The part of us that isn't human | interview with vastbiome

Kovi Bessoff

Peter McCaffrey

Cancer is a harsh diagnosis, condemning patients to months and years of invasive tests and aggressive treatments with shockingly unpredictable response rates. On top of that, patients must endure more harsh tests to monitor the effectiveness of the treatments. Logic expects one drug to follow the same mechanism of treatment for any patient, yet many of these drugs have variable response rates. Depending on the patient, a cancer drug may save a life or it may make the patient sicker. It seems oncologists are missing a key part of human biology, the part of us that isn’t human.

Our bodies are host to as many bacterial cells as human cells, which serves as testament to the importance of bacteria in human bodily function [1]. Each individual hosts a unique collection of bacterial strains to help digest food and defend against colonization by bacteria that may cause harm. This collection of bacteria makes up our microbiome.

Many antibiotics are small modifications upon chemicals that are naturally produced by bacteria to defend themselves against competitive species. That means each individual has a constant supply of a unique set of antibiotics within their gut. Consider that each drug warns of interactive side-effects—the unexpected, and sometimes dangerous, consequences of mixing drugs. This may explain why cancer drugs don’t work on certain patients…

Last year, a team made up of 2 physicians, a data scientist, and a business expert founded VastBiome at Texas Medical Center in Houston, TX. VastBiome is a start-up that works to deconvolute the microbiome, mining our bacteria for potent intel to better understand health. I spoke with 2 of the co-founders, Kovi Bessoff and Peter McCaffrey, with backgrounds in international public health and bioinformatics respectively. Kovi and Peter work towards a vision of accessible and equitable health care that is simple and noninvasive. This is difficult to do with only 4 people; it can be done with a consortium. VastBiome has decided to team up with ARC Laboratories to take their nuanced understanding of our microbiome and make a global impact.

Medical research needs real data from real people. However, gathering this data is expensive and time-consuming—resources that are difficult to access as a start-up company. To circumnavigate this challenge, VastBiome began by mining public data from other scientific journals for clues that may guide future investigations. The team downloaded immuno-oncology data from the public domain, analyzed different samples together, and paired and parsed information based on their hypotheses of chemical data.

But the microbiome is remarkably complex. Traditionally, studies of the microbiome are confounded by the interplay of data. Many times, this complexity introduces challenges in translating discoveries into therapies, such as probiotics which are difficult to dose and quantify.

The papers often included a degree of “hand-waving” with each explanation—characteristic of many microbiome analyses. VastBiome instead identified key operons, mechanisms, and chemicals that are responsible for the results in the papers and used these discoveries to guide future work. This approach allowed VastBiome to explain response status in cancer patients in ways that other papers weren’t able to do.

By better understanding response status and its intricate tie to the microbiome, VastBiome realized that not only can they predict how patients will respond to certain treatments, but—through careful adjustment of the patient’s diet and, therefore, microbiome—could also modify patient response and increase favorable outcomes. Furthermore, VastBiome tested this algorithm with real patients, and predicted response to chemotherapy drugs with remarkable accuracy. The traditional mindset suggests that bacteria are present because they cause infection, it seems now that bacteria may cause response. 

VastBiome’s goal is to map the microbiome, understand the chemical actors and their roles, then use this information to cure patients of anything from cancer, auto-immune diseases, and bacterial infections.

Within the scope of immuno-oncology, VastBiome envisions a future in which analysis of a patient’s microbiome becomes part of the selection and consultation process when considering chemotherapy. Cancer is dire diagnosis and the procedure proposed by VastBiome is noninvasive—especially compared to existing cancer screenings and tests—so patients are expected to be enthusiastic in trying this type of screening. The microbiome is a modifiable factor that explains variation in chemotherapy treatments because it can either recapitulate or destroy the immune system. Treating cancer is about more than chemo.

At the end of the day, VastBiome is working towards realizing more responsible use of antimicrobials. Through a deeper understanding of how the “drugs” produced by our microbiome interact with our therapies, we can make better decisions about how to use our own drugs.

Antibiotics are a shared resource. Like fish in a lake, the more others use a shared resource (in this case, catch fish), the less there is for everyone else. Similarly, the more one person uses antibiotics, the more likely it is that strains will develop that will no longer respond to those drugs. The decisions of individuals impact the greater global community. So we all have a responsibility to use antibiotics sustainably.

According to Kovi and Peter with their experiences as physicians, the responsibility of sustainable antibiotic use falls equally upon doctors and patients. Doctors should not cut corners or prescribe by memory, but rather reference frequently-updated protocol. Additionally, patients should look into antibiotic stewardship at their local hospital or physician’s office. By sharing this responsibility to be informed, we can buy ourselves some time before antibiotic resistant infections render current antibiotics ineffective.

[1] https://www.nature.com/news/scientists-bust-myth-that-our-bodies-have-more-bacteria-than-human-cells-1.19136