Academia Sinica

Lab of Polymicrobial Interaction and Evolution

Yu-Ying Phoebe Hsieh
www.labofpie.org

Research Field

Biology

Introduction

Phoebe grew up in Hsinchu, Taiwan, a city where tradition meets technology, sparking her curiosity early on to carve out her own path. She first discovered her passion for biology during her undergraduate thesis with Gwo-Jen Liaw at National Yang-Ming University. After graduation, she joined Jun-Yi Leu’s lab at Academia Sinica as a master’s student and then a technician. There, her work on genetic buffering ignited her long-term interest in evolution.

She pursued her Ph.D. with Andrew Murray at Harvard University, where she combined genetics, cell biology, and experimental evolution to explore how a single protein evolves to perform distinct roles in mitosis and meiosis—two fundamental but divergent cellular processes.

“Nothing in biology makes sense except in the light of evolution.” For Phoebe, that statement extends further: nothing in evolution makes sense without considering interspecies interactions. During her postdoctoral training with Harmit Malik at the Fred Hutch Cancer Center and Ajai Dandekar at the University of Washington, she investigated how fungi and bacteria compete—and how such microbial battles shape evolutionary outcomes. She discovered that competition for a vital cation, Mg2+, is a novel axis of competition between fungi and Gram-negative bacteria. Such competition profoundly alters antibiotic resistance evolution in bacteria, providing an evolution-guided approach to treat drug resistance more effectively.

Phoebe returns to Academia Sinica in 2025 to launch her independent research group. She’s excited to uncover the hidden rules of microbial "frienemies" and how these microscopic relationships ripple into the larger biological world.

Phoebe is committed to mentoring scientists from all backgrounds and to fostering a collaborative, inclusive research environment. Her lab is a supportive space where junior scientists are encouraged to grow, take intellectual challenges, and drive their own futures.

Outside of the lab, Phoebe is drawn to traditional markets in Taiwan and enjoys making decent meals.  She finds her happiness when exploring nature and traveling with her family.

Microbes—fungi, bacteria, and phages—rarely live in isolation. They constantly interact, cooperating or competing in diverse niches, like soil or within plant and animal hosts. Microbial competition is especially intense in polymicrobial infections, where multiple microbes co-colonize the same host and must contend with nutrient limitation and host immune responses.

How these microbial battles unfold and how they drive microbial evolution remain poorly understood. At the lab of PIE, we study polymicrobial interactions using fungi and bacteria that cause infectious diseases in plants or humans. We are interested in understanding the mechanisms and consequences of polymicrobial competition and how these interactions shape host-microbe dynamics.

Using bottom-up approaches — including functional genomics and experimental evolution —  we study how bacterial pathogens, like Pseudomonas aeruginosa (in humans) and Pseudomonas syringae (in plants), engage with fungal and phage rivals, in both in vitro and in vivo models. Through these models, we aim to uncover fundamental principles of microbial competition and adaptation to complex biotic pressures. Our long-term goal is to harness this knowledge to engineer microbial communities or develop effective antimicrobial strategies for medical and agricultural purposes.


Research Topics

Genetic conflicts in fungal-bacterial competition

Competition is inevitable in polymicrobial communities, where microbes share similar niches and must evolve strategies to secure resources or space. While interbacterial competition is well studied—often involving toxins or nutrient sequestration—less is known about how bacteria compete with fungi. Do bacteria use different molecular arsenals against fungal competitors? And how can we identify these mechanisms systematically?

We view microbial competition as a genetic conflict, where one species expresses an "offense" gene to antagonize another, which must protect itself either by evasion or by expressing a "defense" gene. Using this framework and a genome-wide bacterial fitness screen, we previously discovered that the human fungal pathogen Candida albicans sequesters Mg2+ to suppress the growth of the human bacterial pathogen Pseudomonas aeruginosa. This nutritional competition for Mg2+ is a widespread mode of competition between multiple fungi and gram-negative bacteria.

Building on this foundation, we are interested in understanding the mechanisms through which other Pseudomonas species engage in fungal competition, how diverse fungal species mount defense, and how bacteria and fungi adapt in this arms race.

Genetic conflicts in fungal-bacterial-phage interactions

In polymicrobial communities, bacteria must compete not only with neighboring fungi but also defend themselves against viral predators—bacteriophages. Phages hijack bacterial cellular machinery to replicate; in response, bacteria evolve defenses that block phage entry or replication. At the same time, bacteria are likely to engage in resource competition and antagonism with fungi.

This raises key questions: How do bacteria manage simultaneous selective pressures from both fungi and phages? Does competition with fungi alter bacterial susceptibility to phages, or vice versa? We are interested in understanding the genes bacteria use to defend against fungi, phages, or both, and how these cross-kingdom conflicts jointly drive bacterial evolution.

Polymicrobial interactions at the host-microbe interface

Our previous work revealed that fungal-bacterial competition for Mg2+ alters bacterial adaptation to antibiotics. This indicates that competition may broadly impact how microbes respond or adapt to other stressors, such as host immune defense during infection.

To explore this further, we use plant and animal infection models combined with microbial genetics and genomics, and cell biology experiments. We aim to identify fungal and bacterial genes critical for polymicrobial infections and to understand how cross-kingdom microbial interactions drive the progression of infectious diseases and host response. Ultimately, our goal is to understand how these interactions shape microbial virulence and adaptation in complex, host-associated ecosystems.


 


Honor

2024-2029 Cystic Fibrosis Foundation, Postdoc-to-Faculty Transition Award

2021-2024 Cystic Fibrosis Foundation, Postdoctoral Research Fellowship Award
2021 The Hutch SPAC Course Scholarship Award
2018 Conference Grant, Graduate Student Council, Harvard University
2018 EMBL Advanced Training Centre Corporate Partnership Programme Fellowship
2018 Bernad Davis Endowed Scholarship, Marine Biological Laboratory
2015 Travel Award, KITP Quantitative Biology Summer Research Course
2015 Travel Award, MCO Graduate Program, Harvard University
2010 Traveling Fellowship, EMBO Conference Series: From Functional Genomics to Systems
Biology
2008 Traveling Fellowship, The 2nd Taiwan-Japan Young Researchers Conference on
Computational and Systems Biology
2007 The Research Creative Award, National Science Council, Taiwan
2007 Dean’s Award of Academic Excellence, College of Life Sciences,
National Yang-Ming University


Educational Background

2020–2025 Postdoctoral Fellow, Basic Science Division, Fred Hutchinson Cancer Center
 

2012-2019 Doctor of Philosophy, Molecular, Cellular, and Organism Program, Harvard University


2009-2012 Research Assistant, Institute of Molecular Biology, Academia Sinica

 

2007-2009 Master of Science, Genome Sciences, National Yang-Ming University

 

2004-2007 Bachelor of Science, Life Sciences, National Yang-Ming University

 


Job Description

The intern will work closely with researchers to:

  1. Participate in basic sequence analysis and evolutionary characterization of genes-of-interest
  2. Assay growth phenotype of bacterial mutants
  3. Assist in media preparation and daily passage of microbial cultures for experimental evolution
  4. Analyze experimental data and contribute to data interpretation
  5. Participate in regular research discussions and lab meetings

Preferred Intern Educational Level

  1. Undergraduate (senior year) or Master's level students
  2. A major in microbiology, molecular biology, cell biology, or plant pathology is preferred. A major in biology is required.
  3. Students with a strong interest in evolution, microbial genetics and ecology are especially encouraged to apply.

Skill sets or Qualities

  1. Lab experience in molecular biology, microbiology, or tissue culture.
  2. Sterile techniques are required
  3. Strong motivation to learn, curiosity, and persistence in problem-solving
  4. Good communication skills and willingness to incorporate people's feedback
  5. Ability to work independently and as a team member