Following World War I, Avery devoted most of his research to biochemical studies of the pneumococcus, collaborating most often with Glenn E. Cullen, Hugh J. Morgan, James M. Neill, and Theodor Thjotta. Most of their work on bacterial nutrition and metabolism focused on some of the more practical problems directly relating to their laboratory experiments. For example, one experiment attempted to improve the culture media used for producing large quantities of bacteria and for diagnostic purposes. Later work developed ways to assure the genetic stability of bacteria strains. Underlying much of Avery's research was the hope that through the study of bacterial metabolism they would eventually reach a better understanding of the resistance, recovery, pathogenesis, and epidemiology of pneumonia. Some of their findings had enormous medical significance. By 1921, Avery's laboratory reported that they had fully developed the serum treatment for the most prevalent strain of pneumococcus, type I. Afterwards, his team turned its efforts to developing sera for the other pneumococcal types and also researched pneumococcal enzymes and bacterial nutrition. Although they were never able to develop a successful serum for the remaining types, they did eventually recognize two accessory growth factors in bacterial culture media (later known as heme and cozymase), an important development in the science of bacterial nutrition.
Perhaps the most significant research conducted by Avery in the immediate post-war years, however, was the continuation of work he initiated with Dochez in 1916. Earlier, the two had prepared substances from pneumococcal broth cultures that were specific to the bacteria types. In two papers that were published in 1917, they called these substances "specific soluble substances," or SSS. Avery also found the SSS in the urine of pneumonia patients and developed a diagnostic test that permitted the rapid identification of the pneumococcal type without having to take a culture from the patient, a development that had the potential to dramatically speed the process of diagnosis and treatment of lobar pneumonia.
Avery believed it important to establish the chemical nature of the SSS. As he always did when confronted by a problem whose solution lay outside his field of expertise, Avery reacted in two ways: First, he dedicated himself to acquiring as much knowledge and practical experience as possible on the new topic, in this case, organic chemistry. Second, he recruited talented and knowledgeable researchers to assist him. In order to further his research on the SSS, Avery labored to convince the noted organic chemist, Michael Heidelberger, to take up the issue. When he encountered Heidelberger in the halls of the Hospital, Avery would remove a vial of the SSS from the pocket of his lab coat and agitate it in front of Heidelberger and say, "Michael, the whole secret of bacterial specificity is in this little tube. When can you work on it?" After several such solicitations by Avery, Heidelberger capitulated in 1922 and agreed to work on the SSS problem. Their work led to the conclusion that the SSS was derived from the external bacterial capsule and was responsible for the specific immunological reaction produced in the patient. This capsular substance was eventually identified as a complex polysaccharide, hence Avery's nickname for pneumococcus, "the sugar-coated microbe." After announcing their findings in 1923, Avery and Heidelberger were initially met with skepticism, as most immunologists thought that only proteins could stimulate antibody production.
To convince others of their findings, Avery and Heidelberger pressed on in their research and published several additional papers between 1923 and 1929, when Heidelberger left for Mount Sinai Hospital. Acutely aware of the possibility that the immunological specificity of the soluble substance could be due to a contaminating protein, in 1924, the two brought in an organic chemist, Walther Goebel, who was able to determine with greater precision the molecular structure of the pneumococcal capsular polysaccharides. With Goebel, Avery also initiated a line of research in which they synthesized artificial antigens made from proteins combined with simple sugars, sugar derivatives, and the capsular polysaccharide of pneumococci. Later experiments with synthetic antigens resulted in the production of a serum that appeared to offer some protection against specific types of pneumococci in mice, which one popular news magazine inaccurately claimed as having achieved "Immunity from Saw Dust and Egg White."
While working with Heidelberger and Goebel, Avery determined that encapsulated pneumococci are virulent while non-encapsulated ones are not. He believed that the discovery of an agent that could remove the capsule might also render the bacteria non-pathogenic. In 1927, Avery found himself in the Hospital dining room sitting next to René Dubos, a young graduate student studying soil microbiology and chemistry at the New Jersey Agricultural Experiment Station. Avery struck up a conversation and inquired about his research interests. He became excited by Dubos's dissertation topic: microbial decomposition of cellulose in soil and his isolation of several species of bacteria and fungi that could destroy it. Avery immediately recognized its implications for his own work on the polysaccharide capsule and arranged a fellowship at the Hospital for Dubos. In 1929, Dubos isolated a bacterial enzyme capable of decomposing the capsule of type III pneumococcus. He and Avery went on to isolate and purify the enzyme that they called SIII, which became a significant factor in the purification of the substance that was at the center of Avery's later work on the transforming principle.
Avery and his assistants opened new lines of research within bacteriology, immunology, and chemistry. Although based in sometimes complex theoretical abstracts, the work of the team was driven by the clinical realities of treating pneumonia patients. Avery continued to be frustrated by their inability to develop an effective serum for Types II and III. By increasingly narrowing their focus on the bacterial capsule, he hoped that the development of a means of artificially imitating natural immune processes would lead to effective treatments. Despite the continuous challenges and aggravation, Avery's laboratory was able to clarify many previously puzzling observations in bacteriology and immunology on a systematic chemical basis.