The New York City public school system has quietly replaced breakfast cereals made by the Kellogg Company, the titan whose name is virtually synonymous with cereal, with those from a small California upstart called Back to the Roots.

The switch, which follows a student taste test that began last spring, adds menu options that are lower in sugar and sodium and higher in whole grains. Coming in the nation’s largest school system, and potentially spreading to other large districts that collaborate with New York in bulk purchases, it is one of the biggest signs to date of the inroads that small food companies are making into the mainstream.

But the change also highlights the many hurdles facing small food companies and advocates of better nutrition, years after the federal government started pressing school districts to improve their menus.

Last summer, Kellogg discontinued two Kashi cereals, Berry Blossoms and Honey Sunshine, that were on the schools’ breakfast menu. But instead of replacing them with other Kellogg cereals, the schools opted to buy Back to the Roots cereals because of their better nutritional profile and organic ingredients, said Eric Goldstein, the chief executive of the Office of School Support Services, which oversees food operations of the city’s Department of Education.