The Expanding Role of the Gut Microbiome in CRC

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Encouraging results in melanoma have led experts to explore the gut microbiome in colorectal cancer.  The next hot topic in research may be the gut microbiome's role for the prevention, progression, and management of colorectal cancer.

Patrick Wagner, MD, FACS

Patrick Wagner, MD, FACS

Oncologists who treat patients with colorectal cancer (CRC) have seen benefit with immunotherapy, but many patients are ineligible for this treatment, according to Patrick Wagner, MD, FACS, and this creates a major need for novel intervention for this patient population.

One path that looks enticing to investigators is the gut microbiome and its potential to improve the occurrence rate for CRC and outcome for patients with CRC.

“The number of immunotherapy options are skyrocketing. It's just that a lot of patients aren't eligible for them. We are looking for ways to expand options for patients and even though the microbiome has always been there in the background, we are just learning about how it impacts things and hopefully, it can make more options for patients,” Wagner, surgical oncologist and director of Complex General Surgical Oncology at Allegheny Health Network Cancer Institute, told Targeted OncologyTM.

The gut microbiome affects the development of CRC and its progression.1 The gut microbiome is also associated with controlling the efficacy of cancer treatment and the toxicities of therapeutic agents. This makes therapeutic agents that can control the gut microbiome expected to be among the most effective approaches for helping to combat CRC.2


Investigators like Wagner are interested in learning more about the role of the microbiome regarding the development of malignancies, their progression, and how they may work instead of therapies for patients with CRC. There have been several studies regarding the progression of melanoma and its correlation with gut microbiome composition. For CRC, early studies are underway.

Learning from Melanoma

Zev A. Wainberg, MD

Zev A. Wainberg, MD

The gut microbiome acts as a barrier to other pathogens2 and infections in the intestine. It modulates inflammation by affecting the host immune system. Not only are gut microbiota related to the intestinal inflammation that has a link tumorigenesis, but also modulation of the anti-cancer immune response. As a result, gut microbiota are associated with tumor progression and anti-cancer treatment efficacy.3

“The gut microbiome refers to the phenomenon that in our bodies, we all have 1000s of different bacterial species that are part of the normal balance between healthy and unhealthy. The essential role that the gut microbiome plays is to keep that balance intact. Not all bacteria is bad,” Zev A. Wainberg, MD, told Targeted OncologyTM.

In the melanoma space, tumors have shown to be responsive to immunotherapy and are immunogenic while only a fraction of colon cancers are eligible to be treated with immunotherapy.1 A study examining the gut microbiome in patients with melanoma showed there to be a clear signal of changing and influencing immunotherapy. This discovery was as monumental as the development of checkpoint inhibitors for this patient population, according to Wainberg. Based on the positive results from this trial, researchers are hopeful the same can be seen when the gut microbiome is used in patients with CRC.

“From a cancer perspective, there's been a lot of speculation over the years that altering the gut microbiome can alter the effectiveness of treatments, whether they be chemotherapy or drugs like immunotherapy. There have been some studies...that have suggested that patients can do better or worse, depending on how the gut microbiome is reacting,” added Wainberg, a professor of medicine at University of California, Los Angeles, and co-director of the UCLA GI Oncology Program

Investigating Microbiota in Colon Cancer

Michael G. White, MD, MSc

Michael G. White, MD, MSc

“In colon cancer, there's been a lot of interest. We take a stool sample and run that through an experiment to figure out what organisms are there, and you are going to get 1 answer. But if you look at the tumor itself, you're going to get something potentially different. One of the things that my lab is interested in is looking at how the bacteria in the tumor, not in the stool, impacts the immune recognition of colon cancers in ways that might shape the aggressiveness of the tumor or the prognosis for the patient,” stated Wagner.

From what has been investigated, the gut microbiota can be used as biomarkers to predict the effect of immunotherapy and improve the efficacy of immunotherapy in treating patients with CRC through modulation. There have also been recent advances that have helped experts further understand the role of the gut microbiome, including the development of technologies like 16S rRNA sequencing. With these, investigators have been able to discover microorganisms within the intestine that previously were unable to be identified.

The gut microbiota is made up of bacteria that lives inside the gastrointestinal tract. The 4 main groups of bacteria seen in the gut microbiota include Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria with the most important strains regarding the development of CRC being Bacteroides fragilis, Fusobacterium nucleatum, and Escherichia coli.3 Other bacterial strains linked with CRC are Parvimonas micra, Porphyromonas asaccharolytica, Prevotella intermedia, Alistipes finegoldii, and Thermanaerovibrio acidaminovorans.

“There have been lots of studies along these lines, controlling cancer patients to normal, and seeing what differences there are in the microbiome profile, not down to the level where we have a single agent or a proof of the causative relationship, but just associations. The other thing to know is that in experimental models, it is possible to take the gut microbiome from a cancer patient, give it to a mouse, and that will, under the right circumstances, cause tumors to emerge in the mice. These are heavily altered mice, so they're not they're not normal. They are genetically modified mice, but nevertheless, that is the model that has been shown to transmit cancer risk with the microbiome,” added Wagner.

Studies related to metabolomics and metagenomics also have discussed the effects of the gut microbiome on the human body, as well as others on their involvement in cancer prevention, tumorigenesis, and anti-cancer effects.

Using high-throughput microbiome sequencing, experts have been able to evaluate the microbiome community in tumor-formed and normal colon tissues. This allows for a more informed understanding of the differences between patients with CRC and healthy patients. According to reports, the diversity and richness of the gut microbiome decreases in patients with CRC, and there are even more significant changes in specific microbial groups. These results lead researchers to wonder if this has a greater impact on the mucosal immune response of CRC patients compared with healthy individuals.

Each of these studies shows the close correlation between CRC and the gut microbiome. Still further investigation is warranted to fully understand the effects of the gut microbiome in CRC.

“[The gut microbiome is] exciting and promising. What we find you never know, but there's enough signals to see that there's something here in colon cancer. There is probably an especially meaningful relationship because it is in the gut, and that makes it easier to study,” added Wagner.

Before cancer is diagnosed, there is work being done in the gastroenterology that culd help with disease prevention.

"A number of microbial taxa have been noted in the stool of colorectal cancer patients that suggests a general dysbiosis in patient’s gut microbiome. Interestingly, beyond individual taxa we are beginning to see that specific metabolomic signatures appear to be more correlative and reproducible in colorectal cancer patients. It is also noteable that when we examine bacteria within the tumors of patients with colorectal cancer, oral bacteria such as Fusobacterium Nucleatum and Parvimonas Micra are often observed. These bacteria are technically difficult to isolate from stool but the mechanism and path with which they reach tumors is currently being studied by our group and others. These species appear to create tumoral microenvironments that are both pro tumorigenic and appear to lead to resistance to standard chemotherapies such as oxaliplatin," Michael G. White, MD, MSc, assistant professor of the Department of Colon & Rectal Surgery at The University of Texas MD Anderson Cancer Center, told Targeted Oncology.


Anti-cancer effects on the growth of CRC are often associated with the presence or enrichment of certain intestinal strains. Preclinical studies have evaluated and shown several emerging chemical candidates to induce protective effects against CRC.2

For example, Faecalibacterium prausnitzii, a potential probiotic, can downregulate the NF-kB pathway in gut epithelial cells as it produces hydrophobic microbial anti-inflammatory molecules and prevents colitis. Lactobacillus rhamnosus and Bifidobacterium lactis may prevent abnormal epithelial proliferation in patients who have a history of polyps. These can also better the intestinal epithelial tight junction barrier and research suggests they play a role in suppressing tumor progression and volume in a preclinical CRC model.

These probiotics and their presence are confirmed to induce increasing short-chain fatty acid production, which then leads to apoptosis and inhibiting tumor proliferation.

The administration of probiotics is suggested to restore microbial imbalance and sustain intestinal microbial balance through occupying host tissue and preventing colonization of pathogenic bacteria. Ingestion of some probiotic strains, including Clostridium difficile and Staphylococcus aureus, diminish colonization of pathogens, which supports the use of probiotics to prevent intestinal infection.

In particular, Clostridium difficile (C. diff) infection usually results from bacterial perturbations in the gut with the use of antimicrobials. These lead to gut microbial disturbances being at the core of its pathogenesis. The gut microbiota does a lot to resist the colonization of C. diff, and infection with C. diff impacts the gut microbiome diversity. There is already an established correlation between gut microbial perturbations and C. diff, but with more data on microbial patterns, it is believed that this could be used to predict response to treatment and aid in the appropriate management of C diff.

Probiotics and other commensal microbiota stick to the surface on epithelial cells or mucus and by excluding pathogenic invasion, probiotic intake can lead to lower risks of intestinal infection, subsequent inflammation, and ultimately play a role in the prevention of CRC development, as well as reduce complications in pre-existing patients with CRC.

Though there are still unknowns, investigators believe gut microbiota modulation has the potential to prevent and treat CRC. Preclinical and clinical studies will further evaluate the gut microbiome’s role in CRC and see how it may transition into clinical practice or provide a therapeutic option for high-risk patients.


Some studies have revealed that the composition of the gut microbiome is related to the progression of CRC. In published findings around the development of CRC, many bacteria have affected tumor development and growth.4 It was also seen that the progression of CRC was promoted in a spontaneous CRC mouse model characterized by expression of a tumor suppressor gene, mutated Apc.

One study showed there to be a total of 11 operational taxonomic units (OTUs) which belong to the genera Enterococcus, Escherichia/Shigella, Klebsiella, Streptococcus, and Peptostreptococcus. These were found to be significantly more abundant in the gut microbiota of patients with CRC. Five OTUs belonged to Roseburia, and other butyrate-producing bacteria from the Lachnospiraceae family were less abundant. Additionally, dysbiosis was observed in the gut microbiome of patients with CRC, which may cause the promotion or progression of CRC.3

Research also demonstrated that in patients with CRC, Fusobacterium nucleatum is also significantly increased vs what is observed in healthy patients. Early-stage patients with CRC also have a different microbiome composition compared with advanced-stage patients.

In another study Fusobacterium Nucleatum were more abundant from precursor to late stages when evaluating the gut microbiome in patients with CRC, while Atopobium parvulum and Actinomyces odontolyticus were elevated only in early stages. These data highlight the potential clinical role that species abundance has as a biomarker for disease and progression.4

Gut microorganisms each specifically cause chronic inflammation in the colorectal epithelium and chronic inflammation is 1 of the major causes of CRC. Increased ROS with epithelial cell DNA damage also often induces cancer by the gut microbiome. For example, Fusobacterium Nucleatum and Bacteroides fragilis lead to a tumor-favorable immune microenvironment as they decrease CD3+ T cell density and multiply CD4+CCR6+IL17A+ Th17 cells. Bacterial components also may activate the NF-κB signaling pathway in CRC tumor cells, leading to tumor cell proliferation.

Other bacteria like olibactin-producing Escherichia coliencodes enzymes, the most highly abundant strain residing in the intestine, which is also related to the growth of CRC, are the head of HGF synthesis and induce senescence and tumor growth.

First, Streptococcus bovis is one of the risk factors for and typically is located in the gastrointestinal tract. Streptococcus bovis-induced endocarditis or bacteremia was an early clue to its involvement in colon cancer. The relationship between pro-inflammatory potential of Streptococcus bovis proteins and their carcinogenic properties was seen, noting the correlation between inflammation and colon. Streptococcus bovis also plays an active role in CRC development through an inflammation-based sequence of tumor development or propagation involving interleukin (IL)-1, cyclooxygenase-2, and IL-8.

One of the most widely known strains which is related to the formation of CRC tumors is Fusobacterium nucleatum. In a preclinical study, Fusobacterium nucleatum developed a pro-inflammatory environment and induced neoplasia progression in intestinal epithelial cells. IL-17a was also highly expressed in patients with CRC and they had an abundance of Fusobacterium nucleatum. Fusobacterium nucleatum also induces early carcinogenesis with increased bacterial adherence in the mucosal surface and created Fusobacterium adhesin A, which induces the start of the β-catenin signaling pathway once it joins to E-cadherin, a potent oncogenic stimulator.

Enterococcus faecalis, a gut commensal bacterium, produces a superoxide from the autoxidation of membrane-associated demethylmenaquinone. With infections related to Enterococcus faecalis, DNA damage to intestinal epithelial cells is induced. The amount of Enterococcus faecalis was significantly increased in patients with CRC patients vs healthy individuals, and in in vitro and in vivo studies, Enterococcus faecalis was shown to produce hydroxyl radicals, which are potent mutagens that cause DNA breaks, point mutations, and protein-DNA crosslinking. This adds to chromosomal instability and risk of CRC.

There are other bacteria which influence the formation of CRC, including Enterotoxigenic Bacteroides fragilis, which produces Bacteroides fragilis toxin, causes diarrhea and inflammatory bowel disease, promotes tumors, and Peptostreptococcus anaerobius, which causes a pro-inflammatory immune microenvironment, allows for tumor formation in the intestine, and plays a role in tumor formation by increasing the expression of pro-inflammatory cytokines.

Further research is needed to fully understand the relationship between other intestinal microbes with CRC formation as there are many causative bacteria of CRC that do not have a lot of investigation behind them.


With this knowledge that the gut microbiome has an association with CRC, more studies have focused their efforts on investigating its effect in this patient population. Studies are being conducted with the gut microbiome in combination with various treatment modalities to apply it to clinical cancer treatment, and new advances are being made to learn more about the synergistic effects of the gut microbiome when given with immune checkpoint inhibitors.5

Therapies which modulate the gut microbiome, including administration of probiotics or fecal microbiota transplantation, improve the efficacy of cancer treatment. Administration of antibiotics can reduce the efficacy of oxaliplatin and CpG oligodeoxynucleotides chemotherapeutic agents. The use of antibiotics increases pathogenic bacteria such as Escherichia shigella and Enterobacter, as well as reduces the anti-cancer effect of 5-FU.

Radiation of the pelvic area causes dysbiosis and has the potential to affect the treatment modality of CRC.5 Furthermore, radiation-induced gut epithelial damage worsens the prognosis of CRC patients. These radiation side effects can be ameliorated through fecal microbiome transplantation as well as probiotics administration.

The gut microbiota plays a role in modulating mucosal immunity in the colorectal region, acting to improve the efficacy of immunotherapy by enhancing the CD8+ T cell immune response or short-chain fatty acids metabolite production.5

Preclinical studies have demonstrated changes in the composition of the gut microbiota to affect the initiation of precancerous cancer lesions and disease progression.2 In the colorectal region, gut microbiota can change and influence organs directly. As a result, CRC tends to be affected by the gut microbiome at a higher rate compared with other tumors.

Many published results have demonstrated that the gut microbiome acts as an important key factor in the initiation and progression of carcinoma in the treatment of CRC.4 While some studies have shown that microbiome alterations may be modified to treat patients with CRC, more molecular-based analyses and/or prospective interventional studies must be done in order to yield further results.

“In general, this is an emerging area of science. There are no recommendations that you can give right now. We're trying to expand the number of patients for whom immunotherapy is an option. The vast majority of patients with colon cancer don't have any immunotherapy options, so the point of studying the microbiome is to open the doors to more patients because when immunotherapy works, it really works. The whole point of this entire research is to exercise beyond just epidemiology and understanding what causes cancer. Of course, that is important, but more urgently, can we open the gates to more patients by altering their tumors to make them responsive to immunotherapy? We care because so few people are eligible for immunotherapy right now, so we need to do whatever we can to learn how to turn the tide,” Wagner concluded.

Part of “turning the tide” could mean leaning toward a mor emultidisciplinary approach to addressing colon cancer risk and colon cancer management, according to White.

"Working with our colleagues across disciplines is critical to the successful treatment of patients with colorectal cancers. Especially in patients with locally advanced or metastatic malignancies medical, surgical, and radiation oncology teams are each critical to optimizing patient outcomes. This is really one of the strengths of working at a tertiarycancer center like MD Anderson."

  1. Sehgal K, Khanna S. Gut microbiome and Clostridioides difficile infection: a closer look at the microscopic interface. Therap Adv Gastroenterol. 2021;14:1756284821994736. Published 2021 Feb 23. doi:10.1177/1756284821994736
  2. Kim J, Lee HK. Potential role of the Gut microbiome in colorectal cancer progression. Front Immunol. 2022;12:807648. Published 2022 Jan 7. doi:10.3389/fimmu.2021.807648
  3. Rebersek M. Gut microbiome and its role in colorectal cancer. BMC Cancer. 2021;21(1):1325. Published 2021 Dec 11. doi:10.1186/s12885-021-09054-2
  4. Cass SH, Ajami NJ, White MG. The microbiome: the link to colorectal cancer and research opportunities [published correction appears in Curr Treat Options Oncol. 2022 Apr 5;:]. Curr Treat Options Oncol. 2022;23(5):631-644. doi:10.1007/s11864-022-00960-6
  5. Alrahawy M, Javed S, Atif H, Elsanhoury K, Mekhaeil K, Eskandar G. Microbiome and colorectal cancer management. Cureus. 2022;14(10):e30720. Published 2022 Oct 26. doi:10.7759/cureus.30720
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