Sonny T.M. Lee, Associate Professor


Contact information

136 Ackert Hall

Lab website:


Ph.D. 2016, University of Auckland, New Zealand. Environmental Science/ Microbiology.

Area(s) of Specialization

Metagenomics, Bioinformatics, Microbial ecology, microbial diversity and cultivation.

Research Focus

Our research uses a combination of genomics enabled technologies (metagenomics, metatranscriptomics, metabolomics) to inventory microbial genes, functions and expressions. Combining with chemical and processes data, we create a profile of microbial functions that contribute to critical host-microbes-environment interaction. We validate these multi-omic enabled hypotheses with both laboratory and field manipulations, as well as large-scale surveys. We work with various model systems ranging from plants and soil, to organisms in the ocean and streams, to human gut. Please get in touch if you are interested to learn more about what our lab is doing.

Selected Publications

Tom O. Delmont, Christopher Quince, Alon Shaiber, Özcan C. Esen, Lee Sonny T.M., Sebastian Lücker, A. Murat Eren. 2018. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in the surface ocean. Nature Microbiology 3: 804–813

Lee Sonny T.M., Keshavmurthy S., Fontana Silvia, Takuma Mezaki, Chou W.H., Tang S.L., Chen A. 2018. Transcriptomic response in Acropora muricata under acute temperature stress follows preconditioned seasonal temperature fluctuations. BMC Research Notes 11: 119.

Lee Sonny T.M., Stacy A. Kahn, Tom O. Delmont, Alon Shaiber, Özcan C. Esen, Nathaniel A. Hubert, Hilary G. Morrison, Dionysios A. Antonopoulos, David T. Rubin, A. Murat Eren. 2017. Tracking microbial colonization in Fecal Microbiota Transplantation experiments via genome-resolved metagenomics. Microbiome 5(1): 50.

Lee Sonny T.M., Davy S., Tang S.L. and Kench P. 2017. Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata. Sci Rep 7: 43600.

Lee Sonny T.M., Davy S., Tang S.L. and Kench P. 2016. Mucus sugar content shapes the bacterial community structure in thermally stressed Acropora muricata. Frontiers in Microbiology 7: 371.

Yang S.H., Lee Sonny T.M., Huang C.R., Tseng C.H., Chiang P.W., Chen C.P., Chen H.J., Tang S.L. 2016. Prevalence of potential nitrogen-fixing, green sulphur bacteria in the skeleton of reef-building coral Isopora palifera. Limnology and Oceanography 61: 1078-1086.

Lee Sonny T.M., Davy S., Tang S.L., Fan T.Y. and Kench P. 2015. Successive shifts in the microbial community of the surface mucus layer and tissues of the coral Acropora muricata under thermal stress. FEMS Microbiology Ecology 91(12): fiv142.

View the complete publication list in Google Scholar