequilibrium between H₂S levels and detoxification pathways occurs in colonocytes and shifts its effects toward promoting tumor development (90,91). However, in dysbiosis and at high concentrations, H₂S modulates DNA hypermethylation (inhibits DNA methyltransferase), silences the secreted frizzled related protein 2 tumor suppressor gene and activates NF-κB signaling (92).

The gut microbiota can produce other metabolites, including phenolic compounds (such as flavonoids), lactate and ammonia, which are functional in reshaping the TME and immune responses (93). LPS is a structural component of the outer membrane of gram-negative bacteria (45); LPS is a potent bacterial endotoxin that activates the innate immune system via Toll-like receptor 4 (TLR4) signaling, resulting in chronic inflammation by activating NF-κB signaling and increasing the production of tumor-promoting cytokines, such as IL-6 and IL-8, in gastric and pancreatic cancers (94). Increased LPS levels have also been identified in hepatocellular and gastric cancers (94).

The gut microbiota contributes to TME remodeling within cancer cells by regulating cellular interactions and cytokine production to support cellular proliferation and survival (14). Butyrate acts as an epigenetic regulator in normal colonocytes, inhibits HDAC, induces transcriptional changes to induce apoptosis and supports epithelial barrier integrity in normal colonocytes; however, within the hypoxic TME of CRC, it serves as an energy source, promoting the survival and chemoresistance of tumor cells (33). Lactate is another metabolite produced within the TME, owing to the increased demand for energy sources or by the in-house microbiota (75). By binding to glycoprotein receptors, such as GPR81, it serves as a metabolic substrate for signaling molecules and therefore promotes immunosuppression and angiogenesis in the TME (95). Streptococcus species acidify the gastric TME by producing lactate, resulting in VEGF/MMP9 activation and immune evasion (96,97). Immune evasion is a unique characteristic of the cancer cells within the TME; this phenomenon is facilitated by the activation of inflammatory pathways, such as NF-κB, Wnt/β-catenin signaling and STAT3, which are mediated by secondary bile acids and the production of reactive oxygen species (98). In HCC, the overgrowth of Clostridium scindens was observed under dysbiosis, which is potentially associated with increased conversion of primary bile acids to secondary ones such as DCA (36). As aforementioned, the increased levels of DCA within the TME is mechanistically associated with DNA damage and inflammation resulting in cancerous cell migration, invasion and extracellular matrix remodeling (99,100).

Microbial metabolites, such as SCFA, kynurenine and indole derivatives, influence cancer cell proliferation and tumor growth (8). In dysbiosis, changes in amino acid metabolism by the gut microbiota (such as Lactobacillus) alter the levels of amino acid catabolites such as indole-3-acetic acid and kynurenine, Tryptophan derived catabolites, which can activate aryl hydrocarbon receptors on immune cell surface, promote immunosuppressive phenotypes, reduce T-cytotoxic lymphocytes and mediate immune tolerance in pancreatic ductal adenocarcinoma (93,101-103). In addition, increased ammonia levels, originating from proteolytic bacteria, result in T cell exhaustion and impair antitumor activity. Microbial metabolites also provide nutrients and immune cell energy sources within the TME. The microbiota can also act as proinflammatory mediators. For instance, LPS from gram-negative bacteria (such as Klebsiella) induce epithelial mesenchymal transition in pancreatic cancer by activating TLR4 signaling, resulting in the activation of NF-κB and the release of proinflammatory cytokines such as TNF-α and IL-6(104).

In CRC, some E. coli strains (such as phylogroups B1 and B2) can produce colibactin, a genotoxin that induces chromosomal instability and breakage in double-stranded DNA and exerts somatic mutations in the KRAS gene, resulting in mutagenesis (105-107). In dysbiosis, microbial compounds can also promote the accumulation of reactive oxygen and nitrogen species, thereby intensify oxidative DNA damage and promote lipid peroxidation (44). In addition to directed DNA damage, microbial metabolites such as butyrate (HDAC inhibitor) can induce epigenetic alterations and affect cellular DNA condensation within the TME (33,79).

Microbial biotransformation is a process by which the gut microbiota processes chemical compounds, including dietary substances and xenobiotics (108). Xenobiotics are chemical substances that do not originate intrinsically, such as medications, environmental pollutants, dietary compounds and other chemical substances. The gut microbiota serves a pivotal role in biotransformation and markedly affects the risk of cancer development in the digestive tissues. In dysbiosis, microbial biotransformation may activate carcinogenic compounds, induce DNA damage and affect host detoxification pathways (108).

The microbial metabolism of xenobiotic compounds typically involves two main phases (108). In the first phase, the oxidation, reduction and hydrolysis of xenobiotics are often mediated by analog compounds of cytochrome P450 (cytP450). For instance, aflatoxin B1 (AFB-1), a mycotoxin produced by Aspergillus species; AFB-1, is typically converted by cytP450 to a carcinogenic epoxide. Gut microbiota, such as Lactobacillus, produce enzymes that detoxify AFB-1. Under dysbiosis, overproduction of AFB-1 disrupts DNA structure and leads to HCC (109). The second phase of xenobiotic metabolism involves increasing the solubility and facilitating the excretion of xenobiotic compounds (110). This phase includes conjugation, sulfation and methylation reactions. For example, Bacteroides and Clostridium produce enzymes similar to β-glucuronidase and azoreductase, which metabolize heterocyclic amines, such as polycyclic aromatic hydrocarbons (111). Heterocyclic amines potentially induce mutations in essential genes, such as adenomatous polyposis coli (APC) and KRAS, which are risk factors for CRC. Under dysbiosis, these transformation processes are probably disturbed, resulting in carcinogenesis (112,113).

In dysbiosis, the gut microbiota can reduce dietary nitrates to nitrites, and oral Veillonella and gastric H. pylori convert nitrites to nitrosamines, which are potent mutagens that contribute to gastric carcinoma (114,115). Environmental pollutants, such as heavy metals, can also be detoxified by some microbiota strains, such as Lactobacillus strains, which bind to and reduce the bioavailability and nephrotoxicity of cadmium and arsenic (116,117). Another notable role of the microbiota in the metabolism of xenobiotic compounds is detoxification and drug metabolism (117,118); for instance, Eggerthella lenta inactivates digoxin, a chemotherapeutic agent, and Enterococcus species can detoxify and mitigate the production of cisplatin-induced reactive oxygen species (119).

The intricate association between the gut microbiota and immune response in digestive tumors supports their pivotal role in regulating inflammatory signals, immune cell differentiation, cytokine production and immune checkpoint alterations within the TME of digestive tumors (Fig. 2). The gut microbiota can directly affect the local immunity of the TME within digestive tumors, such as gastric and CRC. Within the gastrointestinal tract, a consistent interplay between the gut microbiota and mucosal immune system is evident. In dysbiosis, pathogenic bacteria such as F. nucleatum suppress local immunity, and in CRC, F. nucleatum inhibits tumor cell cytotoxicity by binding to the T cell immunoreceptor with Ig and ITIM domains receptor on natural killer cells and cytotoxic T lymphocytes (Fig. 3). Dysbiotic microbiota, such as F. nucleatum induce M2-polarization of tumor-associated macrophages and block the production of tumor-suppressor cytokines, such as IL-10 and TGF-β (78,86).

Commensal bacteria are essential for maintaining epithelial integrity and equilibrium between pro- and anti-inflammatory signals. A balanced intestinal microbiota is essential for the host to support immune homeostasis by inducing the maturation of circulating immune cells, including dendritic cells, macrophages and different subtypes of T lymphocytes within secondary lymphoid organs (7,45). Bifidobacterium and F. prausnitzii produce SCFAs, tryptophan derivatives and secondary bile acids that can enter the bloodstream, interact with immune cells and promote anti-inflammatory responses and cytotoxicity of tumor-infiltrating lymphocytes (23,24,29). In addition, microbial translocation has been proposed as a risk factor for premetastatic niches, mainly because of the immune suppression and inflammation induced by microbial metabolites. Some Escherichia strains and Proteus mirabilis have been found to be incorporated into liver metastases from colorectal tumors. In dysbiosis, the translocation of gut microbiota, such as Enterobacteriaceae, results in locally elevated LPS levels and the activation of TLR4 in hepatic Kupffer cells. These events induce the activation of IL-6/STAT3 signaling and the progression of tumor cells in HCC (35,43).

Gut microbiota profiling is useful for predicting therapeutic outcomes, particularly in digestive tumors. Beyond its influence on tumor biology, microbial composition can also affect drug metabolism and determine the efficiency of checkpoint inhibitors and chemotherapeutic agents (7,118,120). Therefore, microbial diversity can be used as a determining factor for whether a patient is resistant or responsive to treatment. For instance, Heshiki et al (121) investigated the intestinal microbiota profile in patients with different cancers and identified a significant microbiota diversity in patients who were responded successfully to treatment than non-responder patients. Based on microbiota profile, the authors developed a machine leaning model to predict treatment outcome indicating a positive correlation between Bacteroides and positive response to treatment, and validated the accuracy of model in a different cohort.

The use of antibodies against immune checkpoint inhibitors, including anti-programmed cell death protein 1, anti-programmed death-ligand 1 and anti-cytotoxic T-lymphocyte associated protein 4, is an emerging therapy that affects T cell-mediated antitumor activity. Currently, gut microbiota composition has been introduced as a predictor of response to treatment with checkpoint inhibitors (12,122). Patients with a microbiota profile enriched in beneficial commensals, such as A. muciniphila and Bifidobacterium, usually respond favorably to treatment (123). These bacteria have the potential to increase antigen presentation, increase effector T-cells levels and promote dendritic cell maturation. Transferring beneficial microbiota to non-responders to immune checkpoint inhibitors is a promising hypothesis for restoring immunomodulatory and therapeutic outcomes in a personalized medicine approach.

Multiple studies on the influence of gut microbiota on treatment outcomes with chemotherapeutic agents have indicated that microbial enzymes can induce the activation or degradation of certain medications (124,125). For example, Mycoplasma hyorhinis produces cytidine deaminase, which inactivates gemcitabine in patients with pancreatic cancer. In addition, Lactobacillus species exert a synergistic effect on 5-FU cytotoxicity by producing thymidylate synthase inhibitors (126).