Gut microbiota and neoadjuvant chemoradiotherapy in locally advanced rectal cancer: a review of current evidence and emerging insights

Abstract

Locally advanced rectal cancer (LARC) presents a significant burden on lower gastrointestinal diseases, with current treatment strategies primarily involving neoadjuvant chemoradiotherapy (nCRT) followed by radical surgery. However, patient responses to nCRT exhibit significant variability, highlighting the need for personalized therapeutic approaches. Emerging evidence suggests that the gut microbiota plays a critical role in influencing both treatment outcomes and toxicity in LARC patients. Intestinal dysbiosis has been linked to LARC progression and may affect the efficacy and adverse effects of nCRT. This narrative review critically evaluates the current literature on the relationship between gut microbiota and nCRT in LARC. Certain microbial taxa, such as Alistipes spp., Akkermansia muciniphila, and Faecalibacterium prausnitzii, have been associated with enhanced therapeutic responses, while others, such as Fusobacterium nucleatum and Enterotoxigenic Bacteroides fragilis, may contribute to treatment resistance and exacerbate adverse effects. We also discuss novel mechanisms by which specific gut microbiota and their metabolites modulate nCRT response distinct from conventional immune regulation, alongside emerging strategies for microbiota modulation, including dietary interventions, probiotics, prebiotics, and fecal microbiota transplantation. Despite challenges in standardizing microbiota analysis and fully understanding the precise mechanisms, microbiota-targeted interventions offer a promising avenue for personalized treatment in LARC, with the potential to improve patient outcomes and quality of life.

Plain language summary

Gut bacteria and treatment before surgery for advanced rectal cancer: a review

What did we study? We reviewed current research to understand how the gut microbiota, which is the community of bacteria living in the intestines, may affect how patients with locally advanced rectal cancer respond to neoadjuvant chemoradiotherapy given before surgery.

Why is this important? Patients respond very differently to chemoradiotherapy. Some benefit greatly, while others experience limited tumor response or significant side effects. Being able to predict who will respond well could help doctors personalize treatment, avoid unnecessary toxicity, and improve quality of life.

How did we do it? We analyzed published clinical and experimental studies that examined links between gut microbiota composition, treatment response, treatment side effects, and biological mechanisms in rectal cancer patients receiving chemoradiotherapy.

What did we find? Studies show that patients with certain beneficial gut bacteria, such as Akkermansia muciniphila, Faecalibacterium prausnitzii, and Alistipes species, tend to have better treatment responses and fewer side effects. In contrast, harmful bacteria like Fusobacterium nucleatum are often associated with treatment resistance and worse toxicity. Gut bacteria and their metabolites can influence immune activity, tumor behavior, and sensitivity to radiation and chemotherapy. Approaches such as dietary changes, probiotics, prebiotics, and fecal microbiota transplantation may help modify these effects.

What does this mean? The gut microbiota has the potential to become both a predictor of treatment response and a target for supportive therapies in rectal cancer. Microbiota-based strategies could support more personalized and effective treatment in the future, although further clinical studies are needed before routine use.

Keywords

dysbiosis gut microbiota locally advanced rectal cancer microbiota modulation neoadjuvant chemoradiotherapy

Introduction

Colorectal cancer (CRC) is the third most commonly diagnosed malignancy.¹ Rectal cancer, accounting for approximately one-third of CRCs, poses a significant global health concern.² It ranks among the leading causes of cancer-related mortality, with 339,022 related deaths reported in 2020, representing 3.4% of all cancer deaths worldwide.³ Early-stage rectal cancer can often be treated effectively with surgery alone, but as the disease progresses, treatment becomes increasingly complicated.⁴ Locally advanced rectal cancer (LARC) refers to tumors that have invaded nearby structures or lymph nodes but have not yet metastasized to distant organs.⁵ The management of LARC typically necessitates a multidisciplinary approach to improve outcomes and reduce the risk of recurrence. Current guidelines recommend neoadjuvant chemoradiotherapy (nCRT) combined with radical surgery and postoperative adjuvant therapy as the standard treatment for patients with LARC.⁶ Effective responses to nCRT can significantly improve local disease control, and, in some cases, patients who achieve a clinical complete response post-nCRT treatment may shift clinical strategies from radical surgery to a “watch and wait” approach.⁶ However, patient responses to nCRT are highly variable. It frequently leads to side effects such as fatigue, gastrointestinal disturbances, depressive symptoms, and more severe conditions like radiation proctitis and myelosuppression, all of which can severely impact quality of life.⁷

The gut microbiota, a complex community of approximately 100 trillions of microorganisms residing in the human gastrointestinal tract, plays a pivotal role in maintaining health and modulating disease processes.⁸ Dysbiosis, or imbalance in the gut microbial composition, has been implicated in the pathogenesis of numerous diseases, notably CRC.⁹ Emerging evidence have indicated that disruption of gut microbiota has been increasingly linked to the development of CRC.^10–17 However, landmark studies have demonstrated that microbial dysbiosis is involved not only in carcinogenesis but also in shaping tumor biology and treatment responsiveness.^18–21 In the context of LARC, dysbiosis has been gradually suggested as a factor that may predict the response to nCRT^22–24 and modulate both its efficacy and toxicity.^25,26 Certain microbial taxa may enhance therapeutic responses by activating immune pathways or metabolizing chemotherapeutic agents, thus improving the therapeutic outcomes of nCRT. Conversely, some may contribute to treatment resistance, promote chronic inflammation, or exacerbate side effects such as gastrointestinal damage and radiation-induced proctitis.^27–29 Collectively, these findings highlight the potential for the gut microbiota to influence treatment responses in LARC, suggesting that microbiota dysbiosis may act as both a biomarker for therapy response and a modifiable factor influencing the effectiveness and toxicity of nCRT. Therefore, elucidating the interplay between dysbiosis and nCRT in LARC may offer exciting prospects for improving patient outcomes.

In this narrative review, we aim to critically assess the current evidence on the relationship between gut microbiota and nCRT in LARC. We will explore how gut microbial composition predicts response to nCRT and affects treatment efficacy and toxicity, delve into the underlying mechanisms of these interactions, and evaluate emerging strategies for microbiota modulation. By synthesizing recent findings, we seek to highlight opportunities for integrating gut microbiota considerations into personalized therapeutic approaches, ultimately enhancing patient outcomes and minimizing adverse effects associated with nCRT.

Literature search strategy

A structured literature search was conducted to identify relevant studies examining the relationship between gut microbiota and nCRT response in LARC. The search covered publications from inception to September 2025 across three electronic databases: PubMed, Embase, and Web of Science. The following core search terms and their combinations were used: “rectal cancer,” “locally advanced rectal cancer,” “neoadjuvant chemoradiotherapy,” “gut microbiota,” “microbiome,” “treatment response,” and “radiotherapy sensitivity.” Boolean operators (AND/OR) and Medical Subject Headings (MeSH) were applied where appropriate. Reference lists of included articles and relevant reviews were also screened to identify additional eligible studies.

Studies were included if they met the following criteria: (i) investigated gut microbiota in the context of LARC or nCRT; (ii) involved human subjects and/or preclinical models exploring mechanistic associations; and (iii) were published as full-text original research articles or review articles in English. Conference abstracts, editorials, case reports, and non-peer-reviewed sources were excluded. Given the emerging nature of this field, both clinical observational studies and mechanistic preclinical studies were considered to provide a comprehensive overview of current evidence. Data were extracted narratively with attention to study design, cohort characteristics, microbiome assessment methods, and key findings.

The gut microbiota and colorectal cancer

The gut microbiota is crucial for maintaining intestinal health, playing a fundamental role in digestion, nutrient absorption, immune system modulation, and protection against pathogens.³⁰ This complex community of microorganisms—including bacteria, archaea, viruses, and fungi—contributes to the integrity of the intestinal barrier and the development of the host immune system.³¹ A balanced gut microbiota is essential for preventing colonization by pathogenic organisms and for modulating inflammatory responses.³² However, increasing evidence indicates that disruptions to microbial balance are closely linked to colorectal carcinogenesis through metabolic, inflammatory, and immune-mediated mechanisms.

Gut microbiota composition varies between healthy individuals and CRC patients

In healthy individuals, the gut microbiota is predominantly composed of bacteria from the phyla Firmicutes and Bacteroidetes, which together constitute over 90% of the gut microbial population. Notably, these two phyla are especially abundant in the colon. Other common phyla include Actinobacteria, Proteobacteria, Verrucomicrobia, and Fusobacteria.³³ At the genus level, common bacteria include Bacteroides, Lactobacillus, Bifidobacterium, Clostridium, and Eubacterium.⁸ This diverse microbial ecosystem maintains intestinal homeostasis through various functions such as fermenting dietary fibers into short-chain fatty acids (SCFAs), synthesizing vitamins, and regulating immune responses.³⁴

CRC is one of the most extensively studied diseases in relation to the gut microbiota. Accumulating evidence demonstrates marked alterations in gut microbiota composition, diversity, and functional capacity in CRC patients compared with healthy individuals. Studies have shown an increased abundance of pathogenic bacteria such as Fusobacterium nucleatum, Bacteroides fragilis, and pathogenic strains of Escherichia coli in the gut microbiota of CRC patients.^12,35 These microbial shifts are not merely associative; mechanistic studies indicate that pro-carcinogenic bacteria promote tumorigenesis by inducing chronic inflammation, releasing genotoxic metabolites, altering epithelial signaling pathways, and suppressing anti-tumor immunity.²⁹ Conversely, there is often a decrease in beneficial commensal bacteria like Lactobacillus and Bifidobacterium, which bear anti-inflammatory and anti-carcinogenic properties.³⁶ The imbalance between harmful and beneficial microbes contributes to a microenvironment conducive to carcinogenesis. Notably, geographic, dietary, and lifestyle differences strongly influence baseline microbiota composition, which may partially account for inconsistent microbial signatures reported across CRC cohorts.

Relationship between gut microbiota and the tumor immune microenvironment in CRC

The gut microbiota profoundly influences the tumor immune microenvironment in CRC. Microbial metabolites, such as SCFAs and secondary bile acids, can modulate local immune responses by affecting the differentiation and function of immune cells like T cells, dendritic cells, and macrophages.^37,38 Certain pathogenic bacteria, such as Fusobacterium nucleatum and Enterotoxigenic B. fragilis, can create a pro-inflammatory environment by activating nuclear factor-kappa B and other signaling pathways. This leads to the recruitment of immunosuppressive cells and the inhibition of anti-tumor immunity.^39,40 For instance, F. nucleatum promotes immune suppression by inducing myeloid-derived suppressor cells, while Enterotoxigenic B. fragilis produces inflammatory toxins that activate the Wnt/β-catenin pathway, enhancing tumor growth and immune evasion, as shown in Table 1. Collectively, these microbial activities shape an immunosuppressive tumor milieu that facilitates cancer progression and reduces responsiveness to anti-cancer therapies.

Table 1.

Specific pathogenic and commensal bacteria and their role in tumor immune microenvironment of CRC.

Bacterial species	Bacteria type	Mechanism in tumor immune microenvironment	Effect on tumor immune microenvironment	References
Fusobacterium nucleatum	Pathogenic	Induces NF-κB activation, triggers pro-inflammatory cytokine production (e.g., IL-6, TNF-α), and promotes immune suppression by inducing MDSCs	Promotes tumor progression, immunosuppression	41, 42
Enterotoxigenic Bacteroides fragilis	Pathogenic	Produces B. fragilis toxin that activates the Wnt/β-catenin signaling pathway; induces IL-17 production by CD4⁺ T cells, creates a pro-inflammatory tumor environment, and impairs anti-tumor immunity	Promotes tumorigenesis and immune suppression	43, 44
Lactobacillus spp.	Commensal	Produces lactic acid and SCFAs (e.g., acetate), which can stimulate T cell differentiation, enhance CTLs function, and improve immune responses	Promotes anti-tumor immunity	45 –47
Bifidobacterium spp.	Commensal	Produces butyrate that strengthens the intestinal barrier, enhances antigen presentation by dendritic cells, and modulates T cell responses	Enhances anti-tumor immunity and maintains gut homeostasis	48 –50
B. fragilis (non-toxigenic)	Commensal	Produces SCFAs that strengthen the intestinal barrier and regulate immune responses; enhances gut homeostasis	Enhances immune function and maintains gut health	51, 52
Faecalibacterium prausnitzii	Commensal	Produces butyrate and acts as an anti-inflammatory agent by suppressing pro-inflammatory cytokines such as IL-6 and TNF-α	Reduces inflammation and enhances anti-tumor immunity	53, 54
Akkermansia muciniphila	Commensal	Enhances mucus layer and gut barrier integrity; promotes differentiation of Tregs that modulate immune responses	Helps maintain immune balance and tumor suppression	55 –57

CRC, colorectal cancer; CTLs, cytotoxic T lymphocyte; IL, interleukin; MDSCs, myeloid-derived suppressor cells; NF-κB, nuclear factor-kappa B; SCFAs, short-chain fatty acids; Tregs, regulatory T cells.

Conversely, commensal bacteria such as Lactobacillus spp., Bifidobacterium spp., and Faecalibacterium prausnitzii enhance anti-tumor immunity by promoting regulatory T cell and cytotoxic T lymphocyte balance, strengthening epithelial barrier integrity, and reducing inflammation. Commensal bacteria also produce metabolites, such as butyrate and lactic acid, that strengthen the intestinal barrier and prevent the translocation of pathogenic bacteria and their toxins, thus reducing inflammation and promoting immune responses.⁵⁸ Importantly, recent studies highlight that microbiota–immune crosstalk may influence not only tumor development but also treatment response, including immunotherapy and chemoradiotherapy outcomes. Understanding this interplay is critical for developing microbiota-targeted interventions aimed at boosting immune responses and improving therapeutic outcomes in CRC or LARC patients.

Gut microbiota as a predictor of nCRT response in LARC

The variability in patient responses to nCRT for LARC underscores the need for reliable predictive biomarkers. In this review, gut microbiota mainly refers to luminal microbial communities measured from fecal samples, which are the most commonly studied and clinically accessible source. At the same time, tumor progression and treatment response may also be shaped by tumor-associated or intratumoral microbiota, namely microorganisms detected within tumor tissue or in close proximity to cancer cells, typically assessed from biopsy specimens. Although these compartments are biologically connected, they may influence tumor biology and nCRT outcomes through different routes. Luminal microbiota may affect host metabolism, systemic immune regulation, and treatment tolerance, whereas intratumoral microbiota may more directly interact with tumor cells and modulate the local immune microenvironment.

Recent research increasingly suggests that the composition of the microbiota could serve as a promising predictor of nCRT response in these patients, as shown in Table 2. However, the predictive value of the microbiota remains inconsistent across clinical studies, largely due to variations in study design, sequencing platforms, sample types (stool vs biopsy), patient demographics, and analytical methods. Identifying microbial profiles associated with favorable or unfavorable treatment responses can help tailor personalized treatment strategies, ultimately improving patient outcomes.

Table 2.

Microbial signatures linked to nCRT response and toxicity in LARC.

Taxa	Country (year)	Sample (method)	Timepoint	Association	References
Shuttleworthia	China (2020)	Stool (16S rRNA)	Baseline	Enriched in responders	59
Several Clostridiales (e.g., Faecalibacterium, Murimonas, Lachnospiraceae incertae sedis)			Baseline	Enriched in non-responders
Bifidobacterium, Butyricicoccus, Clostridium XlVa, Hungatella, Bacteroides vulgatus			During nCRT	Higher in patients without severe diarrhea
Fusobacterium, Peptostreptococcus, Parvimonas, Porphyromonas	China (2021)	Stool (16S rRNA)	On-treatment change vs baseline	Decrease during nCRT	23
Lactobacillus, Streptococcus				Increase during nCRT
Roseburia, Dorea, Anaerostipes			Baseline	Enriched in responders
Coriobacteriaceae, Streptococcus, Fusobacterium				Enriched in non-responders
Dorea, Anaerostipes, Clostridium XVIII				Predict response
Eisenbergiella, Granulicatella, Ralstonia				Predict non-response
Hungatella, Flavonifractor, Methanosphaera	Brazil (2022)	Stool (16S rRNA)	Baseline	Enriched in responders	60
Enhydrobacter, Paraprevotella, Finegoldia				Enriched in non-responders
Collinsella, Alistipes, Christensenella, Faecalibacterium, Ruminococcus, Pavimonas, Akkermansia	Germany (2023)	Tumor biopsy (16S rRNA)	Baseline	Predict response	61
Faecalibacterium sp900539945, Phocaeicola dorei, Gemmiger qucibialis	China (2024)	Stool (metagenomics)	Baseline	Higher in good responders	62
Ruminococcus spp.	Switzerland (2025)	Tumor biopsy (16S rRNA)	Baseline	Predict CR	63
Fusobacterium, Porphyromonas, Oscillibacter				Predict non-CR

CR, complete responders; LARC, locally advanced rectal cancer; nCRT, neoadjuvant chemoradiotherapy.

Microbial signatures associated with nCRT response

Several studies have pinpointed specific microbial taxa correlated with the effectiveness of nCRT in patients with LARC.^23,59,64 Patients who achieve a pathological complete response (pCR) often present with a distinct gut microbiota composition compared to non-responders. A commonly reported feature is increased baseline microbial diversity among responders, which may reflect a more resilient and functionally adaptable microbial ecosystem. For instance, Fan et al.⁶⁴ reported that both the alpha diversity and richness of the microbiota were notably higher in pCR groups than in non-pCR groups. Similarly, Sánchez-Alcoholado et al.⁶⁵ found that responder patients had significantly higher microbial diversity and richness compared to non-responder patients. These findings suggest that a more diverse microbiota might enhance mucosal barrier function and modulate systemic immunity, potentially improving the efficacy of treatment.

In terms of alterations of bacteria taxa, Yi et al. found that nCRT treatment significantly alters the microbial composition, characterized by a reduction in diversity and unevenness. Specifically, Fusobacterium, Peptostreptococcus, Parvimonas, and Porphyromonas demonstrated a significant decrease following nCRT, whereas Lactobacillus, particularly Streptococcus, showed a marked increase.²³ Additionally, certain bacteria such as Roseburia, Dorea, and Anaerostipes, known for their ability to produce butyrate and modulate immune responses, have been correlated to better nCRT outcomes.²³ Conversely, an elevated presence of specific pathogenic bacteria, such as Coriobacteriaceae, Streptococcus, and Fusobacterium, has been linked to resistance to nCRT.²³ For instance, F. nucleatum is known to promote tumor progression by suppressing immune cytotoxicity, which may diminish the efficacy of nCRT.⁶⁶ Furthermore, a recent metagenome shotgun sequencing performed by Chen et al.⁶² revealed that Faecalibacterium sp900539945, Phocaeicola dorei, and Gemmiger qucibialis were found significantly abundant in LARC patients with good response. Understanding these microbial signatures and their potential effects on tumor biology could be instrumental in predicting patient responses to nCRT and guiding more personalized treatment approaches for LARC.

Predictive microbiota-based biomarkers

The identification of microbiota-based biomarkers offers the potential to predict individual responses to nCRT. Integrating microbiota analysis into clinical practice could lead to more personalized and effective treatment plans for LARC patients. Several microbial genera have been identified as potential biomarkers for predicting response to nCRT. Shi et al.⁵⁹ employed statistical analysis of metagenomic profiles (STAMP) and linear discriminant analysis of effect size (LEfSe) to identify Shuttleworthia as enriched in responders, while several bacteria taxa in the Clostridiales order (Faecalibacterium, Murimonas, and Lachnospiraceae incertae sedis) were found to be enriched in non-responders. Yi et al.²³ developed a random forest model incorporating 10 microbial biomarkers that achieved an AUC of 93.57% in the training cohort and 73.53% in the validation cohort, highlighting the potential of Eisenbergiella, Granulicatella, and Ralstonia as microbiota-based predictors of non-response; however, external validation remains limited. Takenaka et al.⁶⁰ used LEfSe to identify specific genera, such as Hungatella, Flavonifractor, and Methanosphaera, as potential predictive markers for nCRT response in responder LARC patients, while non-responders exhibited a higher abundance of genera like Enhydrobacter, Paraprevotella, and Finegoldia.⁶⁰ Additionally, Sun et al.⁶¹ established a predictive classifier and found that Collinsella (AUC = 0.652), Alistipes (AUC = 0.702), Christensenella (AUC = 0.702), Faecalibacterium (AUC = 0.658), Ruminococcus (AUC = 0.652), Pavimonas (AUC = 0.669), and Akkermansia (AUC = 0.689) were significantly associated with the responses to nCRT. And a recent study by Roesel et al.⁶³ analyzed diagnostic biopsies from LARC patients and identified significant differences in intratumoral microbiota between complete responders (CR) and non-complete responders (non-CR). Specifically, a consistent association was observed by LEfSe between the presence of Ruminococcus species and CR, whereas higher abundances of Fusobacterium, Porphyromonas, and Oscillibacter were linked to non-CR. These findings highlight the significant microbial profile differences between responders and non-responders, emphasizing the role of specific bacterial communities in predicting treatment outcomes. Nevertheless, across studies, the overlap in identified microbial biomarkers is minimal, indicating that population-specific, tumor microenvironment-dependent, and diet-related factors strongly influence microbial signatures.

Gut microbiota and nCRT-induced toxicity

The relationship between gut microbiota and the toxicity of nCRT in LARC has gained increasing attention due to its potential role in modulating treatment outcomes. nCRT can induce significant gastrointestinal side effects, including diarrhea, mucositis, and intestinal permeability changes. The diversity and composition of the gut microbiome are thought to be key factors influencing these toxicities. Several studies have demonstrated that loss of microbial diversity and changes in bacterial composition are associated with therapy-related toxicities in cancer patients.^67–71 However, a recent study by Shi et al.⁵⁹ investigating rectal cancer patients undergoing nCRT found no significant differences in the richness and diversity of the gut microbiome between patients with no or mild diarrhea and those with severe diarrhea. These findings suggest that other factors, such as specific bacterial taxa, might be more influential in modulating nCRT toxicity. When specific bacterial taxa were examined, significant differences in the relative abundances of several taxa were observed between the two groups. Notably, Bifidobacterium, several bacteria in the Clostridia class, including Butyricicoccus, Clostridium XlVa, and Hungatella, as well as the Bacteroides genus (particularly Bacteroides vulgatus), were enriched in patients with no or mild diarrhea. These microbial communities may play a protective role in mitigating the severity of diarrhea induced by nCRT, highlighting the potential for microbiome-based interventions to reduce treatment-related toxicities.

Specific mechanisms of gut microbiota influencing the efficacy of nCRT in LARC

The interaction between gut microbiota and nCRT is multifaceted. The gut microbiota plays a crucial role in modulating systemic immunity, influencing inflammation, and affecting drug metabolism, all of which can impact the response to nCRT. Building on the earlier overview of microbiota-associated immune effects within the tumor microenvironment in CRC, this section focuses on mechanisms that are more directly relevant to nCRT efficacy in LARC and minimizes repetition of general immune concepts. In particular, we highlight emerging nCRT-related pathways beyond broad immune modulation, including microbiota-mediated effects on radiosensitivity, tumor metabolism, DNA damage and repair, and direct interactions with chemotherapeutic agents.

Teng et al.²⁵ reported that the presence of B. vulgatus was found to upregulate genes related to nucleotide biosynthesis, potentially aiding tumor survival and contributing to therapy resistance. The study also suggests that B. vulgatus can protect cancer cells from the cytotoxic effects of 5-fluorouracil-induced chemotherapy or radiation treatment. Furthermore, Zhou et al.²⁶ discovered that methylglyoxal (MG), a metabolite derived from the gut microbiota, particularly from Lactobacillus, enhances the radiotherapy response by stimulating the generation of intracellular reactive oxygen species (ROS) and reducing tumor hypoxia. Mechanistically, MG activates the cGAS-STING pathway, increases DNA double-strand breaks, and promotes immunogenic cell death through ROS-induced endoplasmic reticulum stress, which leads to enhanced infiltration of CD8⁺ T cells and natural killer cells into the tumor immune microenvironment. Moreover, MG has shown potential as an effective radiosensitizer and immunomodulator, with the combination of MG and anti-PD1 therapy producing long-lasting complete responses in both irradiated and non-irradiated tumor sites, which offers a promising avenue for improving treatment outcomes in LARC patients. These findings highlight a potential therapeutic avenue for microbiota-derived metabolites to synergize with immune checkpoint blockade and radiotherapy.

Strategies for modulating gut microbiota to improve nCRT outcomes

The growing understanding of how gut microbiota interacts with nCRT has led to the exploration of strategies for microbiota modulation aimed at improving treatment outcomes and reducing toxicities. These approaches can be broadly categorized into dietary interventions, probiotics, prebiotics, and fecal microbiota transplantation (FMT).

Dietary interventions

Diet plays a crucial role in shaping the gut microbiota. Studies suggest that a high-fiber diet can increase the abundance of SCFA-producing bacteria including Lactobacillus, Bifidobacterium, and Akkermansia, potentially enhancing immune function and improving the response to nCRT.^72,73 Diets rich in fiber from fruits, vegetables, and whole grains may not only improve microbiota composition but also reduce the side effects of nCRT, such as diarrhea and mucositis, by promoting gut health and immune homeostasis. For patients with diarrhea, a diet rich in soluble fiber that helps absorb water can be beneficial.⁷⁴

While dietary fiber generally benefits gut health, a recent study has raised concerns about high-dose soluble fiber intake. Research in mice has shown that high doses of soluble fiber but not insoluble fiber can promote colorectal tumorigenesis by dysregulating gut microbiota and metabolites.⁷⁵ This effect was associated with increased tumor number and load, as well as alterations in gut microbial composition, including enrichment of Bacteroides uniformis and depletion of Bifidobacterium pseudolongum.

Probiotics and prebiotics

Probiotics are live beneficial microorganisms that play a crucial role in maintaining health, capable of restoring microbial balance, and alleviating chemotherapy-induced adverse events such as diarrhea and oral mucositis in patients undergoing chemoradiotherapy.^76,77 In recent years, the role of probiotics, particularly strains like Lactobacillus, Bifidobacterium, and Saccharomyces, has garnered clinical attention for their ability to mitigate chemotherapy-induced adverse events, especially chemotherapy-induced diarrhea (CID).⁷⁸ The mechanisms through which probiotics alleviate CID include regulating dysbiosis, modulating inflammatory cytokine production, enhancing immunity, and improving the gut mucosal barrier.^45,79–81 Among these, strains like Lactobacillus and Bifidobacterium have shown promise in reducing CID and protecting the intestinal barrier.⁸² In a randomized clinical trial by Österlund et al.,⁸³ Lactobacillus GG supplementation was found to potentially reduce the frequency of severe diarrhea and abdominal discomfort in CRC patients undergoing 5-fluorouracil-based chemotherapy. However, a more recent clinical study reported contradictory results, finding no significant effect of probiotic supplementation (Lactobacillus and Bifidobacterium) on the severity of CID in CRC patients.⁸⁴ Additionally, Golkhalkhali et al.⁸⁵ reported that CRC patients treated with a combination of Lactobacillus, Bifidobacterium, and omega-3 fatty acids exhibited clinically significant improvement in CID. Mohebian et al.⁸⁶ reported that yogurt combined with probiotics including Lactobacillus spp., Bifidobacterium spp., Streptococcus spp. could lead to better outcome in CRC patients suffering from CID. Overall, probiotics play a significant role in alleviating the side effects associated with nCRT, particularly in improving symptoms such as CID.

Prebiotics, non-digestible food components that promote the growth and activity of beneficial gut microorganisms, have also been investigated for their potential in modulating gut microbiota and improving outcomes in patients undergoing nCRT. Prebiotics, such as inulin, fructooligosaccharides (FOS), and galactooligosaccharides, have been shown to selectively stimulate the growth of beneficial gut bacteria, which may help in restoring microbial balance and supporting gut health during nCRT.⁸⁷ By enhancing the growth of probiotics like Lactobacillus and Bifidobacterium, prebiotics may work synergistically to further improve gut microbiota composition, reduce inflammation, and strengthen the gut mucosal barrier.^88,89 Recent studies have indicated that prebiotics may enhance the beneficial effects of probiotics in mitigating chemotherapy-induced side effects, including diarrhea and mucositis, by promoting a more favorable gut environment.^90,91 For instance, Lactobacillus fermentum together with the prebiotic FOS alleviated 5-fluorouracil-induced intestinal mucositis and improved intestinal barrier function.⁹² Additionally, probiotics combined with prebiotics can influence the efficacy of anti-CRC treatments by affecting the colonization of pathogenic bacteria, such as Clostridium difficile and Staphylococcus aureus, in the intestine.⁹³ They also regulate intestinal immunity and affect the production of SCFAs.⁹³ Therefore, the combined use of prebiotics and probiotics holds great potential for enhancing gut health of patients undergoing nCRT, ultimately leading to better treatment outcomes and improved quality of life.

Fecal microbiota transplantation

FMT is a therapeutic procedure that involves transferring fecal matter from a healthy donor to a patient to restore microbial diversity and function in the recipient’s gut.⁹⁴ This approach has proven effective in treating conditions such as C. difficile infection,⁹⁵ which remains the primary approved indication for FMT. Beyond this, FMT is being explored for broader applications, including its potential role in cancer therapy.

Recent studies suggest that FMT may help re-establish a healthy microbiota in cancer patients undergoing nCRT, potentially enhancing the treatment response and reducing toxicities.⁹⁶ For example, FMT has been shown to alleviate radiation-induced gastrointestinal toxicity, with several clinical studies demonstrating its ability to improve dysbiosis.^97,98 Furthermore, FMT has been shown to reducing intestinal inflammation and improve the gut microbiome in patients with CRC by decreasing the abundance of cancer-promoting bacteria.^89,94 Additionally, FMT has been shown to decrease the abundance of the Firmicutes phylum and increased the abundance of the Bacteroidetes phylum, thereby restoring the gut microbiome’s diversity and composition and shifting it toward a more balanced state that favors healthy microbial functions.^97,99

In animal studies, Cui et al.¹⁰⁰ found that FMT from healthy donors helped to restore gastrointestinal function, improve survival rates, and promote epithelial integrity without accelerating tumor growth. Dong et al.¹⁰¹ found that FMT potentiated the tumoricidal effects of radiation and alleviated intestinal toxicity in CRC mice models by accumulating Roseburia intestinalis in the gastrointestinal tract. FMT has also been shown to increase levels of beneficial metabolites, such as SCFAs, which are associated with improved gut barrier function and reduced inflammation.^102,103

Given these findings, FMT emerges as a promising adjunctive therapy for improving outcomes in cancer patients undergoing nCRT. However, more research is needed to fully understand its role in enhancing therapeutic efficacy, particularly in terms of modulating immune responses and influencing treatment-related side effects.

Discussion

The gut microbiota’s role in modulating the response to nCRT in patients with LARC is increasingly recognized. Specific microbial signatures, including the abundance of certain bacterial taxa like Alistipes spp., are associated with improved responses to nCRT, while others, like F. nucleatum, are linked to resistance. Recent studies have emphasized the predictive value of microbiota-based biomarkers in nCRT response^{23,59,60–62} and have also suggested that the gut microbiota may be useful in predicting treatment-related toxicity. For instance, Clostridium spp. and Alistipes spp. have been found to be significantly more abundant in patients who do not experience adverse events compared to those who do.¹⁰⁴ These findings align with the study by Shi et al., which highlighted Alistipes spp. as a potential predictor of nCRT response.⁶¹ Such specific microbial signatures, with the ability to predict nCRT response or adverse effects, could pave the way for personalized therapeutic strategies in the treatment of LARC in real-world clinical settings.^105,106 However, the current evidence remains heterogeneous, and the translation of microbial signatures into clinically actionable biomarkers requires validation across diverse populations, standardized methodologies, and prospective clinical trials.

Contradictory findings across studies further complicate biomarker development and underscore the limits of genus-level associations. Using 16S rRNA profiling, Shi et al.⁵⁹ reported Faecalibacterium to be more abundant in non-responders than responders, with levels declining post-nCRT among responders. This appears at odds with the broader literature describing Faecalibacterium (notably F. prausnitzii) as a butyrate-producing taxon with anti-inflammatory and immune-regulatory effects.^107,108 In contrast, a shotgun metagenomic study by Chen et al.⁶² identified Faecalibacterium sp900539945 enriched in good responders, suggesting that strain-level heterogeneity—and not the genus per se—may drive response signals. Similarly, the dual role of Streptococcus species in study by Yi et al.²³ further complicates microbiota modulation efforts. While certain strains such as Streptococcus thermophilus exert anti-inflammatory effects,¹⁰⁹ others, like Streptococcus agalactiae, possess virulence factors that may suppress immune responses and hinder nCRT effectiveness.¹¹⁰ Together, these contrasts argue for strain-resolved, function-anchored analyses (e.g., metagenomics/metatranscriptomics with metabolomics), and standardized reporting of sample type and timepoint; without this resolution, clinical translation risks being misleading or ineffective.

Beyond taxonomic correlations, recent mechanistic studies emphasize that microbial influence on nCRT extends beyond immune modulation. While the beneficial effects of gut microbiota metabolites, such as butyrate, in modulating inflammation and supporting immune responses have been well-established, emerging evidence demonstrates direct microbial interactions with tumor metabolic pathways and treatment-induced cell death mechanisms. For example, B. vulgatus upregulates nucleotide biosynthesis genes, contributing to cancer cell survival and therapy resistance.²⁵ In contrast, Lactobacillus-derived metabolites MG enhances radiotherapy outcomes by activating the cGAS-STING pathway and promoting immunogenic cell death.²⁶ These findings indicate that microbial metabolites can act as radiosensitizers or resistance factors, opening new opportunities for combining microbiota-targeted agents with chemoradiotherapy and immunotherapy. However, studies examining these mechanisms in LARC remain scarce, underscoring a critical research gap.

Research has predominantly focused on the gut microbiota, but the tumor-associated microbiome is now emerging as an equally important determinant of treatment response. The intratumoral microbiota directly interfaces with tumor cells and the immune microenvironment, thereby shaping therapeutic sensitivity. Recent integrated microbiome–immune profiling studies in LARC demonstrated distinct intratumoral microbial patterns between responders and non-responders.^61,63 To move beyond associative signals, future work should prioritize paired designs that collect diagnostic LARC tumor biopsies and contemporaneous baseline stool samples for shotgun metagenomics (± metatranscriptomics), enabling concordance/discordance mapping of taxa and functions across tumor and lumen. Such paired datasets would clarify which stool features reliably mirror tumor biology, improve classifier generalizability, and identify stool-based surrogates for hard-to-sample intratumoral features. Complementary approaches—spatial profiling of tumor microbiota (e.g., 16S/ISH or spatial metagenomics) alongside single-cell or bulk immune transcriptomics, longitudinal sampling pre-/mid-/post-nCRT, and standardized protocols for tissue handling and DNA/RNA extraction—should be embedded to strengthen mechanistic inference and cross-cohort reproducibility. Ultimately, integrating tumor- and stool-derived microbial features with host genomics, immune contexture, and clinical covariates in multiscale models may enhance predictive accuracy beyond stool-only biomarkers and better inform organ-preserving strategies in LARC.

Strategies for modulating the gut microbiota offer promising avenues to enhance nCRT outcomes. Dietary interventions, particularly high-fiber diets, increase beneficial bacteria such as Lactobacillus, Bifidobacterium, and Akkermansia, and may support immune function and reduce nCRT-related toxicities. However, dietary composition must be carefully tailored, as the effects of fiber vary depending on solubility, and excessive soluble fiber may promote colorectal tumorigenesis under certain microbial conditions. Probiotics and prebiotics have garnered attention for their potential to alleviate nCRT-induced side effects. Certain strains in Lactobacillus and Bifidobacterium can reduce CID and enhance the gut mucosal barrier. The combination of probiotics and prebiotics is an exciting approach, as prebiotics may enhance the effects of probiotics, improving the gut environment during nCRT. As these strategies are better understood, they could be seamlessly integrated into standardized treatment protocols for LARC, making microbiota-based interventions an ancillary component of care. In addition, FMT has shown promise in restoring microbial diversity, reducing toxicities, and potentially improving treatment responses in cancer patients undergoing nCRT. Although FMT is a powerful microbiota-modifying intervention, its optimal timing, donor selection criteria, long-term effects, and oncologic safety remain unclear and require evaluation in controlled clinical trials.

Despite notable progress, substantial limitations hinder clinical translation. Significant heterogeneity exists in study settings, including timing of sample collection, stool versus tissue sampling, choice of sequencing (16S vs metagenomics), and analytical pipelines, all of which restrict comparability. Population-specific microbiome structures driven by diet, lifestyle, genetics, and environmental exposure further limit generalizability, given that most findings originate from East Asian and European cohorts. Without standardized workflows and multi-center, longitudinal validation, microbiota-based biomarkers may remain population-dependent and non-generalizable.

Overall, the potential for microbiota-based interventions to enhance the efficacy of nCRT and reduce treatment-related toxicities is undeniable. Future research should focus on refining microbiota profiling techniques to identify reliable biomarkers of nCRT response, exploring the mechanisms of microbiota-tumor interactions, and conducting well-designed clinical trials to evaluate the effectiveness of microbiota modulation strategies in LARC patients. Additionally, the incorporation of microbiota-based therapies into multimodal treatment regimens for LARC could provide significant benefits in terms of improving patient outcomes and quality of life.

Conclusion

In conclusion, gut microbiota shapes both response and toxicity to nCRT in LARC, with distinct taxa and functional pathways emerging as candidate biomarkers to identify responders, guide risk stratification, and inform supportive care. Beyond immune modulation, microbial metabolites can directly alter radiosensitivity and therapy-induced stress responses, revealing actionable mechanisms. Microbiota-targeted strategies, including dietary interventions, probiotics/prebiotics, and FMT, are promising adjuncts for enhancing efficacy and mitigating gastrointestinal toxicity, but require rigorous, standardized validation. Key gaps include heterogeneity in sampling and analytics, population-specific effects, limited LARC-focused mechanism studies, and a paucity of interventional trials, including those assessing the intratumoral microbiome. Integrating microbiome profiling with immunologic, metabolomic, and genomic data in prospective, multi-center studies will be critical to deliver reproducible biomarkers and safe, effective interventions. These advances could enable microbiome-informed precision therapy that improves outcomes and quality of life for patients with LARC.

Footnotes

Acknowledgements

The authors would like to thank Dr Jian Chen for his valuable guidance and insightful suggestions throughout the preparation of this review.

Declarations

ORCID iD

Chengzhen Lyu

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