Study level

  • PhD
  • Master of Philosophy


Topic status

We're looking for students to study this topic.


Associate Professor Yi-Chin Toh
Associate Professor
Division / Faculty
Faculty of Engineering
Professor Gene Tyson
Professor of Microbial Genomics
Division / Faculty
Faculty of Health


The human microbiome refers to the collection of micro-organisms that are living symbiotically in the human body (defined as the “microbiota”), their genetic material as well as the surrounding environmental habitat.

It is now appreciated that the microbiome plays an important role in human health and diseases. Various disease states have been linked to dysregulation of the gut microbiota, including neurodegenerative, cardiovascular and metabolic diseases. The composition of the gut microbiome can also affect responses to therapies, most notably in cancer treatment.

With the advent of -omics technologies such as Next-Generation Sequencing (NGS), researchers have successfully identified changes in the gut microbiome that are associated with disease states as well as various host (e.g., age, ethnicity, diet) and environmental factors.

However, associations identified through metagenome wide association studies (MWAs) are correlative, and do not shed insights into causal links and the involvement of any indirect confounding factors. Therefore, there is a need for experimental systems that emulate the gut microenvironment to functionally screen microbial metabolic capabilities, interactions, and environmental factors that shape the gut microbiome.

A key engineering challenge is to create gut bioreactor system that can generate the aerobic (oxygen-requiring) intestinal epithelium and anaerobic microbiota interface since most gut microbes are obligate anaerobes and cannot tolerate oxygen.

Research activities

  1. Design and fabrication of the gut micro-reactor, which comprises of multi-well Transwell array which is coupled to a series of modular, perfusable chambers via reversible interconnections.
  2. Establishment and functional characterisation of a gut epithelium in the micro-reactor.
  3. Perform and functionally validate whether the gut micro-reactor can successful support the coculture of selected anaerobic microbes isolated from human gut microbiome with intestinal epithelium.


The proposed gut micro-bioreactor is specifically designed to operate in an anaerobic chamber while ensuring the viability of the intestinal epithelium. Individual donor microbiome samples can be dispensed into the apical compartments of the Transwell array and be maintained under anaerobic conditions, while controlled-oxygenated culture media will be perfused through the micro-reactors connected to the basal compartments of the Transwell array to sustain the intestinal epithelium without poisoning the anaerobic microbes.

Skills and experience

Candidates are expected to have obtained a first-class honours (or equivalent) undergraduate degree in:

  • chemical engineering
  • biomedical engineering
  • mechanical engineering, or,
  • a related discipline.

Preference will be given to candidates with prior experience in:

  • computer-aided drawing (CAD)
  • 3D-printing, or,
  • related prototyping tools e.g. CNC machining, cell culture, microscopy and biochemical assays.


You may be eligible to apply for a research scholarship.

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Contact the supervisors for more information:

Associate Professor Yi-Chin Toh

Professor Gene Tyson