How the bacteria in your gut could raise colon cancer risk

She didn’t smoke. She didn’t drink. She exercised daily and considered herself a “clean” eater. And yet, at 43, Dana Deighton was diagnosed with stage four gastrointestinal cancer—in the esophagus.

Deighton questioned the “why” and the “how,” like many other young people who are finding themselves frustrated by a surprise diagnosis. “There are so many variables: the environment, what we eat, the buildings we live and work in, our genetics, our own unique biology,” she says. “Our bodies are being challenged every day by forces we can't always see or escape.”

Gastrointestinal cancer cases are expected to double worldwide by 2050, according to a December 2025 report published in the Interdisciplinary International Journal of the American Cancer Society. The report suggests that the biggest increases will be in pancreatic cancer diagnoses and colorectal cancer deaths. Each year, the colorectal cancer rates rise one to three percent, especially in those in their 20’s, 30’s, and 40’s, the Dana Farber Cancer Institute reports. A disturbing rate of young people aren’t just getting diagnosed, but dying from colorectal cancer, which has become the leading cause of cancer deaths in the U.S. in those under 50. And simply pointing to rising obesity rates or the need for more Americans to engage in regular exercise to stay healthy just isn’t accounting for the unprecedented rise, experts say.

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“You can’t separate one factor, and that’s what makes it hard—if it were simple, we’d know,” says Ben Schlechter, gastrointestinal oncologist at the Dana-Farber Cancer Institute in Boston. “But [factors] are linked in weird ways, so there’s a lot of information that tells us what’s going on,”

Research around another theory is underway. At the center of it is an entire microscopic community that lines our digestive tract—the microbiome.

What does the microbiome have to do with colorectal cancer?

The microbiome is a group of tiny organisms in the body that protect us from disease. But there are many reasons it can become imbalanced, potentially affecting cancer development and even how treatment works.

While researchers and doctors are quick to say they don’t know of a single cause for the increased rate of gastrointestinal cancer, including colorectal, the microbiome is becoming a more plausible reason for the rate increases—but is incredibly hard to study, as a glimpse at someone’s microbiome makeup can change day to day due to factors like diet and medications.

One study notes that countries with higher rates of colorectal cancer also reported higher mutation loads of a bacterium in the gut called colibactin. Schlechter says it’s important to note in understanding this study that the endpoint of the colon—the rectum and sigmoid colon—has the most bacteria. This is the part of the colon where the most water has been removed to form stool and his bacterium is more concentrated, potentially causing damage.

He says around 20 to 25 percent of patients have a mutation profile resulting from bacterial injury. “So there's a bacteria, and it makes a toxin, and that toxin injures DNA, and that injury is present in a much higher degree in adults under the age of 50 with colon cancer than adults over the age of 70,” he shares. In addition to the damage the bacterium is likely doing causing cancer, the bacteria itself can play a role by leaving behind a substance that’s been metabolized, and has “turned into something even worse,” he says. That substance is also causing injury.

What can happen in the gastrointestinal tract from an early age

Another study suggests a 23 percent increase in rates of colorectal cancer later in life for infants who were breastfed—not to discourage breastfeeding, which researchers reiterate is healthy, but to point to the potential role of the microbiome in the rise in these cancer rates.

Similar to how water is removed from stool in the colon, breastmilk is “concentrated,” Schlechter says. “Water is extracted and breastmilk comes out. So there’s some substance that can pass through the [mother’s] body, make it into breastmilk. As water is removed to concentrate breastmilk, it’s left behind.”

He also points to the fact that babies are often breastfed from birth, a time when the stage is set for microbiome health going forward. He says the “big three” factors here are that the substance from breast milk is “partially soluble in water, [there is] bacterial involvement, and exposure starts really, really early.”

Later in childhood, the American diet and lack of movement come into play. “We know that kids who are more sedentary and have a diet higher in sugar-sweetened beverages are more likely to have young onset colon cancer,” Schlechter says. “Extra sugar means extra bacterial overgrowth, creating this idea—we can’t prove but we suspect—that bacteria is doing something, we are overfeeding the bacteria, and all these factors are feeding into this toxic mix at the bottom of our colon that results in these young onset colorectal cancers.”

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He adds that obesity in children results in higher rates, and exercise seems to have a potentially protective effect, with lower rates in kids who get plenty of movement. But the full connection between exercise and the microbiome is yet to be fully understood.

“If you take everything—a microbial signature, rapid onset of weight after adolescence, a childhood exposure of sugar-sweetened beverages, kids who didn’t do a sport … kids who are breastfed, you probably only capture a third of the risk,” Schlechter says. “Which means the rest is…who knows.”

Overgrowth and undergrowth of bacteria in the gut might contribute

Schlechter hypothesizes that something changed in the 1960s or ‘70s that started this trend. Cynthia Sears, professor of medicine and oncology at Johns Hopkins University School of Medicine, and microbiome program leader at the Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins in Baltimore, adds that overprescribing antibiotics was common in the 1980s and ‘90s, which can lead to imbalances in bacteria in the microbiome. Sears studies Enterotoxygenic Bacteroides Fragilis, which is transferred from animals to people, originally identified as a diarrheal disease. Then, researchers started to explore its connection to cancer after proving it led to colon cancer in mice. Another gut disease, Clostridioides difficile (“C-Diff”), has become a larger problem in children now, she says.

Imbalances in the gut, such as those from E.coli—which naturally lives in our gut and is helpful unless there’s an overgrowth—can add to the confusion. “There’s a strain of E. coli doing the wrong thing,” Schlecter adds. Similarly, H. Pylori, a bacterium that can be present in the stomach, has been associated with cancer.

“You can’t live without bacteria in your gut, but they can get out of hand,” Schlechter says. Similarly, overuse of antibiotics can impact gut health, as can environmental exposures such as ingesting preservatives, he shares. “You're eating preservatives. They're meant to keep bacteria out of your food, but they can injure bacteria that you need in your gut.”

Sears says it’s “hard to unravel and pull out one bug amongst many” in the microbiome; they’ve identified 11 bugs that have been associated with colon cancer, and in late April, she published a new paper further linking Bacteroides fragilis with colon tumor formation.

What to do to mitigate cancer risk

All of these unknowns about the microbiome, along with hard-to-manage factors, might have young people wondering what they really can do to prevent early-onset GI cancers. When Deighton was diagnosed, she considered what changes might affect her microbiome and overall health. After doing her own research, she decided to move to a plant-based diet to hopefully improve inflammation, she says, which “made sense to her intuitively.”

“Once I made the shift, I never looked back,” she says. “I knew how important it was to stay healthy enough to make it to the next day, for my kids and myself.”

Schlechter says he is careful when discussing risk factors, because some of the patients he sees had none. He says it can imply someone gave themself cancer, but also, risk factors don’t account for some cases.

For example, some of the fittest athletes might be at higher risk. A 2025 study reports triple the number of polyps in the colons of long-distance runners, which the Prevent Cancer Foundation suggests could be due to chronic inflammation from exercise affecting the microbiome.

Experts echo the same: eating whole and less processed foods, lowering sugar intake, exercising, and not smoking or drinking can not only help prevent cancer, but help fight it if you do get it.

In addition to leading a healthy lifestyle, each expert recommends getting a preventative colonoscopy starting at 45 and reporting any persistent GI symptoms to your doctor promptly. 

But, until more research is done, official recommendations on the role of the microbiome will have to wait. For now, Schlechter has a clear message for those worried about getting colorectal cancer: “Every adult 45 and older should undergo screening, whether it’s a colonoscopy or stool-based test,” he says. “If you don’t feel fine, you need to see a doctor.”