When we joined microbiome scientist Jeffrey Gordon's lab at Washington University in 2003 we had no idea how profoundly it would shape our careers and our lives. Coming from different scientific disciplines structural and molecular biology and glycobiology we were united by a shared curiosity about gut microbes and their impact on human health.

Advanced sequencing technologies born from landmark NIH-funded efforts like the Human Genome Project equipped us with the tools to truly decipher the genetic landscape of the gut microbiome and explore entirely new lines of inquiry. It felt like spending your whole life staring at the ocean from the shore and then someone invents a boat suddenly you can venture into the unknown.

A major focus of our research is understanding how diet influences the microbiome to support overall health. One of our most striking discoveries revealed that dietary effects on the microbiome can have consequences across generations. In a study with mice fed a Western-style diet we observed that after just four generations only a fraction of the original microbial diversity remained. It was a powerful realization: not only can poor diet lead to microbial extinctions but those losses can accumulate over generations. Parents with compromised microbiomes may be unable to pass on key microbes to their offspring. Alarmingly, this mirrors what’s happening in human populations today.

These insights didn’t just shape our scientific trajectory they deeply impacted our personal lives. Like many of our colleagues we began adopting diets rich in fiber and fermented foods with the goal of supporting a more resilient microbiome and reducing inflammation.

Two core ideas drive everything we do in our lab. First the gut microbiome is incredibly malleable. Unlike most parts of the body it can be changed often dramatically through something as simple as diet. You can’t alter the cells in your heart by changing what you eat but you can reshape the microbial community in your gut which in turn reshapes your biology. Second the gut microbiome is deeply integrated into every aspect of our physiology. There’s virtually no part of our biology that isn’t influenced either directly or indirectly by it. Everything is connected.

What keeps us rooted in academia rather than moving to industry is the difference in time horizons. Industry focuses on short-term outcomes developing profitable therapies that often serve as temporary fixes rather than addressing the deeper causes of disease. These treatments are important and do help people but they often patch the cracks in a system with underlying structural flaws. In contrast academic research allows us the freedom to explore long-term solutions and get to the root causes like chronic inflammation that underlie many modern diseases. That kind of foundational work simply isn’t feasible under industry’s financial models.

Source: https://news.stanford.edu/stories/2025/05/research-matters-justin-and-erica-sonnenberg