Gut microbiota and the colorectal cancer tumor microenvironment: From carcinogenic mechanisms to therapeutic opportunities

Abstract

Colorectal cancer (CRC) is ranked as the third most common tumor globally, representing approximately 10% of all cancer cases, and is the second primary cause of cancer-associated mortality. Existing therapeutic approaches demonstrate limited efficacy against CRC, partially due to the immunosuppressive tumor microenvironment (TME). In recent years, substantial evidence indicates that dysbiosis of the gut microbiota and its metabolic products is closely associated with the initiation, progression, and prognostic outcomes of CRC. In this minireview, we systematically elaborate on how these microbes and their metabolites directly impair intestinal epithelial integrity, activate cancer-associated fibroblasts, remodel tumor vasculature, and critically, sculpt an immunosuppressive landscape by modulating T cells, dendritic cells, and tumor-associated macrophages. We highlight the translational potential of targeting the gut microbiota, including fecal microbiota transplantation, probiotics, and engineered microbial systems, to reprogram the TME and overcome resistance to immunotherapy and chemotherapy. A deeper understanding of the microbiota-TME axis is essential for developing novel diagnostic and therapeutic paradigms for CRC.

Key Words: Gut microbiota; Tumor immune microenvironment; Colorectal cancer; Tumor stromal cells; Immune cells

Core Tip: This minireview synthesizes current insights into how gut microbiota and their metabolites bidirectionally shape the colorectal cancer tumor microenvironment, moving beyond epithelial barrier disruption to delineate direct immunomodulatory effects on stromal and immune cells. We highlight the translational potential of microbiota-targeting strategies, such as fecal microbiota transplantation and engineered microbes, in reprogramming the immunosuppressive niche to overcome therapy resistance.

INTRODUCTION

Colorectal cancer (CRC) is a major global public health challenge. Its high morbidity and mortality together constitute a heavy disease burden. It ranks third in incidence and second in mortality among malignant tumors globally[1]. The current therapeutic efficacy for CRC remains limited, and the core reason is its immunosuppressive microenvironment. Recent research evidence has shown that the imbalance of intestinal flora and its metabolites is closely related to the occurrence, development, progression, and clinical prognosis of CRC[2]. This minireview discusses the mechanisms of interactions between gut microbiota and different cell populations within the tumor microenvironment (TME), analyzes the effects on the progression of CRC, and further elucidates their translational potential in clinical applications.

MICROBIOTA AND NONIMMUNE CELLS

Gut microbiota affects nonimmune cells in CRC through multiple mechanisms. Some bacteria directly induce DNA damage and impair epithelial barrier integrity in intestinal epithelial cells. Other bacteria modulate the metabolic remodeling of cancer-associated fibroblasts (CAFs) and impact the function of vascular endothelial cells (ECs), thereby contributing to the establishment of an immunosuppressive microenvironment.

EFFECTS OF MICROBIOTA ON INTESTINAL EPITHELIAL CELLS

In CRC patients, especially those with colitis-associated CRC, the microbiota composition of stool and mucosal samples is significantly different from those of healthy individuals[3]. A variety of bacteria can directly damage intestinal epithelial cells and destroy the mucosal barrier through direct or indirect mechanisms, thereby promoting tumorigenesis.

Among these bacteria that disrupt the intestinal barrier and drive tumorigenesis, adherent-invasive Escherichia coli serves as a typical example. It relies on pili-mediated adhesion to colonize the mucosa and induce persistent inflammation, which in turn leads to excessive epithelial proliferation and gradual progression to adenoma and colon cancer[4]. E. coli strains carrying the “pks” pathogenic island encode the genotoxin colibactin, which triggers DNA double-strand breaks and cellular senescence in intestinal epithelial cells, ultimately leading to abnormal proliferation and malignant transformation[5].

In addition, Fusobacterium nucleatum is significantly enriched in tumor tissue samples from CRC patients. Studies have demonstrated that its surface adhesin FadA triggers the β-catenin signaling pathway through binding to E-cadherin, thereby promoting oncogenic transcriptional programs[6]. However, it is still controversial whether the protumor effect of this bacterium is entirely dependent on the inflammatory response.

Similarly, enterotoxigenic Bacteroides fragilis directly splits E-cadherin and disrupts epithelial barrier integrity by secreting the metalloprotease fragilysin. It indirectly activates the STAT3/Th17 immune axis and triggers the secretion of protumor inflammatory factors, thus facilitating the onset and progression of CRC[7].

EFFECTS OF MICROBIOTA ON CAFs

CAFs serve as the core stromal cells within the TME of CRC. These cells remodel the extracellular matrix through the release of diverse signaling molecules, including transforming growth factor (TGF)-β, interleukin (IL)-6, and hepatocyte growth factor, and are crucial in facilitating tumor proliferation, invasion, metastasis, as well as chemotherapy resistance[8,9].

Gut microbiota dysbiosis can regulate the functions of CAFs through multiple pathways, thereby influencing CRC progression. First, the microbiota exerts effects via its metabolites. For example, short-chain fatty acids (SCFAs) can alter the metabolic reprogramming of CAFs, specifically enhancing the glycolysis level of CAFs, which ultimately promotes the formation of an immunosuppressive microenvironment[10].

Beyond metabolites, specific strains within the gut microbiota also exhibit significant differential regulation of CAF functions[11]. For example, Bifidobacterium adolescentis regulates the CD143⁺ CAFs subset, and upregulates expression of the Wingless/Int-1 (Wnt) signaling pathway inhibitor GAS1, thereby inhibiting the occurrence of colorectal tumors. Animal experiments have shown that supplementing this strain can significantly reduce tumor burden and improve prognosis[12]. Conversely, F. nucleatum and its secreted outer membrane vesicles directly activate CAFs, resulting in increased expression of CAF markers (such as fibroblast activation protein and -smooth muscle actin), and facilitating the secretion of proinflammatory factors including IL-6 and TGF-β. This activation enhances the invasive function of CAFs, accelerating tumor progression and chemotherapy resistance. Additionally, microbiota derivatives such as lipopolysaccharide activate CAFs via the TLR/NF-κB signaling pathway, thereby upregulating the CXCL12/CXCR4 axis and promoting epithelial-mesenchymal transition and tumor metastasis[13].

EFFECTS OF MICROBIOTA ON VASCULAR ECs

Vascular ECs are a single layer of flat cells that constitute the inner wall of blood vessels and play a key role in maintaining vascular barrier and regulating substance exchange[14]. In CRC, tumor ECs (TECs) exhibit significant heterogeneity compared to normal ECs, manifested at multiple levels including gene expression, cell phenotype, and functional characteristics. They typically display persistent angiogenic promotion, immunosuppression, and resistance to antiangiogenic treatments[15].

Gut microbiota regulates the functions and behaviors of TECs through multiple complex mechanisms. For example, F. nucleatum upregulates expression of EC adhesion molecule ICAM-1 through activation of the ALPK1/NF-κB/ICAM-1 signaling pathway, thereby enhancing the adhesion between tumor cells and ECs[16]. E. coli C17 impairs the gut vascular barrier via a VirF-dependent type III secretion system. This is characterized by upregulation of PV-1 protein expression, leading to the bacteria entering the bloodstream and establishing a premetastatic niche in the liver, thus promoting liver metastasis of CRC[17]. SCFAs, such as butyric acid, are produced by the microbiota. Specifically, they regulate expression of inflammation- and angiogenesis-related genes in ECs via GPR41/GPR43 receptor signaling. This regulatory effect inhibits abnormal angiogenesis and reduces vascular permeability, ultimately exerting potential antitumor effects[18].

MICROBIOTA AND IMMUNE CELLS

CRC, particularly the microsatellite stable subtype, is generally considered an immunosuppressive or “cold” tumor. The TME of CRC exhibits strong immunosuppressive properties and is enriched with various inhibitory immune cell populations. A pivotal mechanism by which the gut microbiota influences CRC progression is its ability to actively foster an immunosuppressive TME permissive of immune evasion. Microbial dysbiosis and its metabolites collaboratively achieve this by expanding immunosuppressive cell populations and inhibiting cytotoxic effector functions. For instance, microbiota-derived SCFAs such as butyrate exhibit dual roles; while potentially immunostimulatory in certain contexts, they can also promote the differentiation and function of regulatory T (Treg) cells through histone deacetylase (HDAC) inhibition, thereby suppressing antitumor immunity[19]. Pathogenic bacteria exacerbate this immunosuppressive milieu. F. nucleatum upregulates expression of immune checkpoint ligands, such as programmed death protein ligand (PD-L)1, on tumor cells and immune cells within the TME, directly contributing to T cell exhaustion and apoptosis[20]. Microbial metabolism of dietary components generates metabolites that undermine antitumor immunity. The conversion of tryptophan into the immunosuppressive kynurenine by host or microbial enzymes activates the aryl hydrocarbon receptor (AhR) in T cells, leading to cell cycle arrest and functional impairment[21]. This multifaceted interference, via the modulation of suppressive cells, checkpoint expression, and metabolic pathways, constitutes a major determinant of immunotherapy resistance in CRC.

In this section, three immune cells pivotal to the CRC immune microenvironment, including T cells, dendritic cells (DCs), and tumor-associated macrophages (TAMs), are discussed. We further elucidate the potential mechanisms by which gut microbiota and their metabolites modulate the function and phenotype of these cells.

EFFECTS OF MICROBIOTA ON T CELLS

T cells exhibit high heterogeneity in the TME of CRC, and their infiltration density, subtype composition, and spatial distribution are related to the prognosis of patients[22]. The TME of CRC mainly includes several functional subgroups, including cytotoxic CD8⁺ T cells, helper T cells (e.g., Th1, Th17, and Treg cells), memory T cells, and γδ T cells[23]. Numerous studies have shown that the gut microbiota can significantly influence the onset, progression, and treatment response of CRC by regulating T cell responses.

Some symbiotic bacterial genera, such as Roseburia and Faecalibacterium, can induce tumor cells to express chemokines such as CCL5, CXCL9, and CXCL10, thereby promoting recruitment of CD8⁺ T cells and Th1 cells to the tumor site. This enhances antitumor immunity and improves patient survival[24]. Similarly, Bacteroides and Lactobacillus can regulate the IL-12/IL-23 signaling axis, promoting Th1 differentiation and inhibiting the protumor Th17 immune response[25]. Bacterial antigens can activate follicular helper T cells within the intestinal lamina propria, promoting the formation of tertiary lymphoid structures, which further enhances the local T-cell-mediated antitumor immunity[26].

However, the enrichment of some pathogenic bacteria, such as F. nucleatum, is associated with lymph node metastasis in CRC. It may promote immune escape by inhibiting T cell infiltration[25]. Patients responding to immune checkpoint inhibitors (such as anti-PD-1 therapy) often exhibit specific beneficial microbiota characteristics, such as the enrichment of Akkermansia muciniphila and Bifidobacterium. These bacteria can enhance antitumor immune efficacy by activating CD8⁺ T cells and DCs[27].

EFFECTS OF MICROBIOTA ON DCs

In CRC, DCs act as specialized antigen-presenting cells and play a central role in initiating and regulating antitumor immune responses. Their functional state directly affects disease progression: Myeloid DCs (mDCs) typically have immunostimulatory properties, while plasmacytoid DCs (pDCs) are more often associated with immune tolerance[28]. Studies have shown that when the ratio of pDCs/mDCs increases, it is often accompanied by enhanced infiltration of Treg cells, promoting immune escape[29].

The gut microbiota modulates the function of DCs via various mechanisms. For example, Lactobacillus intestinalis facilitates the recruitment of DCs through tumor-derived CCL5, thereby suppressing colorectal tumorigenesis[30]. Conversely, F. nucleatum can weaken the antigen-presenting ability of DCs via the activation of autophagy-lysosome pathways, facilitating CRC immune escape[31]. The metabolic products of the microbiota also exert dual regulatory effects. For example, butyric acid inhibits HDAC and regulates the mTOR/S6K pathway, altering the epigenetic modifications of DCs, which can both inhibit the expression of proinflammatory cytokines and promote the differentiation of Treg cells, thereby exerting both immunosuppressive and regulatory functions in CRC[32]. Additionally, a novel strain (YB328, belonging to the Hominenteromicrobium genus) discovered in the fecal microbiota of patients responding to PD-1 inhibitors can specifically activate intestinal CD103⁺ CD11b conventional DCs, promoting their maturation and migration to the TME, thereby enhancing the activity of CD8⁺ T cells and PD-1 expression, and significantly improving the antitumor efficacy of immune checkpoint blockade therapy[33].

EFFECTS OF MICROBIOTA ON TAMs

TAMs constitute one of the most prevalent immune cell populations within the TME of CRC. They exert a dual function in tumor progression. The classically activated M1 macrophages possess proinflammatory and antitumor growth effects, while the alternatively activated M2 macrophages exhibit anti-inflammatory properties and promote tumor invasion and metastasis[34]. The phenotype and function of TAMs are precisely regulated by various cytokines and chemokines in the TME.

Researchers have revealed that the gut microbiota regulates TAMs via various mechanisms, thus influencing the TME and treatment response of CRC. In particular, F. nucleatum triggers the TLR4 signaling pathway via its adhesin FadA, eliciting the expression of NF-κB and S100A9, facilitating macrophage polarization toward the M2 type, and thereby driving tumor progression[35]. Conversely, A. muciniphila and its outer membrane protein Amuc_1100 can reduce the number of macrophages in the colon and inhibit the occurrence of colitis-related tumors by regulating the ratio of the PD-1⁺ T cells to CD16/32⁺ macrophages via the PD-1/PD-L1 signaling pathway[36]. Additionally, gut microbiota-derived metabolites, such as SCFAs and tryptophan derivatives, can affect macrophage polarization through signaling pathways such as the AhR and β-catenin. In particular, Akkermansia can inhibit tryptophan metabolism, reduce the accumulation of immunosuppressive metabolites, and indirectly inhibit the differentiation of M2-type TAMs[37].

CLINICAL TRANSFORMATION AND APPLICATION

Since the 20th century, research on gut microbiota has rapidly advanced from basic mechanism exploration to clinical application, especially showing significant potential in the prevention, diagnosis, and treatment of CRC.

In terms of diagnosis and prognosis, numerous studies have confirmed that specific microbiota characteristics can be used for the early identification and risk stratification of CRC. For example, the enrichment of F. nucleatum in CRC tissues is significantly associated with later TNM stage, lymph node metastasis, chemotherapy resistance, and poor survival prognosis[38]. Detection of pathogenic bacteria such as pks+ E. coli provides important evidence for disease risk assessment[39,40]. The panel of microbiota biomarkers based on metagenomic sequencing is gradually being introduced into clinical practice, providing new tools for noninvasive diagnosis and individualized prognosis assessment.

The regulation of gut microbiota shows potential to enhance traditional therapies. Currently, the response rate of immune checkpoint inhibitors in patients with mismatch repair intact CRC is low[41]. Fecal microbiota transplantation (FMT) has emerged as a powerful strategy to reverse this resistance by remodeling the TME[42], and several ongoing clinical trials exploring this combination are summarized in Table 1. Its efficacy stems from introducing a synergistic microbial community from responsive donors, which enhances intratumoral infiltration and function of CD8⁺ T cells while suppressing Treg cells and myeloid-derived suppressor cells[43]. This immunomodulation is partly driven by a shift in the microbial metabolite profile, increasing beneficial molecules like SCFAs and inosine that promote antitumor immunity, while decreasing immunosuppressive metabolites such as secondary bile acids[44]. Probiotics and their metabolites also play a role in adjuvant treatment. In particular, the F. nucleatum enriched within tumors can inhibit HDAC3/8 in CD8⁺ T cells via its metabolite butyric acid, induce expression of TBX21, and transcriptionally inhibit PD-1, thereby alleviating T cell exhaustion and enhancing the efficacy of anti-PD-1 therapy[45]. Looking forward, the translational path for FMT involves overcoming challenges in standardization, safety, and donor-recipient matching. The future lies in moving from whole-community transplantation towards precision interventions. This includes the development of defined next-generation probiotics or synthetic microbial consortia that mimic the beneficial effects of FMT without its inherent variability. Combining these defined bacterial products with immune checkpoint inhibitors is a promising strategy to broaden their efficacy in currently resistant CRC populations, ultimately paving the way for more predictable and personalized microbiome-based therapies.

Table 1 Current clinical trials of combining gut microbiota modulation and immunotherapy in colorectal cancer.

Title	Intervention	Patient population	Phase	Trial ID
FMT and re-introduction of anti-PD-1 therapy (pembrolizumab or nivolumab) for the treatment of metastatic CRC	Colonoscopic FMT-IV pembrolizumab + oral FMT capsules	dMMR/MSI-H metastatic CRC; anti-PD-1 nonresponders	II	NCT04729322
FMT capsule + anti-PD-1 for PD-(L)1 resistant digestive system cancers	FMT capsules (1st week: 3 consecutive days; then maintenance dose) + anti-PD-1 therapy (every 2 weeks, up to 6 cycles)	Gastrointestinal cancer	I	NCT04130763
A phase Ib trial to evaluate the safety and efficacy of FMT and nivolumab in subjects with MSI-H, dMMR CRC	FMT capsules + nivolumab	MSI-H, dMMR CRC	Ib	NCT04521075
Pembrolizumab with intratumoral injection of Clostridium novyi-NT	Pembrolizumab + Clostridium novyi-NT + lifelong oral doxycycline	Advanced solid tumors (including CRC)	Ib	NCT03435952
FMT plus tislelizumab and fruquintinib in refractory MSS metastatic colorectal cancer	FMT + tislelizumab + fruquintinib	Refractory MSS mCRC	II	RENMIN-215

FMT: Fecal microbiota transplantation; CRC: Colorectal cancer; dMMR: Deficient DNA mismatch repair; MSI-H: Microsatellite instability-high; MSS: Microsatellite stable; mCRC: Metastatic colorectal cancer; NT: Nontoxic.

Emerging treatment strategies further expand the precision and effectiveness of microbiota intervention. On the one hand, researchers are developing precise antibacterial therapies targeting carcinogenic bacteria (such as F. nucleatum), including specific inhibitors, to eliminate pathogens while maintaining the overall balance of the microbiota[46]. On the other hand, the use of synthetic biology methods to construct engineered bacteria or liposomes for targeted delivery of immunomodulators or anti-cancer drugs to the tumor site has also become a research hotspot. For example, Wang et al[47] developed a liposome-encapsulated antibiotic silver-tinidazole complex (LipoAgTNZ) to eradicate tumor-associated bacteria in primary tumors and liver metastases, while avoiding the induction of gut microbiome dysbiosis.

CONCLUSION

This minireview explores the crucial role of the gut microbiota and its metabolites in the regulation and shaping process of the TME in CRC, and reviews the cutting-edge progress in its clinical translation and application. With growing insights into microbiota-TME interactions, targeting the gut microbiota has become an important therapeutic strategy for CRC. In the future, the precise molecular mechanism and temporal-spatial dynamic rules of the microbiota-host interaction need to be further clarified. Current clinical translation research mainly focuses on three directions: (1) Establish a standardized microbiota detection system and a treatment plan for FMT; (2) Promote intervention strategies to gradually shift from the traditional community level to the strain level and even the metabolite level for precise regulation; and (3) Actively explore the synergistic treatment mode of microbiota regulation combined with immunotherapy, chemotherapy or targeted therapy to comprehensively improve antitumor efficacy and patients’ quality of life. An in-depth investigation of the mechanisms underlying the crosstalk between the gut microbiota and the TME will provide valuable insights for developing therapies against CRC.