Biotech startup leverages Japan’s research strengths to lead in the gut microbiome field

Gut bacteria donors in Yamagata Prefecture

An estimated 40 trillion bacteria inhabit the human gut, and imbalances in this complex ecosystem have been linked to various diseases. Metagen Therapeutics in Tsuruoka City, Yamagata Prefecture is a startup aiming to restore intestinal and overall health by transplanting gut bacteria extracted from the stool of healthy donors into the colon of patients. This emerging therapeutic approach is called “fecal microbiota transplantation (FMT).”

“Making sick people healthy by using the stool of people with excellent gut bacteria.”

Gut bacteria donors are certified through a rigorous process that includes an initial questionnaire screening, comprehensive laboratory testing, and suitability assessments by a physician. Approved donors then visit the Tsuruoka Stool Donation Room on a regular basis to provide samples. “Our screening criteria are far stricter than those for blood donations,” says CEO NAKAHARA Taku. “As a new endeavor, gaining broad understanding and cooperation is essential. We compensate donors up to JPY5,000 per visit and focus on building long-term relationships.”

This emphasis on public engagement distinguishes Metagen Therapeutics from many other biotech startups. In addition, Juntendo University’s clinical trials and research expertise underscore its credibility. The company is also advancing research to develop microbiome-based medicines.

Many Western microbiome companies have focused on treatments targeting Clostridioides difficile infection, a condition for which steady research progress has been made.

However, treatments for inflammatory bowel diseases such as ulcerative colitis have a much larger market. ISHIKAWA Dai, Associate Professor at Juntendo University and the company’s co-founder, has spent many years treating ulcerative colitis using gut microbiota, accumulating a substantial body of clinical data. NAKAHARA speaks highly of him: “His research is the driving force that enables us to be a leader in this field.”

Although many biotech startups struggle at the stage of demonstrating efficacy in humans, “We have already climbed over that first hurdle. The challenges we face from here on are how to prove it works and how to communicate this to society.”

Could Japanese food culture be a strength?

Japan still lacks a biotech startup success story on the scale of Genentech or Amgen, which were founded in the U.S. in the 1970s and 80s. Metagen Therapeutics succeeding will not only benefit patients, but will also help spur the growth of the entire domestic industry, according to NAKAHARA. He founded the company in 2020 following a diverse career as a researcher, a failed entrepreneur in the U.S., and a venture capitalist.

“I am well aware of the difficulty of doing business overseas. That is why JBIC’s expertise in global business development and its support (equity investment in September 2025) were so encouraging. I hope this will lead to new chemistry emerging.”

Scientific studies have suggested that Japan's traditional food culture has a positive impact on gut microbiota. If its secrets can be unraveled, this could be shared with the world as a unique strength of Japan. The company says that it will begin clinical trials in both Japan and the U.S. as part of its drug discovery efforts. Armed with proprietary data and research capabilities rooted in Japan, the company is poised to make major breakthroughs in the global market.

---