Overview

Teaching: min
Exercises: 480 min

Objectives

• Get acquainted with the state of the art of phage research

• Choose one or more papers for inspiration

• Write down 1 or 2 research questions

• Make a plan on how to tackle the questions

To close off this course, we would like to give you the opportunity to design your own research project. A research question does not have to be very profound, it can be simple. Viromics is a new field, the virosphere is huge, and there is a LOT of data, so there are more unanswered than answered questions. Looking back on the course, are there things you are wondering about or want more time to work on? You can also look in literature for inspiration.

Here are a few papers that caught our eye, maybe they inspire you (feel free to find other papers too):

• A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes, by Dutilh et al (2014)
• Bacteriophage evolution differs by host, lifestyle and genome, by Mavrich and Hatfull (2017)
• Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages, by de Jonge et al (2019)
• Virus Bioinformatics, by Pappas et al (2021)
• High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems, by Meaden et al (2022)
• Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats, by Hwang et al (2023)

Choose one type of project

Choose one type of project that better fits your interests:

1. Go into detail into analyses
2. Build a broader research proposal

Detailed Analyses

This type of project is more hands-on. You might write your own script(s), run your own analyses and produce your own plots. The idea here would be to focus on one of the methods/analyses we covered in the course and to go deeper into the analysis. In any case, the question you want to address should be clearly defined.

An example: “What are the differences between functional annotation done with Pharokka and Genomad?”.

Below are what should be included in your documentation/presentation for project type 1

• A brief background on the topic
• A workflow for the steps you plan to take
• A rationale for why you will take those steps
• What will be the inputs and outputs?
• Which programs will (do you plan to) use?

Note that hypotheses do not need be proven. We want to see from you as results:

Output (a table or a figure) Interpretation of the output: what does the data tell you? Does it answer your question? It does not have to. In a negative case, can you say what you might do differently next time

Research Proposal Style

This type of project is more in the style of a research proposal with a broader scope. You should focus on the biological questions and how to address them using viromics.

Your hypothesis and aims should be clear and backed-up by the literature.

Below are what should be included in your documentation/presentation for project type 2

• A brief background on the topic
• Formulate your research question or hypothesis to test
• What informed the question?
• How would you address this question or test the hypothesis? (make a detailed plan)
• Estimate the complexity of the problem

Presentation

• Present the project you worked on
• Limitations
• Things you found particularly interesting
• Any lessons learnt

Your project notes should still go into your lab book

Exercise

1. Once you have an idea of a research question, take some time to talk about your idea with your fellow students. Often your initial idea can be further refined based on discussions with others.
2. Make sure you check the literature: are there any papers that do something related to your question? Find the three papers that are the most closely related to your project, and use them to refine your question.
3. Make a plan for tackling your question(s). The more detail you can add, the better. Think about data sources, bioinformatic methods, possible outcomes, expectations, backup/follow-up plans, hypotheses, and interpretation.

Here, you can find ideas for projects.

Key Points