Postdoctoral Research

Gut microbes growing in water droplets suspended in an immiscible oil
A droplet culture of gut microbes. Single cells are partitioned to single droplets to produce hundred of isolated colonies for examining the function of clonal isolates.

A high throughput assay for microbial function

The diversity of human microbiome, the collection of microbes that lives on and inside us, is vast; particularly in the gut. Gut microbes help us extract energy from our diet by breaking down dietary fiber that we alone cannot. An understanding of what microbes confer the benefits of fiber breakdown would be helpful to improve human health by targeting the gut microbiome. Determining which microbes consume a given dietary fiber is difficult because of the hundred of different kinds of gut microbes in even a single person. We developed an assay to reveal the fiber degradation by hundreds of different microbes at once by combining droplet culture of gut microbes with high throughput DNA sequencing. We found dozens of fiber degrading gut microbes in healthy individuals, but the abundance of these microbes differed across people. In the future, this technique could be employed with human trials of dietary fiber consumption to examine how differences in individuals fiber-degrading microbes contribute to microbiome-mediated effects of human health such as short chain fatty acid production by gut microbes. This microbial assay is also applicable to other problems in microbiology, such as understanding which microbes degrade human-targeted drugs or are differentially affected by antibiotic treatments.

Doctoral Research


(above) Cross-sectional view of a scaffold seeded with mouse bone marrow stromal cells. Maximum intensity z-projection of a 100 micron stack acquired by 2-photon microscopy.

Bone tissue engineering

The goal of bone tissue engineering is to safely regenerate bone in response to injuries or surgical procedures where patient bone is in limited supply. The basic approach employs marrow-derived adult stem cells loaded in a delivery scaffold capable of providing the microenvironmental cues necessary for bone regeneration.  For my doctoral work I addressed the following questions:

  1. What is the detailed progression of bone repair in a scaffold based system?
  2. How do host and donor cells interact with a biomaterial to form new tissue?
  3. What is the ideal proto-tissue prior to implantation?
  4. What is the ideal scaffold design for bone tissue engineering?

In doing so,  I: (1)  designed and tested scaffolds for delivering cells to an injury site and provide a bridge between undamaged host tissue, and (2) used 2-photon live animal imaging to gain insight into the cellular dynamics of the repair.

FIG. 1| Electron micrograph of scaffolds for bone regeneration. Scaffolds are used deliver cells to a site of injury and to provide a pathway for migration of host and donor cells. This particular scaffold is primarily made of type-I collagen fibers.

FIG. 2| Visualizing cells in a live animal. 2D (left) and 3D (right) 2-photon acquired images showing osteoblast cells (bone makers, GREEN) and the surrounding collagen matrix (BLUE). This image was taken in a mouse skull. 2-photon microscopy allows our team to visualize cells in living tissue.

Master’s Thesis

Microfluidics for stem cell culture

Stem cell fate depends on physical and chemical cues in the cell microenvironment; which can be more accurately controlled within a microfluidic system. In particular, chemical gradients can be stably produced in microfluidic systems. For instance, this would be advantageous for examining how cells respond to different concentrations of a signalling molecule.  To help establish this approach, I developed a continuous-flow microculture system for mouse embryonic stem cells. I examined the flow conditions for the growth and self-renewal of primary mouse embryonic stem cells cultured in the device. The optimal culture medium flow rate through the system is key to providing correct mechanical and chemical levels for growth. This work provides a practical description of the fabrication and use of a microculture system for stem cells. In the future, the cell microenvironment may be perturbed with different chemical cues to examine cell response. Villa, M.M. et al., Biomed Microdevices 12, 253, 2010.

Top row: Primary mouse fibroblasts cultured in the system during development.
Bottom row L to R: Close up of the microsystem, 2 microsystems hooked up to a syringe pump, and syringe pump providing perfusion for microsystems within a cell culture incubator.