Skip to main content

What do we do? Getting started

Our works centers on the genetic basis for microbial influence of animal traits. Established students in the lab focus on one of three technical areas, below.

A few tips / thoughts for students who want to get started in research:

  • Any research will do. As a young graduate student trying to choose a research lab I was told, "A good scientist can get excited about any problem." I also believe strongly in its corollary, that you can learn how to be a great scientist by doing good work in almost any field. Frankly, the topics investigated by and methods used by most research labs on campus would be an excellent springboard for almost any field of scientific inquiry after you graduate. You're learning to identify and work through a problem cogently. This link (scroll to bottom) will help you identify anyone in the college you might want to begin with: Faculty research interests
  • Just start. There is a strong correlation between washing dishes and success in the lab. Most students who are starting off have far more time than expertise to fill it with. Wash some dishes. I personally believe that the cause here is that motivated students work hard at whatever they're given. As the Savior said: "He that is faithful in that which is least is faithful also in much. (Luke 16:10)
  • Read. I love doing experiments and analyzing data, but reading is often way more effective (some smarter person already solved your problem).
  • Reach out to me. Email me and we can discuss how you might get started. Usually, I'll encourage students to start with one of these. You can throw yourself into it and move on in a month or two; or you can move through slowly over a semester or two.
    • Wash dishes
    • Do some computer tutorials
    • Start learning to pick axenic fly eggs
    • Start learning to do DNA extractions or other basic pipet work
    • Enter and curate handwritten datasets
  • What will you produce? Your career goals will determine how much you might want to get out of a lab experience, but most students will benefit from conducting a research project - independently or while being mentored by another student - and presenting those findings at a meeting, and then writing and publishing them. Nothing will help your applications to graduate school more than publishing a paper. This can also be really important for students bound for professional school.
  • Get paid! Write and receive funding for a CURA proposal ($1500 for you, $1500 for research supplies).
  • What will I do long-term? Most students in the lab work one one of three classes of projects.
    • Animal microbiomes. Analyze the microbiome of a 16S dataset from samples we collected or got from collaborators (we've had human, deer, otter, alpaca, crayfish, and, of course, Drosophila samples, usually poop). You'll work exclusively on a computer for this, and will need R and shell coding (we can train you!).
    • Host-microbe evolution. We're really interested in how microbes affect animal evolution. We study natural fruit fly populations to do this, including evolution in the lab and outside in special enclosures at the greenhouse. We also manipulate their rearing conditions in the alb (different temps, humidities, etc), and work with genotypes adapted to different locations.
    • Design-your-own. We have a fairly formulaic approach to this.
      • Find a trait you can measure in fruit flies. There are thousands of possible traits. Do your reading and find something!
      • Develop the assay in the lab and test if the microbes impact it by comparing between bacteria-free and bacteria-colonized flies
      • If it does, screen the effects of 40-50 microbes on the trait
      • Perform MGWA to predict the bacterial genes that impact the trait
      • Use bacterial mutants from our library to confirm the predictions
  • My lab is always looking for motivated students. Please e-mail me if you want to discuss more!
  • See more details below.
  • Note that all students will need to complete safety training before they can begin working in the lab:
    • For 'Life Sciences General Lab Safety Training' you can self enroll in the training course on in the Life Science catalog and selecting the needed training courses.
Drosophila Behavior, Physiology, and Genetics.
The fruit fly Drosophila melanogaster is a superb model organism for investigating animal responses to associated microbes, including in mammals. It has a culturable, low diversity microbiota, and many of its behavioral and physiological traits are strongly influenced by microbiota. We dissect the contributions of specific microbes to these traits by first eliminating colonizing microbes from Drosophila embryos, and then inoculating embryos with target microbial species of interest. We also draw on vast community resources in the Drosophila field to understand how host genotype dictates and responds to the presence of particular microbial taxa.

Undergraduate-led project:
Microbial Genetics
We use genetic approaches to dissect the mechanistic basis for bacterial influence of animal traits. Most bacteria that associate with Drosophila are readily cultured and are amenable to genetic interrogation. These approaches are increasingly supported by genomic tools, including next-generation sequencing-based approaches. We are also interested in developing genetic approaches in bacteria that are recalcitrant to standard laboratory culture and mutagenesis techniques.

Undergraduate-led collaboration:
To support both of the research areas above we use comparative and statistical genomic approaches that require use or modification of existing bioinformatics tools, or development of new approaches. We are particularly focused on our recent development of a metagenome-wide association pipeline as a surrogate for a functional genetic screen. This approach successfully predicted bacterial genes that affect host traits from phenotypic data collected from a relatively small number (41) of mono associated hosts. We are currently developing this and other tools for public dissemination.

Undergraduate-led project: