As one of the most aggressive human malignancies, PC remains a formidable clinical and biological challenge marked by silent onset, delayed detection, and profound therapeutic resistance. The pancreas is a vital organ that performs both exocrine and endocrine functions, playing a crucial role in digestion, nutrient absorption, and metabolic regulation. However, its deep anatomical location and the asymptomatic nature of early disease stages often delay diagnosis until the malignancy is advanced and incurable (1). Among pancreatic neoplasms, PDAC accounts for over 90% of cases and is one of the most lethal solid tumors. This malignancy is marked by a complex and immunosuppressive TME that promotes metabolic reprogramming and facilitates interactions between diverse cellular populations, contributing to rapid progression and limited therapeutic response (2). Globally, it ranks as the 12th most diagnosed cancer, yet its mortality rate remains disproportionately high (3). Survival rates for PDAC are alarmingly low, with only ∼18% of patients surviving 1 year after diagnosis and just 11% surviving 5 years (4, 5). These outcomes are largely attributed to delayed detection and intrinsic resistance to therapy.

Imaging remains the cornerstone of PC diagnosis. Multidetector computed tomography (CT) is the preferred modality for initial evaluation, while ultrasonography and magnetic resonance imaging (MRI) provide complementary anatomical resolution (6, 7). In efforts to overcome diagnostic delays, innovative tools such as the PAC-MANN blood-based assay have been introduced. This platform utilizes magnetic nanosensors to quantify protease activity, and when combined with CA 19-9, achieves 85% accuracy in detecting early-stage PC using only 8 μL of blood. Delivering results within 45 min, it represents a rapid, cost-effective, and scalable strategy, particularly advantageous for resource-limited settings (8).

Beyond classical diagnostics, the human microbiome has emerged as a fundamental regulator of systemic physiology and oncogenesis. Comprising bacteria, viruses, and fungi, this “hidden organ” orchestrates host metabolism, immunity, and inflammation (9–15). The intestinal microbiome, in particular, is indispensable for lifelong immune development and tolerance. Disruption of its homeostasis, termed dysbiosis, has been implicated in gastrointestinal, metabolic, cardiovascular, and neuropsychiatric disorders (9, 16–18). Microbial ecosystems also inhabit anatomical regions once considered sterile. The genitourinary tract, for instance, hosts a unique microbiome influenced by age, hormonal milieu, and host-specific factors, though reproducibility across studies remains limited due to methodological variability in sampling and sequencing (19). Increasingly, evidence indicates that the gastrointestinal microbiome plays a critical role in pancreatic tumorigenesis. Alterations in microbial composition and function can modulate local and systemic inflammation, immune regulation, and xenobiotic metabolism-mechanisms directly relevant to PC initiation and therapeutic resistance (20–23).

Recent translational frameworks now position the microbiome as a mechanistic and clinically actionable component of oncology, advancing from correlation to intervention-ready models. Multi-omic evidence links microbial pathways, nucleotide salvage, bile-acid remodeling, and tryptophan–kynurenine metabolism to immune evasion, stromal remodeling, and therapeutic resistance in PDAC, supporting the development of microbiota-informed diagnostics and adjunctive strategies such as live biotherapeutics and precision nutrition (24, 25). For low-biomass niches like the intrapancreatic and biliary microbiomes, standardized sampling, contamination control, and functional readouts (metatranscriptomics, metabolomics) are essential for reproducible biomarker discovery (13, 26). Parallel evidence indicates that early-life microbial imprinting, shaped by delivery mode, breastfeeding, and maternal microbiota, programs immune tone and metabolic set-points that persist into adulthood. Early dysbiosis, particularly altered Bifidobacterium and Lactobacillus transmission, may predispose individuals to chronic inflammation and metabolic reprogramming conducive to PDAC development. Integrating function-first profiling with life-course microbial determinants could refine PDAC risk stratification and accelerate translation from discovery to personalized interventions (27, 28).

Within the urogenital niche, dysbiosis has been linked to urinary pathologies, whereas dominance of Lactobacillus species such as L. crispatus supports urogenital health, while L. gasseri is often associated with dysbiotic states, reflecting species-specific effects on mucosal stability (29). Similarly, the oral microbiome contributes to pancreatic carcinogenesis, with pro-inflammatory taxa including Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans potentially translocating to the pancreas via hematogenous or lymphatic routes and altering its immune milieu (30). Furthermore, the intrapancreatic microbiome, enriched with Fusobacterium, Pseudomonas, Enterobacter, and Malassezia, has been shown to shape immune cell infiltration, influence chemotherapeutic efficacy, and modulate disease aggressiveness and prognosis (22).

Recent metagenomic profiling has revealed that PDAC harbors a distinct microbial ecosystem with functional links to tumor metabolism and immunosuppression. Multi-omic integration demonstrates that specific microbial taxa contribute to reprogramming of amino-acid and lipid metabolism, while simultaneously dampening interferon signaling and cytotoxic lymphocyte infiltration (31). These findings suggest that microbial metabolic pathways operate as co-drivers of pancreatic tumor biology, aligning with emerging evidence that the gut–pancreas axis orchestrates oncogenic inflammation and immune escape (32).

Beyond initiation and immune escape, the microbiome actively engineers metastatic fitness and organotropism in PDAC. Gut and intratumoral taxa calibrate EMT, desmoplasia, angiogenesis, and immune surveillance, conditioning pre-metastatic niches and shaping therapy response. In parallel, tumor-derived extracellular vesicles encode integrin “zip codes” that direct tissue targeting, such as α6β4/α6β1 biasing lung uptake and αvβ5 engaging liver Kupffer cells, remodeling distant sites via cytokine induction, ECM dynamics, vascular leak, and immune suppression. This tumor-microbe-host circuitry also alters drug bioavailability and ICI efficacy: gut metabolites (SCFAs, bile-acid and tryptophan derivatives) reprogram endothelium and myeloid compartments, while Gammaproteobacteria can inactivate gemcitabine; circulating microbial DNA/metabolite signatures capture these states and predict outcomes. Operationalizing organotropism, especially PDAC’s liver/peritoneal tropism, by pairing microbiome-informed biomarkers with EV-guided niche biology could sharpen surveillance, risk stratification, and treatment timing (12, 33).

This review synthesizes the mechanistic dimensions through which the microbiome shapes PC biology across four interrelated niches-gastrointestinal, oral, urogenital, and intrapancreatic. We elucidate how microbial communities modulate the pancreatic TME, influence immune signaling and metabolism, and alter treatment responsiveness via drug biotransformation and immune regulation. Collectively, these insights highlight the microbiome’s growing significance as both a diagnostic biomarker and a therapeutic target in the evolving landscape of PC management.

Among the various microbial ecosystems in the human body, the gastrointestinal microbiome emerges as a critical regulator of systemic immunity, metabolic signaling, and inflammatory pathways (16) (Figure 1). These functions are increasingly implicated in the pathogenesis of PC. Alterations in gut microbial composition, particularly reduced diversity, have been observed in patients with PC. It has been reported a significant shift in gut microbiota populations, characterized by an increased abundance of Bacteroides and a decreased proportion of Proteobacteria, compared to healthy controls (34, 35). Emerging data link gut microbiota dysbiosis to tumor-promoting inflammation, including enhanced expression of pro-inflammatory cytokines such as tumor necrosis factor-alpha (TNF-α), a hallmark of chronic inflammatory states (36). Although transient inflammation is protective, its persistence fosters a pro-carcinogenic microenvironment that supports malignant transformation.

Systemic and local inflammatory pathways converge in PC, where metabolic disorders such as obesity, type 2 diabetes, and chronic pancreatitis exacerbate gut microbiota dysbiosis and compromise intestinal barrier integrity. This disruption facilitates microbial translocation to pancreatic tissue through mesenteric or lymphatic routes (37). Integrative metabolomic analyses reveal that depletion of Faecalibacterium and Akkermansia perturbs bile-acid and tryptophan pathways, activating pro-inflammatory signaling cascades that favor epithelial–mesenchymal transition and tumor initiation (38, 39). However, these metabolic circuitries, particularly the bile-acid and tryptophan–kynurenine axes, have been more comprehensively characterized in metabolic disease, colorectal cancer, and inflammatory bowel disorders, indicating that their mechanistic roles in PDAC require further validation (40–43).

Recent mechanistic studies further reveal that chronic inflammation reshapes the tumor immune microenvironment through myeloid-cell reprogramming. Specifically, CSF1R⁺ tumor-associated macrophages suppress cytotoxic CD8⁺ T-cell infiltration and effector function, generating an immunosuppressive niche that supports tumor persistence. Targeted depletion of this subset restores antitumor T-cell activity and reduces tumor burden, highlighting the CSF1/CSF1R axis as a promising immunotherapeutic target in PC (44).

Beyond immune modulation, the gut microbiome exerts systemic effects through the microbiota-gutbrain axis. Microbial species such as Lactobacillus and Bifidobacterium produce key neurotransmitters, including γ-aminobutyric acid (GABA), serotonin, and dopamine, that influence both vagal signaling and immune tone (45). This bidirectional communication system integrates neural, endocrine, and immune signals, modulating not only emotional and behavioral responses but also inflammatory pathways (46). Nevertheless, most mechanistic insights into microbiota-derived neurotransmission originate from neuropsychiatric, metabolic, and gastrointestinal disease models, with only indirect evidence linking these neuromodulatory pathways to PDAC biology. Consequently, their contribution to pancreatic tumorigenesis should be regarded as emerging rather than definitively established (47).

Shifts in the balance of dominant phyla, such as Firmicutes and Bacteroidetes, can significantly impact host metabolism and immune regulation, contributing to the development of metabolic syndrome, chronic inflammation, and tumorigenesis (48). Lastly, these findings position the gastrointestinal microbiome as a central but heterogeneously validated driver of PC pathogenesis, combining well-established inflammatory mechanisms with several promising neuroendocrine and metabolic pathways.

Traditionally viewed as a sterile fluid and passive filtrate of systemic physiology, urine is now recognized as a dynamic biofluid capable of capturing early molecular changes associated with disease processes, including PDAC (49) (Figure 1). Emerging evidence suggests that urine harbors a range of biomarkers, including metabolites linked to glucose dysregulation, chronic inflammation, and cancer-associated cachexia, that can distinguish PDAC patients from healthy individuals even before the onset of clinical symptoms (50). One promising avenue involves urinary exosomal microRNAs, which are protected within lipid vesicles and reflect oncogenic signals emanating from the TME. These vesicle-encapsulated molecules exhibit remarkable stability, making them attractive candidates for non-invasive early detection (51). Although the composition of the urinary microbiota itself remains underexplored in the context of PDAC, the molecular cargo of urine may indirectly reflect host-microbiota interactions or microbial-driven metabolic shifts that contribute to tumor initiation and progression (52).

Crucially, urine does not merely mirror metabolic disturbances; it may also encode immunological and microbial alterations relevant to cancer biology. This broad molecular representation has led to the development of multiplexed biomarker panels, which integrate proteins, metabolites, and non-coding RNAs (53–55). Such combinatorial strategies consistently outperform single-analyte diagnostics in sensitivity and specificity, offering a robust approach to address the clinical challenges posed by PC, a malignancy characterized by marked heterogeneity and rapid progression (56). Collectively, urine has emerged as a powerful non-invasive matrix capable of capturing early molecular signals of malignancy in PC, supporting its integration into risk-stratification workflows.

Homeostasis between the human host and its resident oral microbiota is essential for maintaining normal physiological function (Figure 1). The oral microbiome, one of the most diverse microbial ecosystems in the body, is shaped by a range of factors, including age, sex, oral hygiene, diet, and immune status. Dominant genera commonly identified in the oral cavity include Streptococcus, Haemophilus, Leptotrichia, Porphyromonas, Prevotella, Propionibacterium, Staphylococcus, Veillonella, and Treponema (30). Constantly exposed to exogenous microorganisms through breathing, eating, and drinking, the oral cavity functions as a dynamic interface between host immunity and the external environment (84). This continuous microbial influx complicates the distinction between resident and transient species. Nevertheless, accumulating evidence indicates that specific oral pathogens can disseminate beyond the oral cavity, via saliva, biliary pathways, hematogenous spread, or lymphatic transport, to distant organs such as the gastrointestinal tract and pancreas, where they may alter local microenvironments and promote tumorigenesis (85).

In a Chinese cohort comparing the oral microbiota of individuals with PC, benign pancreatic disease (BPD), and healthy controls (HC), significant compositional differences were observed. Proteobacteria dominated the oral microbiota of healthy and BPD groups, while Bacteroidetes predominated in the PC group (85, 86). At the family level, Leptotrichiaceae, Actinomycetaceae, Lachnospiraceae, Micrococcaceae, Erysipelotrichaceae, Coriobacteriaceae, and Moraxellaceae were enriched in PC, whereas Porphyromonadaceae, Campylobacteraceae, and Spirochaetaceae were depleted (87). Nonetheless, the relative abundance of these taxa exhibits substantial variation across geographic cohorts, sample sources, and sequencing methodologies. These inconsistencies highlight the necessity of standardized analytical frameworks and cross-cohort validation to ensure reproducibility and accurate interpretation of oral microbiome-cancer associations (88, 89). Notably, PC patients exhibited elevated levels of pro-inflammatory and immunosuppressive oral pathogens such as P. gingivalis and A. actinomycetemcomitans, which activate inflammatory cascades and impair immune surveillance (90). Conversely, reductions in commensal taxa like Leptotrichia and Fusobacterium nucleatum suggest that both pathogenic overgrowth and loss of beneficial species may drive carcinogenic processes (87).

Once considered a sterile site, the pancreas is now recognized as a host to a distinct, low-biomass microbiome that becomes enriched and metabolically active during PC progression. However, this assertion must be interpreted with caution given the well-documented challenge of distinguishing genuine intrapancreatic microbial signals from reagent or procedural contaminants inherent to low-biomass tissues. Such contamination risks can confound sequencing-based analyses, underscoring the need for rigorous negative controls, contamination-aware bioinformatic filtering, and functional validation to confirm true microbial presence and activity (91, 92). Evidence indicates that both commensal and pathogenic microorganisms can translocate from the gut or oral cavity to the pancreatic tissue, where they reprogram the TME through immune modulation, inflammatory signaling, and metabolic interactions (93, 94).

In PDAC, the intrapancreatic microbiota is predominantly composed of taxa from the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with recurrent enrichment of genera such as Fusobacterium, Pseudomonas, Enterobacter, Escherichia, Klebsiella, Streptococcus, Bifidobacterium, and fungal species such as Malassezia (22, 95). These microbial populations contribute to tumorigenesis by promoting both innate and adaptive immune suppression, expanding myeloid-derived suppressor cells (MDSCs) and regulatory T cells, while attenuating cytotoxic CD8⁺ T-cell activity (36). Notably, F. nucleatum and Malassezia spp. accelerate PDAC progression by activating complement pathways, driving NF-κB dependent inflammation, and enhancing stromal fibrosis (21, 96).

In contrast, long-term PDAC survivors display a unique microbial signature characterized by higher alpha diversity and enrichment of Pseudoxanthomonas, Saccharopolyspora, and Streptomyces, taxa linked to robust antitumor immune responses and improved overall survival (22). This compositional heterogeneity underscores the potential prognostic value of intrapancreatic microbial profiles.

Beyond tumorigenesis, intratumoral bacteria influence therapeutic efficacy through metabolic interactions and immune modulation. Certain taxa are capable of enzymatically modifying anticancer drugs, thereby contributing to variable treatment responses and chemoresistance in PDAC (21). Moreover, microbiome-driven transcriptional reprogramming within the tumor compartment promotes epithelial-to-mesenchymal transition and favors basal-like PDAC subtypes, which are associated with poor prognosis (95). Deep-sequencing of intratumoral microbiota has recently delineated core microbial consortia associated with stromal remodeling and therapy response. Enrichment of Pseudomonas aeruginosa and Klebsiella oxytoca correlates with elevated IL-1β and TGF-β signaling, potentiating desmoplasia and immune exclusion (97). Conversely, tumors harboring Bifidobacterium longum and Streptococcus mitis show enhanced MHC-I expression and improved responsiveness to gemcitabine (98).

Altogether, these insights position the intrapancreatic microbiome as a dynamic and therapeutically relevant axis in PDAC biology, where precision modulation, via antibiotics, probiotics, or fecal microbiota transplantation (FMT), holds potential to enhance chemotherapeutic efficacy, sensitize tumors to immunotherapy, and reshape future paradigms in PC management (94, 99, 100).

Dysbiosis refers to an imbalance in the composition and function of the commensal microbiota, disrupting host-microbe equilibrium and predisposing to disease (101). In healthy individuals, the microbiota plays a central role in maintaining immune homeostasis, regulating metabolism, and suppressing opportunistic pathogens (102). However, when microbial balance is disturbed, a cascade of pro-inflammatory responses can be initiated. This inflammatory milieu disrupts host biochemical pathways and immune defenses, creating a permissive environment for disease progression and oncogenesis (103). In PDAC, dysbiosis-driven chronic inflammation has been linked to enhanced infiltration and activation of CD8⁺ T cells, an immune response that paradoxically coexists with an immunosuppressive TME (104).

Specific microbial taxa have been shown to influence both the immune landscape and therapeutic response in PDAC. Certain Gammaproteobacteria harbor cytidine-deaminase enzymes that metabolize gemcitabine into inactive derivatives, illustrating how microbial enzymatic activity can directly influence pharmacologic efficacy and therapeutic outcomes in PDAC (105). Another key oncomicrobe, Fusobacterium nucleatum, a Gram-negative anaerobe typically resident in the oral cavity, has been detected in both colorectal and pancreatic tumors. Under pathological conditions, it disseminates systemically, promoting tumor growth, immune evasion, and epigenetic silencing of tumor suppressor genes through hypermethylation and microsatellite instability. Mechanistically, F. nucleatum enhances secretion of IL-8 and CXCL1 and disrupts the centrosomal protein CEP55, facilitating malignant transformation (106, 107). Enterococcus faecalis, a Gram-positive facultative anaerobe, also emerges as a relevant organism in PDAC. Normally residing in the gut, E. faecalis has been detected in pancreatic juice and tissue of patients with suspected malignancy. Its resistance to alkaline environments enables survival in the pancreatic duct, where it may invade host cells via endocytosis, supporting its role as a potential microbial biomarker for PC (108).

While classically linked to gastric carcinogenesis, Helicobacter pylori is increasingly associated with pancreatic tumorigenesis. Two primary mechanisms have been proposed: (i) chronic infection leading to depletion of antral D-cells and reduced somatostatin, which in turn elevates secretin and bicarbonate secretion, inducing pancreatic ductal hyperplasia; and (ii) bacterial overgrowth and gastric hypoacidity fostering N-nitrosamine formation, potent carcinogens that cause DNA damage and neoplastic transformation (10, 109).

Another notable oral pathogen, P. gingivalis, has also been linked to PDAC. Primarily associated with periodontitis, P. gingivalis can invade the pancreas and trigger systemic inflammatory responses (110). Once established in the pancreatic tissue, it releases peptidyl-arginine deiminase (PAD), which promotes the formation of neutrophil extracellular traps (NETs). These, in turn, stimulate the release of pro-tumorigenic chemokines such as CXCL1, CXCL2, and neutrophil elastase, contributing to fibrosis, metastasis, immune evasion, and enhanced tumor proliferation (12, 33, 111).

Together, these microbial communities orchestrate chronic inflammation, immune dysregulation, epigenetic remodeling, and metabolic interference with chemotherapy, progressively transforming the TME into an immune-suppressive, pro-tumorigenic niche that underscores the microbiome’s role as a mechanistic driver and clinically actionable target in PDAC (112, 113).

The human gastrointestinal microbiota, primarily composed of four dominant phyla: Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, plays a fundamental role in the development and modulation of both the innate and adaptive immune systems (114). Disruptions to this microbial balance, or dysbiosis, can lead to chronic inflammation, genomic instability in pancreatic acinar cells, and impaired antitumor immune surveillance, key factors in the pathogenesis of PDAC (37).

Epidemiological data consistently implicate the oral microbiota as a contributor to PC risk. Elevated oral abundance of P. gingivalis (OR 1.6; 95% CI 1.15–2.22) and A. actinomycetemcomitans (OR 2.22; 95% CI 1.16–4.18) has been significantly associated with increased PDAC susceptibility (90). Beyond individual species, a meta-analysis of eight observational studies reported a higher incidence of PC in individuals with periodontitis (RR 1.74; 95% CI 1.41–2.15) and in edentulous subjects (RR 1.54; 95% CI 1.16–2.05), independent of confounders such as age, smoking, diabetes, or alcohol use (115). Expanding on these associations, pooled data from 14 observational studies (n = 1,276; 285 PDAC, 342 chronic pancreatitis, 649 controls) revealed enrichment of Actinomyces, Bifidobacterium, Veillonella, and Escherichia-Shigella, alongside depletion of Firmicutes in PDAC cohorts (116). Similarly, retrospective biliary tract analyses identified dominant Gram-negative taxa, E. coli, Klebsiella spp., and Pseudomonas spp., in PDAC but not in extra-pancreatic malignancies, suggesting their involvement in sustaining localized inflammatory and pro-tumorigenic signaling (117).

The well-recognized association between chronic pancreatitis and PC further underscores the oncogenic role of persistent inflammation (118). Inflammation-induced remodeling of the TME drives PDAC progression. The PDAC TME is dominated by a dense desmoplastic stroma, constituting up to 90% of the tumor mass, rich in pancreatic stellate cells, fibroblasts, macrophages, neutrophils, regulatory T cells, and myeloid-derived suppressor cells (MDSCs). This fibrotic niche, defined by hypoxia, acidity, and poor perfusion, facilitates immune evasion and therapeutic resistance (119). Elevated systemic concentrations of IL-6, IL-8, and IL-10 have been linked to reduced overall survival in PDAC patients (HR 0.204, 0.303, 0.336; all p < 0.05), highlighting their prognostic significance (120). Mechanistically, microbial dysbiosis triggers Toll-like receptor (TLR) activation in monocytes, promoting their M2 macrophage polarization and IL-10 secretion, thereby suppressing cytotoxic T-cell responses. TLR-mediated signaling also supports MDSC expansion and Th2 differentiation while impairing Th1 and CD8⁺ T-cell activity (121). Key cytokines within the TME, including GM-CSF and CXCL1, further sustain metastatic potential and chemotherapy resistance (111). These findings delineate a microbiome-immune axis that orchestrates chronic inflammation, immune tolerance, and stromal remodeling in PDAC. Microbial dysbiosis emerges not merely as a byproduct of disease but as a central driver of tumor-promoting immunity, positioning the microbiome as a promising frontier for biomarker discovery and targeted intervention in PC (122).

Integrative analyses underscore that the microbiome-immune-stromal triad governs PDAC evolution. Single-cell transcriptomic and metagenomic coupling demonstrated that microbial lipopolysaccharide and peptidoglycan signatures activate tumor-associated fibroblasts, inducing CXCL12-mediated immune sequestration and chemoresistance (38). This microbial-stromal axis adds a new mechanistic layer to chronic inflammation and may explain why anti-inflammatory interventions alone yield limited efficacy (97).

Current therapeutic strategies for PC primarily involve surgical resection, when feasible, in combination with adjuvant systemic chemotherapy, with or without radiotherapy. Commonly employed chemotherapy regimens include gemcitabine monotherapy, gemcitabine plus capecitabine or cisplatin, and folfirinox (a combination of fluorouracil, leucovorin, irinotecan, and oxaliplatin) (123). Despite these interventions, treatment outcomes remain poor, with minimal improvement in long-term survival. Both chemotherapy and radiotherapy disrupt intestinal mucosal integrity, promoting dysbiosis characterized by loss of microbial diversity and functional imbalance. This microbial disruption aggravates gastrointestinal toxicity, manifested as nausea, vomiting, and diarrhea, and impairs anti-tumor immunity, further limiting therapeutic efficacy (124, 125).

Bacterial cytidine deaminase converts gemcitabine into its inactive metabolite, 2′,2′-difluorodeoxyuridine, thereby reducing intracellular drug availability and fostering chemoresistance. This mechanism, identified in Gammaproteobacteria such as E. coli and Klebsiella pneumoniae, exemplifies the metabolic interplay between tumor-associated microbes and pharmacologic response. Translational evidence links elevated microbial cytidine-deaminase activity with diminished chemotherapeutic efficacy in PDAC, underscoring the potential of microbiome-targeted strategies to restore drug sensitivity and improve patient outcomes (21, 105, 126).

Certain gut taxa counteract these adverse effects by enhancing immune surveillance and metabolic homeostasis. Bifidobacterium and Faecalibacterium, for instance, ferment dietary substrates into SCFAs such as butyrate, which exert potent anti-inflammatory and immunomodulatory functions (127). Butyrate enhances cytotoxic responses by stimulating CD4⁺ and CD8⁺ T cells to produce interferon-γ (IFN-γ), facilitating tumor-infiltrating lymphocyte recruitment and malignant cell clearance (128). Conversely, intestinal dysbiosis can attenuate chemotherapy responsiveness. In a murine model, Kesh et al. showed that diabetic mice with altered gut microbiota developed resistance to gemcitabine/paclitaxel compared to non-diabetic controls, underscoring the microbiome’s influence on pharmacodynamics (129).

The PDAC immune landscape is further shaped by checkpoint pathways such as PD-1/PD-L1 and CTLA-4, which suppress T-cell activity. Immune checkpoint inhibitors (ICIs) restore anti-tumor immunity by blocking these inhibitory signals (130). Notably, antibiotic-induced microbial depletion increased PD-L1 expression and enhanced ICI efficacy in PDAC mouse models (21). Yet some microorganisms foster chemoresistance. E. coli and Saccharomyces cerevisiae express cytidine deaminase, which inactivates gemcitabine by converting it into 2′,2′-difluorodeoxyuridine (126). In a cohort of 712 early-stage PDAC patients, antibiotic administration within 1 month of chemotherapy initiation improved overall survival by 37% and cancer-specific survival by 30%, though at the cost of increased treatment-related toxicity (131). Similarly, concurrent antibiotic use in metastatic PDAC was associated with higher rates of hematological toxicity, including anemia, thrombocytopenia, leukopenia, and neutropenia (132).

Microbiome modulation has therefore emerged as a promising adjunctive strategy. Probiotic-derived metabolites such as ferrichrome from Lactobacillus casei trigger p53-dependent apoptosis and DNA fragmentation in chemoresistant cancer cells, reducing tumor burden in murine models (133). Likewise, butyrate produced by Firmicutes preserves epithelial barrier integrity and suppresses neoplastic transformation in gemcitabine-treated mice (134). Another promising approach is FMT. In a seminal study, Riquelme et al. transplanted fecal samples from long-term (>5 years) and short-term (<5 years) PDAC survivors into murine models. Mice receiving microbiota from long-term survivors exhibited significantly reduced tumor growth, suggesting that specific microbial configurations may contribute to better clinical outcomes (22). Building on these findings, a phase I clinical trial (NCT04975217) is currently evaluating the safety and efficacy of FMT in PDAC patients undergoing surgical resection (71). While preclinical studies highlight the therapeutic promise of microbiota modulation, translation into routine clinical practice remains limited, and robust, randomized trials are essential to determine efficacy, safety, and durability of response in humans.

Building on this rationale, integrative immunotherapy platforms now combine checkpoint modulators, oncolytic or vaccine approaches, and engineered immune cells within microbiome-aware frameworks. These strategies exploit microbial influences on antigen presentation, cytokine balance, and myeloid polarization, aligning with chronotherapy-based and aI-assisted response modeling (135). However, some mechanistic frameworks, such as the proposed neuro-immune–microbiota axis, are supported largely by studies in colorectal, gastric, and neuroinflammatory disease models rather than pDAC-specific evidence. in these systems, neuropeptides (e.g., CGRP, substance P, VIP) reshape fibroblast activation, myeloid behavior, and lymphocyte trafficking, processes that may be relevant to PDAC but remain insufficiently validated in this tumor type (136, 137). Parallel advances nonetheless suggest that neuronal stress and neuromodulatory signaling could influence stromal architecture and immune tone. Accordingly, we present the neuro-immune–microbiota axis as an emerging, hypothesis-generating concept that warrants targeted mechanistic investigation before clinical integration in PDAC (17).

The intricate interplay between the gastrointestinal, urogenital, oral, and intrapancreatic microbiomes and PC highlights a paradigm shift in our understanding of tumorigenesis, inflammation, and therapeutic resistance. Mounting evidence demonstrates that the microbiota is not merely a bystander but an active participant in modulating pancreatic oncogenesis, immune evasion, and chemoresistance (29, 86, 103). The gut microbiome influences PC onset and progression through dysbiosis, metabolite dysregulation, and immunosuppressive signaling, an axis that holds significant diagnostic and therapeutic potential (9, 10). Concurrently, urogenital microbiota signatures, particularly urinary metabolites and exosomal microRNAs, have emerged as promising non-invasive biomarkers (51). The oral microbiome, especially species such as F. nucleatum and P. gingivalis, has been associated with increased PC risk, suggesting potential utility in early detection through salivary or dental microbiota screening (90). Notably, the pancreatic TME harbors a low-biomass but metabolically active intratumoral microbiota, composed mainly of Fusobacterium, Pseudomonas, Klebsiella, Escherichia, Streptococcus, Bifidobacterium, and Malassezia species, which promotes immune suppression, modulates antitumor immunity, and inactivates drugs like gemcitabine through microbial enzymes (93). Throughout this review, we distinguish mechanisms supported by direct PDAC evidence from those inferred from other malignancies or systemic disease models, explicitly framing the latter as emerging and hypothesis-generating axes.

Emerging evidence positions the microbiome as a metabolic, immunologic, and stromal integrator of pancreatic carcinogenesis. High-resolution multi-omic datasets reveal that intratumoral microbial genes regulating nucleotide salvage and SCFA synthesis predict immunotherapy responsiveness and survival (31, 98). Likewise, microbiota-driven metabolic rewiring, particularly involving the tryptophan-kynurenine and bile-acid axes, defines the inflammatory and immunometabolic trajectories of PDAC progression (32). These insights expand the conventional view of dysbiosis beyond compositional shifts, highlighting functionally active microbial pathways that interface with oncogenic signaling and therapeutic resistance. At the same time, several of these functional links are more robustly established in colorectal and hepatobiliary cancers or metabolic disease than in PDAC, underscoring the need for dedicated pancreas-focused validation. In parallel, comparative work has exposed substantial cross-cohort and platform-dependent variability in microbial signatures, showing that many candidate “oncomicrobes” and risk scores lose discriminatory power when transferred across populations, especially when derived from 16S rRNA sequencing rather than shotgun metagenomics or multi-kingdom profiling. Consequently, future PDAC microbiome frameworks must integrate robust, harmonized pipelines (including shallow shotgun metagenomics, virome/mycobiome interrogation, and standardized analytical workflows) to move from cohort-specific associations toward reproducible, clinically actionable signatures (147, 161–163).

Beyond composition alone, an emerging temporal layer has been proposed to integrate the gut–pancreas axis with host clocks: peripheral circadian oscillators in the gut and pancreas coordinate immune tone, metabolic flux (e.g., bile-acid and tryptophan pathways), and barrier function, while diurnal microbiota rhythms reciprocally entrain clock gene programs in distal tissues (164–167). To date, these circadian–microbiome interactions have been demonstrated predominantly in metabolic and gastrointestinal disease models rather than in PDAC-specific cohorts. Disruption of this bidirectional circuit, by shift work, irregular feeding, or metabolic stress, induces dysbiosis, amplifies inflammatory signaling, and degrades antitumor immunity in experimental systems, raising the hypothesis that similar perturbations could contribute to pancreatic tumor promotion and therapy resistance (20, 165, 166). We therefore consider the circadian–microbiome–pancreas axis a conceptual, hypothesis-generating framework that requires targeted mechanistic and clinical studies in PDAC. Conceptually, microbe-host control of gene regulation extends to epigenetic remodeling: in virus-driven cancers, oncoproteins rewire DNA methylation and histone marks to sustain immune evasion and oncogenic transcriptional states, an instructive paradigm that underscores how exogenous biological agents can durably program host chromatin and suggests analogous, testable mechanisms for microbiome-linked PDAC biomarkers and interventions (111, 168).

Mechanistically, inflammation remains central. Microbiota-induced immune dysregulation, including T cell exhaustion and myeloid cell reprogramming, drives tumor progression and therapy failure (44). Certain bacteria, such as Enterococcus faecalis and H. pylori, have been shown to invade pancreatic tissue, exacerbating inflammation and mutagenesis (108). Bacterial colonization of the pancreatic TME is now recognized not as incidental but as functionally active. Intratumoral microbiota may directly contribute to chemoresistance through enzymatic drug degradation, particularly against gemcitabine, and modulate immunosurveillance. Microbiota-driven inflammatory circuits, particularly those involving LPS-TLR4 and downstream cytokine signaling, remain pivotal in sustaining immune evasion and tumor progression (52, 105, 112). Emerging research highlights that the microbiome also modulates therapeutic response. Strategies such as FMT, narrow-spectrum antibiotics, or probiotic regimens are being explored to improve immunotherapy outcomes or reverse drug resistance. These approaches are especially relevant in the era of precision oncology, where patient-specific microbial signatures could inform individualized treatments (14, 49, 71). Yet, recent low-biomass and contamination-aware re-analyses caution that some earlier associations between intratumoral bacteria and gemcitabine inactivation or ICI response may have overestimated microbial contribution, emphasizing the need to corroborate sequencing-based findings with culture, metabolomics, gnotobiotic models, and spatially resolved host–microbe mapping before translating them into routine clinical practice. Single-cell and spatial multi-omic studies that jointly profile fibroblasts, myeloid cells, lymphocytes, and microbial or microbial-derived signals are poised to refine which immune–stromal circuits are truly microbiome-dependent versus driven by tumor-intrinsic programs (169–171).

Looking forward, the microbiome stands as both a risk factor and therapeutic ally in PC, a duality that, if effectively decoded, may revolutionize prevention, early diagnosis, and individualized therapy in this highly lethal malignancy (20, 166). Harnessing multi-omic profiling to disentangle the complex host-microbiome-tumor crosstalk offers a promising avenue to identify mechanistic drivers and actionable biomarkers. Integrative analyses combining metagenomics, transcriptomics, metabolomics, and immunomics have already revealed microbial fingerprints with diagnostic and therapeutic relevance (21, 132). Prospective, longitudinal clinical trials are urgently needed to evaluate the efficacy and safety of microbiome-informed diagnostics and therapeutics in PC (111). In this context, enthusiasm for urine-based and serum-based biomarker panels must be tempered by evidence that diagnostic performance often attenuates in pre-diagnostic, screening-like settings compared with retrospective case–control cohorts, and that analytical variability across platforms can substantially affect sensitivity and specificity. Harmonized pre-analytical protocols, external quality assessment schemes, and regulatory-grade validation (including multi-center, multi-ethnic cohorts) will be required before microbiome-derived or microbiome-reflective biomarkers can be responsibly incorporated into PDAC surveillance algorithms for high-risk populations (75, 172).

The coming decade may well redefine PC management through the lens of microbial ecology. Integrative microbiome profiling will likely transform microbial ecosystems into actionable determinants of therapeutic precision, bridging the gap between microbial biology and individualized cancer management, and positioning microbiome modulation as a cornerstone of next-generation PC prevention and treatment (37, 167, 168). Key priorities will include (i) establishing international PDAC microbiome consortia with shared biobanking and harmonized sequencing pipelines; (ii) embedding microbiome endpoints into interventional trials of chemotherapy, radiotherapy, and immunotherapy; (iii) rationally designing microbiome-targeted interventions (live biotherapeutics, diet-based strategies, narrow-spectrum antibiotics, engineered phages, or FMT) with clear mechanistic hypotheses; and (iv) ensuring that data and analytical tools remain openly accessible to accelerate replication, meta-analysis, and translation. If these goals are met, the microbiome may transition from a descriptive biomarker of PDAC to a controllable axis of disease modification and therapeutic optimization.