He pioneered the use of culture media to grow microorganisms, and, with food chemist James N. Currie, developed a process to mass-produce citric acid using Aspergillus.

The next year he spent as a science teacher in a Danville high school, before returning to Lake Forest College to receive his Master's degree in 1897.

[1] In 1902, Thom went to study with George F. Atkinson at Cornell University; two colleagues included Benjamin Duggar and Herbert Hice Whetzel, who both later became noted botanists.

[1] Two years later, he accepted a position as dairy mycologist, working with Herbert William Conn, in charge of "cheese investigations" at the Storrs Agricultural Experiment Station in Connecticut.

"[1] Selman Waksman, who would later be another key contributor to antibiotic development, spent some months in 1915-1916 at the USDA in Washington, DC under Thom, studying soil fungi.

Thom's work with the food chemist James N. Currie in 1916–17 enabled them to develop a process to mass-produce citric acid using Aspergillus, and a few years later, the first large-scale mold fermentation factory had been established in Brooklyn, New York.

This early work ultimately led to the Department of Agriculture's establishing four Regional Research Laboratories in 1938 that were devoted to industrial mold fermentations.

[5] In 1929,[6] a year after discovering penicillin, Alexander Fleming published a well-known paper in which he identified the mold Penicillium rubrum as the one responsible for creating the drug.

[7] With Thom's assistance, they identified the organism as Penicillium notatum and, in 1941, developed a method to scale up production at the Department of Agriculture's Northern Regional Research Laboratory in Peoria, Illinois, which ultimately resulted in an inexpensive supply of the drug.

[9] "During his active career in the Department of Agriculture [Thom] identified thousands of cultures for other investigators all around the world, taking little cognizance of the credit that he might or might not receive.

In one of Thom's important contributions to the field, he led the research group responsible for advances that enabled the control of cotton root rot, which at the time was a major problem in the southwestern United States.