Exploring the Hidden Potential of Our Microbiome in Cancer Research
Like many researchers worldwide engaged in human genome studies, scientist Mark Driscoll held the belief that decoding the DNA sequence would ultimately lead to breakthroughs in cancer treatment. During his tenure as a leader in next-generation sequencing (NGS), a technology that enables the reading and analysis of our genetic material, Driscoll and his team achieved several remarkable milestones. Notably, they sequenced the DNA of James Watson, one of the co-discoverers of the double helix structure of DNA, and assisted Nobel Prize winner Svante Pääbo in decoding the Neanderthal genome. However, the anticipated solution to cancer eluded them.
Yet, Driscoll remains undeterred in his mission. He is now convinced that the key to unlocking cancer cures lies not in our genes, but rather in an unexpected source: our gut microbiome. “When we didn’t crack the cancer code, it was disheartening,” Driscoll reflects. “Over the last decade, researchers have noted, ‘Whenever there’s colon cancer, certain bacteria are present. The same goes for pancreatic and breast cancers.’ These consistent observations motivated me to pivot my focus towards the gut microbiome, which hosts approximately two million bacteria, each possessing its unique set of 3,000 to 5,000 genes.”
To further this research, Driscoll established his own company, Intus Biosciences, headquartered in Connecticut. His objective is not only to enhance cancer diagnosis and treatment but also to tackle issues related to irritable bowel syndrome (IBS), particularly as bowel cancer rates surge globally, especially among individuals under fifty in Western nations. In the UK, early-onset bowel cancer cases have surged by 25 percent in the past decade.
To approach this challenge, Driscoll developed a groundbreaking test named GutID, which identifies every strain of bacteria in the human gut microbiome. This test provides scientists—and fortunate individuals who take it—with a comprehensive overview of their gut health. The results are beautifully displayed in a multicolored pie chart, featuring bacterial strains with names that sound almost lyrical: Segatella, Sutterella, Prevotella, Roseburia, along with a spectrum of newly documented bacterial strains.
“Human DNA hasn’t changed significantly over recent generations,” explains Paul Denslow, CEO of Intus Bio and a British professional with a background in finance and biotechnology. “Despite the immense resources devoted to studying the 23,000 human genes, we must turn our attention to the two million bacterial genes residing in our bodies, which we know have evolved in the last few decades due to changes in diet, food production methods, and antibiotic use—coinciding with the alarming increase in cancer rates.”
Having gathered a few thousand test samples and formed collaborations with prestigious institutions such as Imperial College London and Oxford University, Denslow is eager to make Driscoll’s innovative test accessible to a broader audience.
Should healthy individuals, or those with no familial cancer history, consider testing? “Gut bacteria is a fundamental driver of health outcomes,” asserts Denslow. “The aim is to analyze these bacteria to help people manage their health proactively, potentially avoiding or delaying the onset of diseases. This is something individuals can track and positively influence.”
As a middle-aged woman, I find myself amid rising cancer statistics, despite not presenting concerning gut symptoms or having a family history of cancer. I have been bombarded with recommendations to consume kefir and kombucha, yet I enjoy a wide-ranging diet that includes ultra-processed foods. Despite knowing better, I often find myself reluctant to part with favorites like marbled steak and fatty salami.
Although I wouldn’t have spent £349 on the GutID test if I weren’t reporting on it, I am intrigued by the opportunity to explore my microbiome further. However, I am also cautious, taking into account the perspective of Emily Leeming, a microbiome scientist at King’s College London and author of Genius Gut (Penguin, £18.99), who suggests that such tests might not yield actionable insights. “Microbiome testing isn’t advanced enough yet to provide any real advice that we cannot obtain for free elsewhere,” she cautions. “These tests are extremely costly and often promise benefits that lack sufficient credible evidence.”
The test itself is straightforward. I collect a small sample using a plastic scoop, place it in the provided envelope, and await my results. A month later, I receive a detailed 20-page report titled “Core Gut Insights,” which includes an overall score out of 100 and several key findings. To my delight, I score 74, a rating deemed “good” by the report and “very good” by Elena Panzeri, the specialist microbiome nutritionist who will help me interpret the data.
In a subsequent test six months later, my score is recalibrated to 68, as the GutID database has expanded, allowing for a more standardized comparison. Nevertheless, the overall news remains positive. I have no presence of fusobacteria, which Driscoll identifies as a common factor in research surrounding gut bacteria and cancer, typically found in individuals with cancer or those severely ill from foodborne illnesses. “People often question whether it’s causation or correlation,” he explains. “We know that these bacteria exist prior to the onset of cancer. Recent studies have indicated that these bacteria can indeed cause DNA breaks leading to cancer.”
Moreover, my gut microbiome exhibits good diversity, with sufficient levels of bacteroidetes and firmicutes (represented in purple and tan on my microbiome wheel) that constitute a healthy microbiome. However, I do have a few unwelcome guests, including a rare pathogen named mycoplasma, which is not a welcome inhabitant of my gut, alongside a low quantity of probiotics.
In preparation for my follow-up test, I discuss strategies for improving my gut bacteria with Panzeri. I begin taking two probiotics, Thorne bacillus coagulans and Optibac Every Day, and I increase my intake of fiber and polyphenol-rich foods, such as green tea, kefir, berries, dark chocolate, extra virgin olive oil, and almonds. My goal is to achieve a perfect score, something Driscoll almost attained after 14 weeks of enhancing his diet, which had consisted of “black coffee all morning, peanuts all afternoon, and whatever was for dinner.” He started with a score of 28, which remained stable for 14 months, but after following Panzeri’s dietary advice, his score skyrocketed to 92.
Colorectal surgeon James Kinross, who investigates bowel cancer and the gut microbiome at Imperial College London, utilizes the GutID test in his clinical practice. “These are not diagnostic tests,” he clarifies. “We use them to gain functional insights into the gut health of the patients I treat.” When asked if he had utilized an alternative test before GutID became available, he admits, “I hadn’t. Previous direct-to-consumer microbiome tests often employed short-read 16S sequencing, which fails to provide species or strain level identification.”
Zoe is the most recognized gut health test in the UK, a company that popularized the consumption of fermented foods and self-examination of one’s stool. Co-founder Professor Tim Spector recently criticized 16S testing in comparison to Zoe’s metagenomic approach, which employs a tool called MetaPhlAn to analyze over 5 million genes. Previously, Zoe identified 15 “good” and 15 “bad” bacteria for users but expanded its list to 50 of each in 2024.
However, independent experts raise concerns about how we classify and communicate information about bacteria to the general public—namely, non-scientists like myself. “There’s no definitive classification of good or bad bacteria,” states Professor John S. Tregoning, a vaccine immunology expert at Imperial. Tregoning experimented with gut microbiome tests for insights in his recent book Live Forever? A Curious Scientist’s Guide to Wellness, Ageing and Death (One World, £18.99). He did not pay for the test but conducted it through work. Should individuals invest £200 or more in these tests? “Absolutely not!” he exclaims. “Invest your money in activities that enhance your social life, such as joining a tennis club, choir, or dance class. My book’s underlying message is to prioritize spending on enjoyable physical activities with friends.”
What about the advancements in tests like GutID? “The testing process sounds promising,” he acknowledges. “What they are doing represents the best available methodology. However, interpreting the data can be complex. If you’re curious, it might be worth exploring, but it’s primarily for personal interest rather than a definitive health guide.”
“I’m not suggesting their approach is incorrect, but the complexities of gut microbiome science make it challenging to draw clear conclusions,” he adds. Like me, Tregoning exhibited low levels of probiotics in his 16S test, but found that consuming Yakult did little to boost those levels.
After two months of following Panzeri’s dietary advice, I took my second test. However, I also indulged during the festive season, enjoying mince pies drenched in brandy cream. I’m thrilled to learn that my score has increased to 76, and the unwelcome mycoplasma has diminished to a “reasonable slice,” as Driscoll describes it. Even better, it has been supplanted by more beneficial bacteria. Similarly, Tregoning experienced little change in his probiotics, but a strain associated with IBS, known as proteobacteria, has seen a slight uptick in my results.
Experts agree that there is much to learn about our health from the gut microbiome, which holds the potential for groundbreaking medical discoveries. Kinross has high hopes for the near future: “In the next five years, we will witness the emergence of validated biomarkers for bowel cancer screening and risk reduction. I am optimistic this will lead to significantly improved patient outcomes.”
Will I take the test again? After my second test, I was prescribed a five-day course of antibiotics for a toothache—my first antibiotic treatment in a decade. Driscoll describes this as “setting fire” to my gut bacteria. Naturally, I’m intrigued and agree to test the hypothesis with another sample, which I send off two weeks after completing the antibiotics course. I await the results with keen anticipation. While I’m not personally financing this experiment, I recognize how easily such health investigations could become addictive—and for someone on a writer’s budget like mine, this fascination might not be the most practical pursuit.
