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Join the Knight Lab

The Knight lab is a fast-paced, extremely collaborative research environment that requires highly talented people who can work both independently and as part of multidisciplinary teams. Typically, successful members of the lab work on multiple projects, where each project requires collaboration among people with different skills within and outside the lab. We are primarily focused on developing the next generation of large scale microbiome technologies (laboratory and computational), with applications in systems ranging from the environment to industrial applications to human disease. We recommend applying for positions early: this allows for improved planning for projects to help you get started quickly, and to explore funding opportunities if necessary. The following guidelines are based on our observations over a decade of individuals who have been highly successful in our environment.

Please send requests to Antonio Gonzalez ( and cc Yna Villanueva (





In general, successful students started relatively early, allowing sufficient time to build up the interdisciplinary skills required to make large impacts in their respective fields. Within the lab, there are lots of opportunities for different kinds of programs and experiences. In general, at least 10 hours/week commitment over a quarter, or full-time work over the summer, provide optimal experiences. Options include (1) academic credit for independent study, (2) paid student work in the wet lab, (3) software development (see a list of our projects here) or data analysis, and (4) senior thesis, and (5) capstone project options. Note that each program has its own set of rules for a senior thesis or capstone project but, in general, you will need to write a final document based on some intellectual contribution to a project. If you want to do a project that centers around a specific system, e.g. looking at the microbiome effects of a specific gene knockout in a mouse, you are much more likely to be successful doing your project in a lab that works on that specific system and collaborating with us, which is also possible. Projects which an undergraduate makes a substantial intellectual contribution too are an opportunity for authorship, which forms a valuable component to graduate school applications; we’ve had many undergraduates successfully transition to graduate programs and include both programs the lab is affiliated with and other academic institutions.

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Prospective Graduate Students

For most programs at UCSD, you do NOT directly apply to a laboratory, but rather must first be accepted into a specific program.  We welcome rotation students from many programs in our lab. You can apply to any program/department in UCSD. Some of the programs we work with frequently are:

Once you’ve been accepted: A successful rotation experience involves identifying one specific person in the lab who you’ll work closely with, typically on an existing project (because most microbiome projects take more than a quarter to plan, execute, and analyze the data from, and we want you to have a successful experience to get a flavor of what research is like). The key to a successful rotation is building up connections to many different people in the lab and getting a sense of what’s available. We typically use an apprenticeship system, where you initially contribute to several ongoing projects/analyses, then develop an interest area (e.g. obesity, coevolution, energy) or a technology (e.g. correlation networks, 3D visualization, tree topology display) and then integrate or contribute to many projects around that interest area. Notably, we typically do not do projects in-house that focus on a specific system (e.g. recruiting a patient cohort to examine the effects of the microbiome on metformin treatment in type II diabetes). If you want do that type of project with a microbiome component, you should choose a lab that does that type of research and collaborate with us; however, if you want to integrate a dozen such datasets and draw general conclusions, our lab could be a great fit.

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Post-doctoral Positions

We welcome applications from all skills and expertise; however, our general wet lab infrastructure is set up for next generation sequencing. We have observed success with the following general tracks:

  1. Develop technology in the wet or dry lab and apply it broadly to many systems with various collaborators. We have lots of funding to support this model
  2. Come in with your own funding and/or via a funded collaborator on campus (we will help you write collaborative grants and/or write letters of support) to pursue a specific interest area using technologies developed in the lab. Note that we cannot fund you to come here and analyze samples from your previous specific project. We are interested only in supporting people who can develop new tools (laboratory or computational) rather than applying existing ones.

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Visiting Scholars

Visitors who are supporting their own costs, including any associated laboratory costs for reagents and sequencing, are always welcome, pending a screening interview to assess fit with the lab and plausibility of the suggested project in the time allotted. Ensuring your project lies within the research scope of the lab will increase the chances of a successful collaboration. In general, we can not fund your trip or housing costs, although if you are writing a grant we are happy to write you a letter of support or other documentation indicating approval of your visit.

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Visiting Industry Fellow

If you are an industry scientist, we have a program available to accept Industry Fellow through the UC San Diego Center for Microbiome Innovation. Please contact Sandrine Miller, Executive Director of CMI ( for more information on how your company can support your career growth by letting you join this program. Note that your project needs to remain within the scope of the lab. If outside, other labs under the CMI umbrella, may be proposed to you as an alternative lab.

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We can always use motivated unpaid volunteers on American Gut and other citizen-science or otherwise unfunded projects. If you don’t fit into one of the categories above, consider this approach. In general, because of the amount of paperwork required to make a new hire, we can not offer paid short-term positions, internships for people who are not already at UCSD in a formal capacity, etc.

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