Role of gut microbiome in colorectal cancer: a comprehensive umbrella review protocol

Abstract

Introduction

Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related death globally. Growing evidence links gut microbiota dysbiosis to CRC, with several reviews reporting consistent microbial alterations in CRC patients that may serve as non-invasive biomarkers. However, findings vary across studies, and consensus on key microbial taxa is lacking. This umbrella review aims to clarify: (1) the association between gut microbiome composition and CRC development/progression, (2) specific microbial taxa linked to CRC risk, (3) the role of microbiome diversity in CRC outcomes and (4) potential microbial biomarkers for diagnosis, prognosis and treatment response.

Methods and analysis

This umbrella review will follow the Joanna Briggs Institute (JBI) Umbrella Review Guidelines and adhere to the Preferred Reporting Items for Overviews of Reviews. A comprehensive search will be conducted across MEDLINE (PubMed), Embase, CINAHL and key systematic review databases, including the Cochrane Database, JBI Evidence Synthesis and Database of Abstracts of Reviews of Effects, without language restrictions. The search strategy will use a combination of Medical Subject Headings terms and free-text keywords with Boolean operators. The review questions were developed using the Population, Concept and Context framework. Only high-quality (as determined by the JBI Critical Appraisal Checklist for Systematic Reviews and Research Syntheses), peer-reviewed quantitative systematic reviews with or without meta-analyses will be included. Overall effect estimates extracted from systematic reviews, with the number of studies that inform the outcome, will be presented.

Ethics and dissemination

No ethical approval is required since the work is carried out on published documents. Findings of this review will be disseminated among relevant stakeholders through multiple scientific avenues, including presentations at both national and international forums and manuscript publication in an open-access journal.

PROSPERO registration number

PROSPERO 2025 CRD420251035257. Available from:

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251035257.

STRENGTHS AND LIMITATIONS OF THIS STUDY.

• Rigorous methodology in accordance with the Joanna Briggs Institute Umbrella Review Guidelines.

• Transparent reporting according to the Preferred Reporting Items for Overviews of Reviews.

• Evidence compiled solely from high-quality systematic reviews and meta-analyses with predetermined eligibility criteria.

• May be limited by heterogeneity of study populations, microbiome profiling techniques and outcome definitions of the included reviews.

Introduction

Colorectal cancer (CRC) is one of the most prevalent and lethal malignancies worldwide, accounting for nearly 10% of all cancer cases and ranking as the third most common cancer and second leading cause of cancer-related mortality globally.¹ According to the Global Cancer Observatory (GLOBOCAN), CRC was responsible for over 1.9 million new cases and 904 019 deaths in 2022.¹ Furthermore, by 2040, the burden of CRC is projected to increase to 3.2 million new cases with 1.6 million deaths. Most of these cases are predicted to occur in countries with a high human development index.² Changes in dietary habits, sedentary lifestyles, population ageing, smoking, alcohol consumption and obesity were implicated in the rising trends in CRC.³ While advancements in screening and treatment exist, the persistent challenges in early detection and demographic disparities continue to hinder optimal survival rates for CRC patients.⁴

The human gut harbours a vast and diverse microbial community that interacts with multiple organ systems through a complex, multidirectional axis.⁵ Gut microbiota play a crucial role in host–microbe interactions, influencing neural, endocrine, humoral, immunological and metabolic pathways. The majority of these microorganisms are non-pathogenic and maintain a symbiotic relationship with the host, contributing to immune defence against harmful pathogens. Disruptions in the balance of gut microbiota, known as dysbiosis, have been associated with a range of health conditions, including anxiety, depression, hypertension, cardiovascular diseases, obesity, diabetes, inflammatory bowel disease and cancer.⁵

Several mechanisms have been proposed linking gut microbiota to carcinogenesis: (1) proteolytic fermentation associated with high protein intake increases the production of phenolic compounds, amines, ammonia, N-nitroso compounds and indoles, all of which have a carcinogenic impact on epithelial cell differentiation and proliferation,⁶ (2) chronic inflammation by microbial products and cytokines such as interleukin-1β, interleukin-6 and tumour necrosis factor-α,⁷ (3) genotoxicity through bacterial toxins such as colibactin produced by Enterobacteriaceae induces DNA damage,⁸ (4) modulation of inflammatory responses, alteration of immune surveillance and regulation of systemic immune functions contribute to the promotion or inhibition of cancer development through microbiome-driven mechanisms.^{9 10} Understanding the intricate relationships between gut microbiota and CRC could lead to novel therapeutic strategies, including probiotics or dietary modifications aimed at restoring a healthy microbial balance.¹¹ Ongoing studies exploring the potential of faecal microbiota transplantation as a method to manipulate the gut flora offer promising avenues for enhancing treatment efficacy and patient outcomes in CRC therapy.¹²

A preliminary literature search for umbrella reviews on this topic was conducted across multiple databases, including MEDLINE (via PubMed), Embase, CINAHL, the Cochrane Database of Systematic Reviews, the Database of Abstracts of Reviews of Effects (DARE), Joanna Briggs Institute (JBI) Evidence Synthesis, PROSPERO and JSTOR. The search yielded only a single relevant publication.¹³ However, this review did not adhere to JBI guidelines and was not registered with PROSPERO. Additionally, the review lacked a clearly defined objective or research question. Given these limitations, we found conducting another umbrella review on the same topic to be justified.

Several systematic reviews and meta-analyses have investigated the association between gut microbiota and CRC, consistently reporting alterations in gut microbial composition among CRC patients.14,16 Specific microbial species, including Fusobacterium nucleatum, Bacteroides fragilis, Peptostreptococcus stomatis, Gemella morbillorum, Parvimonas spp, Solobacterium moorei and Clostridium symbiosum, were found to be significantly enriched in CRC patients across various geographical regions,¹⁴ with depletion of beneficial bacteria such as Faecalibacterium prausnitzii, ¹⁷Bifidobacterium spp, ¹⁸Prevotella copri¹⁷ and Roseburia spp,^{10 19} which have anti-inflammatory and protective effects. Second, the gut microbiome has been investigated as a potential biomarker for CRC detection.¹⁴ Several studies have explored the potential of gut microbiome signatures as non-invasive biomarkers for CRC screening.¹⁵ Third, microbiota-driven resistance to chemotherapy and immunotherapy has been described.²⁰ Dysbiosis may influence the efficacy of chemotherapy and immunotherapy, with certain bacteria promoting resistance to fluoropyrimidines²¹ and immune checkpoint inhibitors.²⁰ Microbiome modulation through probiotics, prebiotics and faecal microbiota transplantation is being investigated as an adjunctive strategy to improve treatment outcomes.²²

Some of the inconsistent findings across reviews are that while most studies report dysbiosis in CRC patients, there are variations in specific microbial signatures across studies, likely due to differences in geographic populations, sequencing methods and study designs.²³

Despite the growing number of systematic reviews and meta-analyses exploring the relationship between the gut microbiome and CRC, significant gaps remain in synthesising and critically appraising the available evidence. There is a lack of consensus regarding which microbial taxa have the strongest and most consistent associations with CRC, the strength and direction of associations (protective versus harmful microbes), variations in findings across different populations and study methodologies, and the clinical applicability of microbiome-based interventions and biomarkers.

Different terminology has been used in the literature to describe this methodological approach, including ‘overviews of reviews’, ‘reviews of reviews’, ‘summaries of systematic reviews’ and ‘systematic reviews of systematic reviews’.²⁴ By conducting this umbrella review, we aim to: (1) critically appraise the quality and reliability of existing systematic reviews using the JBI Critical Appraisal Checklist for Systematic Reviews and Research Syntheses,²⁵ (2) identify areas of agreement and inconsistency across systematic reviews, (3) provide a comprehensive synthesis of the gut microbiome’s role in CRC development, progression and treatment response, (4) highlight evidence gaps and propose future research directions to improve microbiome-based interventions for CRC.

Given the increasing recognition of the gut microbiome as a key player in CRC pathogenesis and treatment response, it is imperative to synthesise the highest quality evidence available. This umbrella review will apply rigorous methodological standards to critically appraise and integrate findings from systematic reviews and meta-analyses, ultimately advancing our understanding of the gut microbiome’s role in CRC and informing future research and clinical applications.

Findings from this umbrella review would: (1) inform clinicians whether gut microbiome-based interventions (eg, probiotics, prebiotics or faecal microbiota transplantation) could be integrated into CRC prevention or treatment strategies, (2) guide future research by identifying methodological limitations in existing systematic reviews, (3) support personalised medicine approaches by exploring microbiome-based biomarkers for CRC risk stratification and treatment optimisation.

Review questions

The review questions were developed as per the Population, Concept and Context framework recommended by JBI guidelines.²⁵ The primary research question is: ‘what is the association between gut microbiome composition and the development or progression of CRC?’

Secondary research questions include: (1) which specific microbial taxa are associated with an increased or decreased risk of CRC? (2) How does gut microbiome diversity influence CRC outcomes? (3) What microbial biomarkers can be used for diagnosis, prognosis and response to treatment?

Method

The protocol has been registered in PROSPERO (PROSPERO 2025 CRD420251035257. Available from: https://www.crd.york.ac.uk/PROSPERO/view/CRD420251035257). This review will be conducted in accordance with the JBI umbrella review guidelines²⁵ and will be reported according to the Preferred Reporting Items for Overviews of Reviews.²⁶ The planned commencement date for this review is August 2025, with its completion anticipated by September 2026.

Patient and public involvement

None. No patients or the public were involved in the design or conduct of our research.

Inclusion criteria

• Type of participant: adults (≥18 years) diagnosed with CRC.

• Phenomena of interest: role of the gut microbiome.

• Outcomes: microbial influence on the risk, progression, survival and treatment response of CRC, along with therapeutic strategies and microbial biomarkers.

• Context: systematic reviews and meta-analyses relevant to the topic involving all genders and races without geographical restrictions.

• Type of studies: peer-reviewed quantitative systematic reviews, with or without meta-analyses, will be included in the proposed umbrella review, with no language restrictions applied. Only high-quality systematic reviews (as determined by the JBI Critical Appraisal Checklist for Systematic Reviews and Research Syntheses) will be included.²⁵

Exclusion criteria

Reviews will be excluded if:

• They are narrative reviews or scoping reviews.

• They do not specifically distinguish CRC from other gastrointestinal cancers.

• They focus solely on animal models without human data.

• They are theoretical or rely primarily on text and opinions as the main source of evidence.

Search strategy

A comprehensive search strategy will be implemented across multiple databases, including MEDLINE (via PubMed), Embase, CINAHL and major repositories of systematic reviews, including Cochrane Database of Systematic Reviews, JBI Evidence Synthesis and DARE. A combination of Medical Subject Headings (MeSH) and free-text keywords combined with Boolean operators (AND, OR) will be used to create the search query. The search strategy created for the MEDLINE is given: (((“Gastrointestinal Microbiome”[MeSH] OR “Microbiota”[MeSH] OR “Dysbiosis”[MeSH]) OR (gut microbiome OR gut microbiota OR intestinal microbiome OR intestinal microbiota OR gut flora OR intestinal flora OR microbial diversity OR bacterial composition OR dysbiosis)) AND ((“Colorectal Neoplasms”[MeSH] OR “Colonic Neoplasms”[MeSH] OR “Rectal Neoplasms”[MeSH]) OR (colorectal cancer OR colon cancer OR rectal cancer OR CRC OR colorectal carcinoma OR colonic tumo#r OR rectal carcinoma)). Search filters will be applied to limit results to systematic reviews and meta-analyses. Reference lists of included reviews will be hand-searched for additional relevant reviews.

A search for grey literature will aim to identify eligible systematic reviews from reports of governments and non-governmental organisations. We will search CORDIS, the primary source of results from European Commission-funded research (https://cordis.europa.eu/), and websites of the National Institute for Health and Care Research (https://www.nihr.ac.uk/) and the Agency for Healthcare Research and Quality (https://www.ahrq.gov/).

Study selection

After initial removal of duplicates, articles will be imported into the web-based application Rayyan.²⁷ The study selection process will involve two independent reviewers screening studies:

1. Title and abstract screening: articles that fail to meet the inclusion criteria will be excluded.

2. Full-text screening: the full text of potentially eligible reviews will be obtained and assessed.

3. Disagreements will be resolved through discussion or consultation with a third reviewer.

The study selection process will be detailed in a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) flow chart.

Methodological quality assessment

• The methodological rigour of the included systematic reviews will be evaluated using the JBI Critical Appraisal Checklist for Systematic Reviews and Research Syntheses.²⁵

• To obtain an overall appraisal of each review, the following quality thresholds are defined: low quality (0–49% of the criteria met), moderate quality (50–74% of the criteria met) and high quality (75% or more of the criteria met). Results of the quality appraisal will be presented visually using a traffic light scheme to display the score of each item in each review (green for ‘yes’, red for ‘no’, yellow for ‘unclear’ and blank for ‘not applicable’). The overall methodological quality will be described in the final report.

• The final synthesis will include only systematic reviews rated as high quality (75% or more of the criteria met).

Data extraction

Data will be extracted independently by two reviewers using a standardised extraction form including:

• Study details (author, year, country, journal).

• Review type (systematic review, meta-analysis).

• Number of included studies and sample size.

• Microbiome-related findings (specific microbial taxa, diversity indices).

• Association with CRC (risk, progression and treatment response).

• Methodological quality score (JBI Critical Appraisal tool).²⁴

Data synthesis and summary of evidence

A narrative synthesis will summarise the information regarding the citation details; study population and number of participants; the setting and context; the number of databases sourced and searched; the date range of database searching; the date range of included studies that inform each outcome of interest; the number, types of studies and country of origin of primary research studies in the included research synthesis; the instrument used to appraise the primary studies in the research synthesis and the rating of their quality; the outcomes reported by the included reviews that are relevant to the Umbrella Review question, and the type of review and the method of synthesis/analysis employed to synthesise the evidence as well as any comments or notes on the Umbrella review.

Overall effect estimates extracted from systematic reviews, number of studies that inform the outcome, number of participants from included studies and the heterogeneity of the results of included reviews will be reported in a tabular form. Any overlaps of original research studies in each of the included research syntheses will also be presented. The overall certainty of the evidence will be appraised using the Grading of Recommendations Assessment, Development and Evaluation framework.²⁸ Systematic reviews with articles that have been retracted will be clearly identified and will not be included in the synthesis.

Ethics and dissemination

Ethical approval was not required, as this is an umbrella review using already published systematic reviews on the topic of interest as our data source.

The umbrella review will adhere to the JBI Umbrella Review Guidelines and follow the PRISMA 2020 reporting guidelines to transparently illustrate the study selection process and critical appraisal findings. The final report will be submitted to a high-impact peer-reviewed journal and presented at international oncology and microbiome conferences.