Fuqua joined the IU faculty in 1999, coming from Trinity University in San Antonio, Texas, where he was an assistant professor.
Prior to that, he was a postdoctoral fellow in microbiology at Cornell University. Fuqua earned his Ph.D. in Microbiology from the University of Maryland, College Park, in 1991, and his B.S. in Biology from Old Dominion University in Norfolk, Virginia, where he graduated magna cum laude. At IU, Fuqua advanced from assistant to associate professor in 2005 and then to professor in 2008.
He has been a project leader for the Center for Genomics and Bioinformatics (2006-10)- and directed the Microbiology Program (2006-09). Fuqua led the Department of Biology National Institutes of Health Training Grant in Genetics, Cellular, and Molecular Sciences for four years and was associate chair for research and facilities from 2009−2012, followed by Department of Biology chair from 2013-2017.
Fuqua's research interests broadly focus on the mechanisms and consequences of microbial interactions, including pathogenesis and symbiosis. His seminal contributions to many fields of microbiology—including quorum sensing, plant-bacterial interactions, exopolysaccharide synthesis, biofilm formation, and microbial community structure—led to Fuqua being elected a Fellow of the American Association for the Advancement of Science in 2012, and a Fellow of the American Academy of Microbiology. Fuqua's other honors include receiving the Indiana Branch of the American Society for Microbiology's Outstanding Researcher Award, appointment as the American Society for Microbiology Waksman Foundation Lecturer from 2005−2007, receipt of IU's Trustees Teaching Award in 2005, and the Outstanding Junior Faculty Award in 2003. He also received the Department of Biology’s Senior Class Award for Teaching Excellence in Biology and Dedication to Undergraduates in 2004.