Skills
Transmission Dynamics of Pathogens from the Population Genetics Perspective
Strain-Level Phylogeny Reconstruction Using Metagenomic Data
Development of Genomic Databases and Supporting Algorithms for Data Mining
The Anthropocene is a term used to denote the time in which humankind has become a planetary force for change1. Although its starting point is disputed — ranging from the Neolithic Revolution (12,000–15,000 years ago)2 to as recently as the 1960s3 — it is undeniable that, as humanity keeps transforming itself and nature, the entire biosphere is experiencing unprecedented, human-associated pressures.
Many bacteria have emerged with novel adaptive strategies and, in turn, have profoundly affected us. Mycobacterium tuberculosis, for example, may have benefited from the use of fire: soot particles and fire-related lung injuries fostered its coexistence with host immune cells4. Various Salmonella lineages become more active during leaps in human productivity: some settle down in livestock breeding and strengthen their adaptations in farm animals5, others thrive in urban sewage networks and evolve into highly dangerous pathogens6.
Enhanced adaptability tends toward two extremes — either reinforcing traditional ecological routes or breaking away from them entirely — thereby reshaping microbial transmission dynamics.
To build a genomic framework for analysing the adaptive strategies and transmission pathways of microbes in the current epoch, my colleagues and I have pursued three research directions above. To me, these very skills serve as evidence that I myself am adaptively evolving to (and alongside) microbial research — a perfect illustration of co-evolution! 😆
The Anthropocene: IUGS-ICS Statement. March 20, 2024. ↩︎
Archaeological assessment reveals Earth’s early transformation through land use. Ellis, Erle; Goldewijk, Kees Klein; Gaillard, Marie-José; Kaplan, Jed O.; Thornton, Alexa; Powell, Jeremy; et al. August 10, 2019. Science. https://doi.org/10.1126%2Fscience.aax1192 ↩︎
Anthropocene now: Influential panel votes to recognize Earth’s new epoch. Subramanian, Meera. May 21, 2019. Nature. https://doi.org/10.1038/d41586-019-01641-5 ↩︎
Controlled fire use in early humans might have triggered the evolutionary emergence of tuberculosis. Rebecca H. Chisholm; James M. Trauer; Darren Curnoe; and Mark M. Tanak. July 25, 2016. PNAS. https://doi.org/10.1073/pnas.1603224113 ↩︎
Centralized industrialization of pork in Europe and America contributes to the global spread of Salmonella enterica. Heng, Li; Yilei, Wu; Dan, Feng; Quangui, Jiang; Shengkai, Li; Jie, Rong; et al. May 09, 2024. Nature Food. https://doi.org/10.1038/s43016-024-00968-1 ↩︎
Mary Mallon (1869-1938) and the history of typhoid fever. Filio, Marineli; Gregory, Tsoucalas; Marianna, Karamanou; George, Androutsos. November 19, 2012. Ann Gastroenterol. ↩︎