Tumor-Resident Bacteria: Mechanisms of Carcinogenesis, Metastasis and Clinical Implications

Abstract

The human microbiome constitutes an intricate ecosystem comprising bacteria, viruses, fungi, and archaea, which are localized across different anatomical sites, including the skin, oral cavity, respiratory system, and gastrointestinal tract. The microbiota (the microbial community within the body) plays a crucial role in cancer by affecting its initiation, progression, and treatment response. Genomic instability, chronic inflammation, and metabolite production are some features that are responsible for initiation. It is a major regulator of the immune system. Though some beneficial microbes promote anti-tumor immunity it can create an immunosuppressive tumor microenvironment, enabling cancer to evade immune destruction, affecting cancer therapy efficacy. The rapid advancement of high-throughput sequencing has yielded increasing evidence for the existence of a microbial community within tumor tissue. It is crucial to explore the mechanisms of intratumor microbe migration, their potential carcinogenic roles, the defining features of different types of tumor-associated microbes, the methodologies used in tumor microbiota research, and the clinical value of targeting these microbes in cancer therapy. The diverse environments provided by various tissues and organs critically influence host–microbe interactions.

Keywords

microbiology - infection - cancer pathology - tumor-resident bacteria

Introduction

The human microbiome constitutes an intricate ecosystem comprising bacteria, viruses, fungi, and archaea, which are localized across different anatomical sites, including the skin, conjunctiva, oral cavity, saliva, respiratory system, gastrointestinal tract, seminal fluid, uterus, and ovarian follicles. The diverse environments provided by various tissues and organs critically influence host–microbe interactions. Recently, the interest has shifted from the tumor-associated microbiota to tumor-resident bacteria (TRB) for their critical regulatory role in cancer biology, depending on the rapid development of high-throughput next-generation gene sequencing, 16S rRNA gene sequencing, and state-of-the-art in situ spatial-profiling technologies. This has yielded increasing evidence for the existence of a microbial community in low-abundance microniches of the highly immunosuppressive, challenging tumor microenvironment (TME) within tumor tissue. The collective evidence positions the TRB not as mere contaminants but as integral, functional components of the TME, fundamentally shaping the course of the disease. It is worthwhile to examine origin of microbiota, mechanisms of intratumor microbe migration, their intricate interactions with the TME, their potential carcinogenic roles, the defining features of different types of tumor-associated microbes, their dual influence on both tumor suppression and promotion and metastasis, the methodologies used in tumor microbiota research and the clinical value of targeting these microbes in cancer therapy, drug response, and immunotherapy. The human microbiota consists of trillions of microorganisms and a second genome that is distinct from the human genome, and their collective gene count exceeds that of the human genome by over 150-fold.[1]

It plays a significant role in human health.[2] Though the presence in tumor was predicted in the 19th century, contamination issues blocked any progress. Marshall and Warren isolated Helicobacter pylori from the gastric mucosal biopsy specimens of a chronic gastritis patient in 1984, and in 2006, colibactin from gut bacteria of the Enterobacteriaceae family was shown to cause DNA damage and carcinogenesis.[3]

Accurate genetic testing of TRB and fungus is done in the early part of the present decade using next-generation sequencing (NGS) and 16s rRNA technology.[4] [5] TRB are foundational to be lodged inside the cancer and immune cytoplasm. Niño et al[6] used in situ spatial-profiling and could locate them in highly immunosuppressive microniches amongst plenty of CD66b+ myeloid cells in arginase1 and CTLA-4 rich environment, raising a possibility of interaction between TRB and TME components.

Origin of Intratumoral Microbiota

There are four proposed mechanisms for the microbiota being found in tumors: mucous membrane barriers, for tumors near mucosal sites (e.g., lung, colorectal, pancreatic cancers), a compromised mucosal barrier during tumorigenesis can allow colonizing bacteria to invade the TME. This, however, is unlikely for tumors far from mucosal surfaces. Tumor-adjacent normal tissue: the similarity between the microbial spectrum in cancer tissue and normal tissue in the vicinity suggests the latter as a possible source. However, the direction of spread (normal to tumor, tumor to normal, or local expansion) remains unclear. The gut–organ axis: the microbiota from the gut may reach various tumor sites via this pathway.[7] This has been shown by detecting the Malassezia taxon in pancreatic cancer. Hematogenous spread (circulatory system): the bloodstream can act as a conduit for bacteria to reach tumors. Yu and colleagues used a few fluorescent Escherichia coli, Vibrio cholerae,

Typhimurium and Listeria monocytogenes bacteria, which reached the urinary bladder and distant organs like the brain without detectable bacteremia.[8] This process is facilitated by (1) Passive mechanisms: leaky, disorganized tumor vessels allow bacteria to passively access the tumor from the blood. (2) Active mechanisms: specific interactions, such as the bacterial Fap2 protein binding to the Gal-GalNAc molecule overexpressed on some cancer tissues (e.g., colorectal and breast cancer), enable selective adherence and infiltration.[9] A key example is Fusobacterium nucleatum, which traveled to tumors from the mouth via this Fap2-mediated mechanism. Migration and colonization may happen through multiple routes: the same bacterium, such as F. nucleatum, can utilize different migration routes, including both hematogenous spread (from the mouth via transient bacteremia) and direct translocation (descending the digestive tract). Comparative genomic analyses of microbiota from various sites (fecal, oral, normal, tumor) can help trace the origin and migration patterns of TRB, such as suggesting the nasopharynx as the source for bacteria in nasopharyngeal carcinoma or the oral cavity for Porphyromonas gingivalis in pancreatic cancer. Regardless of the source, the immunosuppressive, nutrient-rich, and hypoxic TME creates ideal conditions, an attractant for bacterial colonization and persistence. Facultative and obligate anaerobes are particularly drawn to hypoxic and necrotic tumor regions, which offer nutrients and protection from immune responses.[10] Bacteria employ sophisticated strategies to survive in the TME, including manipulating host cell cytoskeleton to avoid phagocytosis, disrupting endosomal membranes to evade bacteriolysis, and forming protective biofilms (immune evasion).

Role in Carcinogenesis

The presence of specific bacteria within tumors (TRB) is a critical factor in the initiation and progression of various cancers. The oncogenic potential of these microbes is multifaceted, primarily by inducing chronic inflammation, altering the TME, disrupting key signaling pathways, and causing direct DNA damage. Microbes use specific adhesins and toxins to infiltrate host cells and manipulate internal regulatory networks. Certain bacterial strains produce genotoxins or reactive oxygen species that induce DNA adducts and double-strand breaks, foster persistent inflammation, and promote the infiltration of supportive immune cells (like Th17 cells). Fusobacterium nucleatum (CRC, Pancreatic, Breast Cancer): F. nucleatum is linked to advanced disease and poor outcomes. Its FadA adhesin binds to E-cadherin, activating the Wnt/β-catenin signaling pathway.[11] This process is reinforced by Annexin A1 (ANXA1) in a positive feedback loop. F. nucleatum also promotes CRC stemness via its metabolic product, formate, and activates the TLR4/MYD88/NF-κB cascade, leading to miR-21 upregulation.[12] Helicobacter pylori (gastric cancer): classified as a Type I carcinogen, H. pylori uses its HopQ adhesin to bind to gastric cells, enabling the delivery of the virulence factor CagA. CagA disrupts cell proliferation and apoptosis pathways, fostering a pro-inflammatory TME. Streptococcus anginosus (gastric cancer): this bacterium promotes epithelial cell transformation by activating the MAPK pathway after its TMPC protein binds to the ANXA2 receptor.[13] Bacteroides fragilis (colonic tumorigenesis): enterotoxigenic strains (ETBF) promote chronic inflammation and colonic tumorigenesis by activating the IL-17-dependent NF-κB signaling pathway. Escherichia coli (DNA damage): certain pks+ strains produce the genotoxin colibactin,[3] which directly induces DNA damage (adducts and double-strand breaks), contributing to genomic instability and a distinctive mutational signature in CRC patients. These findings suggest that TRB can be key targets for cancer prevention and treatment, as seen in the chemopreventive effect of Aspirin, which modulates F. nucleatum growth and adhesin expression and reduces the expression of its pro-tumorigenic adhesins (FadA and Fap2).

Certain anaerobic bacteria, such as Clostridium sporogenes strains and Bifidobacterium longum, use their capabilities to survive in oxygen-free cancer environments and could cause cancer cell death.[14] [15] Salmonella typhimurium can use the β-catenin pathway of type III secretion system effector AvrA in gut cells, thus causing tumor growth.[5] Fostering pro-tumoral phenotypes: in lung cancer patients, commensal bacteria produce MyD88-dependent IL-1β and IL-23 producing myeloid cells and IL-17-producing and Vγ6/Vδ1+ T cells. The Fap2 protein of Fusobacterium nucleatum inhibits immune cells through TIGIT when cancer cells secrete CXCL16/RhoA/IL-8 and miR-1246/92b-3p/27a-3p exosomes. Inhibiting Cytotoxicity: F. nucleatum and P. gingivalis use iNKT cells and chitinase 3-like-1 protein (CHI3L1) for tumor growth.[16] P. gingivalis and F. nucleatum use neutrophils and macrophage infiltration for growth promotion.

Influence the Host Immune System

Fostering pro-tumoral phenotypes: in lung cancer patients, pulmonary commensal bacteria stimulate myeloid cells to produce MyD88-dependent IL-1β and IL-23, which can activate the proliferation of IL-17-producing and Vγ6/Vδ1+ T cells, leading to inflammation and promoting tumor cell growth. The Fap2 protein produced by Fusobacterium nucleatum can engage with the immune checkpoint protein TIGIT, thereby suppressing the function of immune cells. Fusobacterium nucleatum-infected colorectal cancer (CRC) cells secrete exosomes enriched with miR-1246/92b-3p/27a-3p and containing CXCL16/RhoA/IL-8. Inhibiting Cytotoxicity: F. nucleatum and P. gingivalis convert iNKT cells to a pro-tumoral state and suppress cytotoxicity by upregulating checkpoint protein chitinase 3-like-1 protein (CHI3L1).[16] P. gingivalis also recruits suppressive tumor-associated neutrophils, while F. nucleatum favors M2 macrophage infiltration.

Conversely, some TRB promote anti-tumor immunity. Lactobacillus reuteri releases postbiotics (like I3A) that activate CD8+ T cells to boost IFN-γ and enhance anti-PD-L1. Bifidobacterium uses STING signaling to enhance dendritic cell antigen presentation, aiding anti-CD47 therapy.[17] Pancreatic cancer tissue harbors an abundant microbiome that selectively interacts with toll-like receptors in pancreas cancer transform CD4+ cells to TH1 and activates CD8 T cells.

The effects are thus paradoxical. F. nucleatum causes chemoresistance but can enhance anti-PD-1 therapy in MSS CRC by repressing PD-1 via bacterial butyric acid. Finally, the bacterial peptides on HLA suggests TRB based cancer vaccines.

Chemo-Resistance

TRB can modify the effects of anti-cancer drugs, similar to gut microbes. This influence, known as chemoresistance, occurs through both direct enzymatic modification and indirect mechanisms altering the TME. For example, Gammaproteobacteria in pancreatic cancer can directly inactivate the chemotherapy agent gemcitabine using the enzyme cytidine deaminase.[18] Similarly, E. coli in CRC metabolizes 5-fluorouracil (5-FU), protecting both cancer cells and susceptible bacteria like F. nucleatum, thus promoting recurrence. Indirectly, F. nucleatum causes 5-FU resistance through BIRC3 and activates autophagy.[19] Another bacterium, Lactobacillus iners, may cause resistance to both radiation and gemcitabine by rewiring tumor metabolism through increased bacterial L-lactate. Understanding how TRB alters drug efficacy is crucial for developing targeted interventions to overcome treatment resistance.

Role in the Metastatic Process

TRB are active participants, not passive passengers, in the complex process of cancer metastasis. Evidence shows specific bacteria, including F. nucleatum and B. fragilis, persist and remain viable in both primary tumors and distant metastases (e.g., liver or lung), confirming their ability to migrate. TRB promotes metastasis through several mechanisms: for example, the modulation of cell adhesion and epithelial-mesenchymal transition (EMT) is driven by F. nucleatum, which facilitates cancer cell adhesion to vascular endothelial cells and promotes extravasation by activating the NF-κB pathway to upregulate ICAM-1, while also enhancing cell migration and EMT by upregulating lncRNA EVADR.[20] Furthermore, Cytoskeleton Reorganization is a mechanism where intracellular bacteria help circulating cancer cells survive fluid shear stress and promote colonization at distant sites by reorganizing the host cell's actin cytoskeleton. Finally, premetastatic niche formation occurs when tumor-resident E. coli C17 disrupts the gut vascular barrier and translocates to the liver, creating an inflammatory premetastatic niche that facilitates subsequent cancer cell seeding, aligning with the “seed and soil” hypothesis. The observation that microbial community composition is often organ-specific supports the idea of microbial tropism, where certain bacteria may precondition organs, making them more favorable for metastatic establishment. Identifying these migrating species is key to new prognostic biomarkers ([Fig. 1] and [Table 1]).

Fig. 1 The role of tumor microbiome in cancer development and treatment.[11]

Table 1 Migration routes of organism and sources

Mechanism	Primary source	Example pathogen	Targeted cancer
Mucosal breach	Local mucosa	Local flora	Lung, colorectal
Gut–organ axis	Intestines	Malassezia	Pancreatic
Hematogenous	Oral cavity/blood	F. nucleatum	Breast, colorectal
Direct translocation	Nasopharynx	Local microbiota	Nasopharyngeal

Clinical Applications of Intratumoral Microbiota

In recent decades, antimicrobial treatment has emerged as a strong player in oncology,[7] utilizing two approaches: (1) activating immunity with bacterial antigens or products. (2) in drug delivery or using engineered bacteria.[21] They destroy cancer cells by invasion or anaerobic growth.[14] Though nano and other technology has been helpful[22] lots remain to be done in complying with biosafety measures when using them clinically

Bacteria for Therapeutic Intervention

Microbiotherapy is a novel cancer strategy with roots tracing back to Coley's toxins in 1891.[23] Newer approaches primarily involve activating anti-tumor immunity with microbial antigens or using bacteria as engineered drug delivery vectors. Various bacteria, including Clostridium, Bifidobacterium, and E. coli, are explored due to their ability to invade and colonize tumors, often exploiting anaerobic conditions for destruction.[14] Innovative strategies are now leveraging microbes for cancer therapy, primarily through fecal microbiota transplantation to modulate gut microbiota, and through engineered probiotic bacteria.[24] Advances in synthetic biology allow the reprogramming of live bacteria into safe, immune-stimulating carriers that deliver therapeutic agents, such as cytokines (e.g., engineered E. coli delivering IFN-γ) and metabolic products, directly to tumor sites to minimize off-target effects. Other approaches exploit molecular mimicry, where bacterial peptides structurally homologous to tumor antigens (like FLach peptides) are used to prime the immune system against tumors.[25] Bacteria can also be used to induce the release of novel immunogenic peptides via endoplasmic reticulum stress, representing a unique source for cancer vaccine development. Furthermore, the introduction of immunogenic species, such as H. hepaticus, can promote the formation of tumor-associated tertiary lymphoid structures, which are associated with boosting anti-tumor immune responses and potentially improving outcomes in immunotherapy.[26]

Methods to Study Intratumor Microbiota

Profiling TRB using NGS technologies, like whole-metagenome shotgun sequencing (WMS) and 16S rRNA gene sequencing, faces significant challenges.[27] The main difficulty stems from the low bacterial DNA biomass in tumors and the overwhelming presence of host DNA, demanding careful experimental design and rigorous controls to mitigate environmental contamination. Advancements include using multi-region 16S rRNA sequencing (e.g., the 5R method) for better resolution and employing microbial enrichment kits to prepare samples for high-resolution WMS. Since NGS primarily shows correlation, it must be complemented by functional approaches. Imaging-based methods, such as FISH, in situ spatial-profiling technologies assess presence, while culturomics helps confirm bacterial viability. Mechanistic insights require advanced co-culture protocols using 3D systems like “inverted” organoids or microinjection techniques, which mimic the natural host–microbe interface.[28] [29] Moving forward, an integrative, multimodal strategy combining more sensitive sequencing, optimized enrichment, and robust in vivo and in vitro models is essential to overcome current limitations and establish the causal roles of TRB in tumor biology. Newer software, QIIME, is now used for sequencing and metacentric studies, and the field is ever-increasing.

Conclusion

TRB exhibits a dual role, either promoting or hindering tumor progression and therapeutic efficacy, underscoring the need for selective interventions. Strategies to deplete detrimental TRB must overcome the lack of specificity associated with broad-spectrum antibiotics, which risk eliminating beneficial microbes and inducing dysbiosis. Promising alternatives include targeted delivery systems, such as liposomes (e.g., LipoAgTNZ) that specifically eliminate tumor anaerobes without affecting the gut, and bacteriophages, which can precisely target and penetrate bacterial biofilms (like those of F. nucleatum).[29] Despite technical progress, critical questions persist regarding the causal, temporal, and spatial relationships of TRB within the TME. Fully unraveling these complexities, including unexamined microbe–microbe interactions, requires an integrated, multimodal methodological approach combining advanced imaging, sequencing, culturomics, and robust in vivo and in vitro studies.

Conflict of Interest

None declared.

Patient Consent

Not applicable as it is a review work.

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Publication History

Article published online:
28 February 2026