[3] Fraser has authored more than 300 publications with more than 50,000 citations, edited four books, and served on the editorial boards of nine scientific journals.

[5][6][7][8] In 1995, Fraser was part of the team to first sequence the complete genome of a free-living organism—Haemophilus influenzae—the bacterium that causes lower respiratory tract infections and meningitis in infants and young children.

[10] Fraser's work on the 2001 Amerithrax investigation led to the identification of four genetic mutations in the anthrax spores that enabled the FBI to trace the material back to its original source.

She is an expert in microbial forensics and the growing concern about dual uses – research that can provide knowledge and technologies that could be misapplied.

[12] Past and current studies funded through these initiatives aim to explore the dynamic interactions between high-priority pathogens, hosts, their microbiota, the immune system, and the environment, with the goal to provide a comprehensive understanding of the determinants of infectious disease with hypothesis-driven research using high-throughput "-omics" technologies.

[18][19][20] Fraser's current research is part of the Human Microbiome Project and is focused on how the structure and function of microbial communities in the human gastrointestinal tract change in association with diseases such as obesity and inflammatory bowel disease, and how these communities respond to interventions including oral vaccination and probiotics administration.