Research Projects
Leveraging multi-omics and machine learning to identify key roles of gut archaea and fungi for metabolic dysfunction-associated steatotic liver disease (MASLD)

Metabolic dysfunction–associated steatotic liver disease (MASLD) is a growing global health burden. Its development is shaped by a complex interplay between host metabolism, lifestyle factors such as diet, and the gut microbiome. While previous studies have largely focused on the role of bacteria, recent evidence points to significant contributions from gut archaea and fungi, which can produce bioactive metabolites such as endogenous ethanol and aromatic compounds that may influence liver fat accumulation and inflammation. Yet their mechanisms remain poorly understood due to limitations in taxonomic and metabolic profiling and the difficulty of cultivating these organisms.

This project aims to systematically investigate cross‑kingdom microbial metabolism in MASLD by integrating human cohort data, mouse models, meta‑omics analysis and community metabolic modelling. It aims to characterize archaeal and fungal metabolic pathways, explore cross-feeding within the microbiome, and experimentally validate key microbial roles through enzyme kinetics, engineered strains, in vitro co-culture systems, and in vivo perturbation models. The ultimate goal is to identify previously overlooked microbial players and pathways driving MASLD progression, paving the way for microbiome‑based diagnostics and therapies.

We are looking for motivated PhD and MPhil students with a solid background in pharmacology, pharmacy, microbiology, molecular biology, immunology, bioinformatics, or related fields. Experience in wet lab techniques such as microbial culture, DNA/RNA extraction, PCR, metabolomics workflows (LC–MS/MS, GC–MS), cell culture, and animal experiments is highly valued. Skills in bioinformatics, multi‑omics data analysis, and programming (Python and R) are a strong advantage. Applicants should meet standard English language requirements (e.g., IELTS ≥6.0 overall, no sub-score <5.5, or TOEFL iBT ≥80).

Students will gain hands-on experience in cutting-edge microbiome and MASLD research, multi‑omics technologies, community metabolic modelling, and host–microbe interaction studies, while receiving training in scientific writing and presentation. Candidates should send a CV and cover letter outlining their qualifications and motivation to Dr. Shan Zhang (shanbio@hku.hk).

Dr S Zhang, Department of Pharmacology and Pharmacy

Dr. Shan Zhang is a microbiologist and bioinformatician. She obtained her Ph.D. in Microbiology and Immunology from the School of Biotechnology and Biomolecular Sciences at the University of New South Wales (UNSW), Sydney, Australia, in 2022. During her Ph.D. program, she visited the Medical Systems Biology Lab at Christian-Albrechts-University in Kiel, Germany, in 2019 as a visiting scholar. After completing her Ph.D. degree, she pursued postdoctoral fellowships at UNSW (from March 2022 to July 2023) and at HKUST (from August 2024 to March 2025). In March 2025, she joined the Department of Pharmacology and Pharmacy, LKS Faculty of Medicine at the University of Hong Kong (HKU), as a Research Assistant Professor.

During her Ph.D. program and postdoctoral research, her projects focused on the evolutionary adaptation of microbial symbionts to a symbiotic lifestyle, particularly through the integration of multi-omics approaches (e.g., metagenomics and metabolomics) to study sponges, the common ancestor of all animals, which allows to identify ancestral and conserved features in animal host-microbiome symbioses. Her expertise in cutting-edge bioinformatics techniques, such as genome-scale metabolic modeling, facilitates the exploration of metabolic interactions within host-microbiome symbioses. Additionally, she excels in integrating both culture-independent and culture-dependent approaches to investigate these topics and applies them to various host systems, ranging from animals (e.g., human, sponges and corals) to plants (e.g., seaweeds, wheat and tea).

After joining the Department of Pharmacology and Pharmacy, Dr. Zhang’s research has focused on the symbiotic relationships between the host gut and its associated eukaryotic (fungi) and prokaryotic microorganisms (bacteria and archaea), aiming to better understand host health and microbial physiology. 

Biography
ORCID
shanbio@hku.hk

For more information or to express interest for this project, please email the supervisor or the specified contact point in the project description.  Interested candidates are advised to enclose with your email:

1. your CV,
2. a brief description of your research interest and experience, and
3. two reference letters (not required for HKUMed UG students seeking MRes[Med]/URIS projects).

Information on the research programme, funding support and admission documentations could be referenced online at the Research Postgraduate Admissions website. General admission enquiries should be directed to rpgmed@hku.hk.

HKUMed MBBS students interested in the Master of Research in Medicine (MRes[Med]) programme may visit the programme website for more information.  

HKUMed UG students interested in the Undergraduate Research Internship Scheme (URIS) may visit the scheme’s website for more information.