In addition to his role as a researcher at Kitasato Institute, Omura also did research for Kitasato University’s School of Pharmaceutical Sciences. In 1969, he acquired his doctorate degree in Pharmaceutical Sciences at University of Tokyo with a paper titled "Research on the Structure and Activity of Leukomycin".
Then in October 1969, at the age of 34, Omura was promoted to be Associate Professor of Pharmaceutical Sciences at Kitasato. After that, Omura submitted a series of papers on the synthesis of protein such as pneumococci. In 1970, he obtained his other doctorate in Chemistry from Tokyo University of Science.
When these series of theses had finally settled down, Omura felt there was nothing left for him to do when he went to the lab. His wife Fumiko had instantly noticed this change and took her husband to a specialist. The doctor said Omura was too keen on his research and that he should take up a hobby or pastime.
Besides playing golf, Omura went to the onsen（hot spring）to distract himself. However, he did not recover easily. At that time the Pharmaceutical Society of Japan had planned an overseas trip for people who wishing to attend the International Pharmaceutical Society meeting. Omura and Fumiko decided to join the tour as a couple.
In August 1969, the couple left Japan for a tour of Europe. It was their first overseas trip. This trip had greatly influenced Omura 's thoughts, actions, and outlook on the world. It also gave him a chance to see Kitasato from the outside. He was astonished to find the international prestige established by Kitasato Institute.
When Omura visited the pharmaceutical company Boehringer Mannheim (current Roche) in Germany, a bust statue of Shibasaburo Kitasato was installed in the corner of the company lab. Omura was surprised when he saw this. This company was established by Emil Adolf von Behring, a German researcher who was awarded the first Nobel Prize in Physiology and Medicine. Behring studied serum therapy in collaboration with Shibasaburo Kitasato and received the Nobel Prize for its success. However, much of the research was not possible without Shibasaburo. The statue was installed to acknowledge his contribution. Omura was impressed by his forerunner’s fame, and came to realize Kitasato Institute’s international reputation.
Before, Omura thought that there would be limits to continue his research in chemistry because Kitasato was an institute for medical doctors. However, in Europe, Omura finds out that Kitasato’s name was much widely known than he had imagined. His perception of Kitasato Institute changed completely. He decides to base his research at Kitasato and to protect and nurture Kitasato’s name as one of Japan’s top research institutes.
Next to the lab where Omura worked was a group looking for antibiotics. Researchers on the team seemed to be struggling. They would look for beneficial substances produced by microbes, but they may not find anything for a whole year. After an elated “discovery,” they would be disappointed to find that it was something already known. By observing such researchers, Omura reaches a decision:
“My work is to determine structure of substances found by others, but is this really genuine research? I am building my research on other people’s achievements. I must do my research to find new substances on my own.” After that, Omura shifts his work to discover new substances besides determining structures.
Around March 1971, Omura goes to see Yukimasa Yagisawa about his research methods. Yagisawa worked at Japan’s National Institute of Health (current National Institute of Infectious Diseases) and he was a permanent member of the Japan Antibiotics Academic Association (current Japan Antibiotic Research Association). “Why don’t you study abroad in the US? Studying in the USA will bring you a new horizon," he advised. At that moment, Omura felt his vision clear up. Yagisawa explained that the American research environment is exciting and efficient.
Consequently, Omura decides to travel to Canada and the US for a month. Because an international conference on antibiotics was going to be held near Montreal, Canada, he was going to look for an institute willing to invite him as a researcher.
After the conference, Omura visited University of Montreal, Harvard University, Massachusetts Institute of Technology, Wesleyan University and exchanged views with professors specializing in antibiotics.
After returning home, Omura acted immediately. His wife Fumiko also had a positive feeling about studying abroad in America. Omura had typed up application letters in English to appeal himself and mailed it to five universities.
As soon as he sent the letters, a reply came by telegram from Professor Max Tischler at Wesleyan University. Omura would be accepted as a visiting professor at an annual salary of 7000 US dollars.
Other universities had replied back, too. Omura was surprised at these unexpected responses. They suggested that American colleges regarded highly upon Omura's achievements.
Omura has written all of his papers in English, and the presentations he made during the visits went well, too. Moreover, he was highly evaluated for having excellent skills in determining the structure of substances.
In a memo, Omura had compiled all the employment conditions offered by each university and compared them with Fumiko. The problem was the salary. One position offered as much as 15,000 dollars while another offered 7,000 dollars. The difference was twice as much.
In Japan back then, one US dollar was equal to 360 yen. All the salary offers were much higher than any offer he could get in Japan. Fumiko was frank. "Why don’t you take the job that offers the highest salary?” But, Omura felt indebted to Wesleyan University’s Professor Tischler for his sincerity. He had immediately telegrammed
Omura. Moreover, Omura had a very good impression of Professor Tischler when they first met in the United States.
But the salary offer was the lowest of all. In the end Omura decides to study at Wesleyan, thinking that "there must be something great waiting for me to compensate for the salary." Omura was at the crossroads of his life. Omura and Fumiko unfolded the map of America and pondered about the foreign university yet to be seen. And the couple started their preparation to leave for the US.