Probing Life with Light

Both my current research and long-term career goal are devoted to microbiome imaging. It primarily focuses on the development and application of cutting-edge optical imaging technologies complemented with state-of-the-art multi-omics approaches to gain a comprehensive understanding of host/microbe-microbe interactions that underpin microbiome-related human diseases.

My PhD research under Dr. Ji-Xin Cheng’s mentorship focused on the development and application of label-free chemical imaging techniques to reveal hidden biomarkers in human diseases and human pathogens. Specifically, I achieved glycated hemoglobin (HbA1c) quantification in single red blood cells using transient absorption microcopy as an innovative approach to diagnose Type 2 diabetes (Dong et al. Science Advances 2019) and deciphered mechanism of action of the gold standard antifungal drug, amphotericin B, using polarization-sensitive stimulated Raman scattering microscopy (Dong et al. Science Advances 2021). More recently, driven by my ingenue curiosity on a serendipitously observed photobleaching phenomenon under transient absorption microscopy, I discovered two endogenous chromophores in human pathogens, staphyloxanthin and catalase, as the underlying molecular targets of antimicrobial photohterapy that are subject to photolysis (Dong et al. Advanced Science 2019; Hui#, Dong# et al. Advanced Science 2020; Dong et al. Advanced Science 2022; Dong et al. JCI Insight 2022). These findings have become breakthroughs for the field, and opened new translational opportunities to combat superbug infections (5 granted patents and a startup, Pulsethera, spun off for their clinical translation and commercialization).

Seeking more microbiology questions and trainings, I joined Forsyth as a postdoc and switched my gear studying host/microbe-microbe interactions under the mentorship of Drs. Gary Borisy, Wenyuan Shi, and Xuesong He. By coupling optical imaging with multi-omics, I elucidated the role of intracellular lipid droplets in episymbiotic host-microbe interactions (Dong et al. The ISME Journal 2024) and identified and then developed a Fusobacterial RNA-binding protein as a novel class of host-derived antimicrobials for targeting colorectal cancer-causing Fusobacterium nucleatum (Dong et al. International Journal of Oral Science 2025; Yang#, Dong# et al. The ISME Journal 2023). Since joining Forsyth, I have been particularly spearheading the development of next-generation multiplex fluorescence in situ hybridization (FISH) imaging for interrogating microbiome atlas and host/microbe-microbe interactions. More specifically, I developed an expansion microscopy-based multiplex FISH imaging technology (Dong et al. Proc. Natl. Acad. Sci. U.S.A. 2024) that enables the seamless integration of expansion-mediated single-cell functional imaging with biogeographic mapping. I further co-invented multiplex FISH probes and methods (Dong et al. manuscript in preparation 2025) that allow high-throughput whole-mount imaging that was previously conceived impossible. These advances are expected to profoundly open new avenues for microbiome studies.

“Seeing is believing” and “Discovery can be made by simply watching”. This was how Antonie van Leeuwenhoek trailblazed the microworld using his microscope and became the father of microbiology. This is also why modern optical imaging plays an indispensable role in understanding host/microbe-microbe interactions, particularly considering their spatial, temporal, functional, and molecular resolving power in a complex environment. I am enthusiastic to pursue a career in microbiome imaging. 

Awards/Recognitions

2024                    Rising Star in Engineering in Health, co-hosted by BU, Cornell, JHU, Columbia

2024-2029      NIH/NIDCR K99/R00 Award

2024                    Ned Lally Award, Mini-Symposium for Young Investigators, IADR

2024                    Susan Kinder Haake Travel Award, IADR Microbiology/Immunology Session

2024                    QPC Lasers Young Investigator Best Paper Award, SPIE Photonics West

2023                    Forsyth Pilot Grant, Forsyth Institute & Harvard School of Dental Medicine

2023                    Session Chair on Biophotonics, PQE2023 Conference

2022-2024      NIH/NIDCR T90 Postdoctoral Fellowship

2022                    Best Poster Award, Northeast Symposium on Biomedical Optics

2021                    Forsyth Professional Development Program Grant, Forsyth Institute

2021                    Forsyth Pilot Grant, Forsyth Institute & Harvard School of Dental Medicine

2018                    SPIE Translational Research Award (1/300+ applications), SPIE

2018-now        Committee Member, Photonics for Infections & Inflammatory Diseases, SPIE Photonics West

2017-now        >30 invited talks/seminars at national and international conferences/institutes