Born in Sendai in 1871. After graduating from the Imperial University College of Medicine (now the University of Tokyo Faculty of Medicine), he joined Kitasato Shibasaburō's Institute for Infectious Diseases. In 1897, as a dysentery epidemic swept Japan with over 90,000 cases and many deaths, Shiga undertook to identify the pathogen and discovered the dysentery bacterium as a gram-negative bacillus, announcing his finding in 1898. The bacterium was later named Shigella after him — the first bacterium with a genus name derived from a Japanese. He then studied in Germany under Paul Ehrlich, learning chemotherapy and immunology. On his return he served at the Institute for Infectious Diseases, as president of Keijō Imperial University (now Seoul National University), and at the Kitasato Institute, engaging in research and education. He also left achievements in the study of leprosy. He received the Order of Culture in 1944 and died in 1957 at 85.

A calm and tenacious experimenter. Amid the confusion of a major epidemic and the danger of infection, he pinned down the causative organism through painstaking bacterial culture and animal experiments. A true heir of the German-style bacteriology trained under Kitasato, he was also, no less than his master, passionate about cultivating the next generation.

Shiga's discovery is the first monument on which a Japanese name was inscribed in the global science of infectious disease. Shigella as a genus name lives on in medical literature to this day and appears in textbooks around the world. Dysentery prevention saved many lives through the twentieth century, and his contribution ranks at the top of the history of public health. In Sendai the Shiga Kiyoshi Memorial and at the Kitasato Institute commemorative facilities remember him as one of the great figures of modern Japanese medicine.