Dr Nguyen has been involved in characterising the virulence traits of a Gram-negative bacterium Porphyromonas gingivalis and other periodontal pathogens in the pathogenesis of periodontal disease. These studies include the elucidation of the maturation pathway of a group of proteases from P. gingivalis, the identification of new proteases in other periodontal bacteria and the discovery of a novel heme-uptake system in P. gingivalis.

Currently, in between his lectureship commitment for the Faculty of Dentistry at the University of Sydney, Dr Nguyen has also been involved in the supervision of PhD and Masters students at the Institute of Dental Research, Westmead Millennium Institute. He is also actively engaging in collaborative research work with various international groups in the USA, Sweden, UK, Brazil and Poland.

Dr Nguyen's research has been published in high-impact journals, such as Molecular Microbiology and the Journal of Biological Chemistry.