PS Webinar Series- PhD Exit Seminar: Pathogen detection and microbial community compositions during fungal infections

Abstract - Devastating fungal diseases threaten global food security and plant and animal populations, highlighting the need for rapid and accurate identification of fungal pathogens. Disease outcomes are defined not only by causative pathogens but are influenced by diverse microbial communities known as microbiomes at sites of infection. In this seminar, I will describe two examples of metagenomics sequencing to detect fungal pathogens of wheat and humans, using a portable sequencer in a standard molecular biology laboratory. The data revealed that this method is robust and capable of diagnosing all fungal pathogens tested. I also identified the bacterial genus Pseudomonas as co-present with the fungal pathogens Puccinia and Zymoseptoria but not Pyrenophora. Next, I will present a method development project that aims to compare different sequencing and analysis strategies to improve sequence-based fungal identification. I constructed two mock fungal communities, and generated four datasets for each mock community using different sequencing strategies. I then compared different classification algorithms and databases for each dataset. I found that the most accurate classification pipeline depended on a particular alignment algorithm against a specific database. Secondly, I developed a new parameter named alignment proportion, and further improved the classification accuracy by applying more stringent cut-offs to it. Overall, my thesis work illustrates new approaches to the detection of a broad range of pathogens and associated microbes. Using mock fungal communities, I further outline a practical guide for the design of species classification strategies using sequencing data, which improves our toolkit for understanding the biology of fungi.

Biography - Looking back, I can hardly believe that I have already been in Canberra for nearly seven years. I grew up in China and did my Bachelor degree at Xiamen University, before going abroad for the first time to pursue a Master degree at RSB. I did my Masters’ research year with Prof. John Rathjen and Dr. Benjamin Schwessinger (while Dr. Schwessinger was a DECRA Fellow), and fortunately enough was able to continue to the PhD degree with the help from Prof. Eric Stone since April 2017. My major has changed several times, as my Bachelor degree was in chemical biology, followed by a Master’s project in molecular biology, and finally my PhD project was in microbiology and bioinformatics. Generally, I am most interested in fungal biology. My research is largely focused on their interactions with plant hosts (wheat for now), other fungal pathogens and the microbial communities. Other than research, my interests span from different kinds of food to many outdoor activities including hiking, fishing, skiing and mountaineering.