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Your Checklist to Working With an Emerging Model Organism

With the advent of the ‘omics era, it is becoming more common to explore biological phenomena in non-model organisms. Advances in technology have enabled us to quickly turn little-studied non-model and understudied model organisms into emerging models for which we have sequencing data. Before this was possible, scientists would pick the best fit for their biological question from a narrow range of classical model organisms that had been established over decades with great effort and cost. Examples of classical model organisms include Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila Melanogaster. It seems hard to believe that these were themselves non-model organisms once. Have a look at the wonderful journey of C. elegans in the words of Sydney Brenner. [1] The use of this narrow collection of models, however, limits the range of phenomena that can be feasibly investigated as well as our full understanding of biological mechanisms. Using non-model organisms gets around both problems.

Working with a non-model organism can make one feel like something of an adventurer, exploring uncharted biological territory. It can lead to incredible shifts in perspective—yours and that of the field—and be extremely satisfying. However, it can also lead to frustration and disappointment as you watch established protocols fail and realize the lack of access to sequences and stock centers.

Are you considering using a non-model organism to answer your research questions? Should you take the leap? Here is a checklist of factors to weigh carefully before you make the decision.

Reasons to Use a Non-Model Organism

  1. Non-model organisms are particularly well suited to evolutionary studies, which require sampling from a specific location within the tree of life. Non-model organisms have therefore become a very popular choice in fields such as evo-devo.
  2. Are you studying a trait that is absent in classical models? For instance, you can’t study regeneration in an organism that does not grow back its body parts.
  3. How accessible is your phenomenon of interest in classical models? You can imagine how much easier it would be to study the function of a gene family in a plant that has one or two members rather than tens of them. In cases like this, a non-model organism can save you time, money, and mental sanity.
  4. Are there advantages when it comes to commercial applications in your non-model organism? Is it particularly well suited to metabolite extraction or to being grown at scale? Maybe you’re interested in valuable metabolites that are hard to produce efficiently in model organisms? This was the case for the alga Dunaliella salina, [2] which naturally produces lots of beta-carotene.

Practical Considerations

  1. How easy is it to grow your non-model organism? If it is already in use in some labs, are there established protocols that work consistently across labs? During my PhD, I spent most of my first year working out how to convince Marchantia polymorpha, my emerging plant model, to grow, make babies, and let me extract its nucleic acids and cell wall under our lab conditions. By the end of my PhD, I still had not published my work. If your time is constrained (e.g., you cannot stick around to complete your project as a postdoc, or you have a short contract) and you are considering an academic career, you should give this point some thought.
  2. How fast is the life cycle of your non-model organism? This impacts the nature and number of the experiments you can do during your contract, potentially entailing longer timeframes for publication.
  3. How much space do you need given the size of the organism? Will you have enough space to run parallel experiments?
  4. What type of equipment will you need? Do you have to set up special growth chambers?
  5. Nowadays, many biologists can order mutants and plasmids with a few clicks from stock centers. You will not have that luxury, I’m afraid. In fact, there might not even be a published genome available for your organism, and standard commercial kits may not work.

Benefits of Using a Non-Model Organism

Collaborative Environment

Whether you join an existing community or build one from scratch, you can expect a collaborative environment when it comes to non-model organisms. After all, everyone is facing similar challenges. New protocols need to be established, existing ones need to be modified, and unforeseen technical challenges have to be overcome. All this is much easier when you can discuss setups and ideas with other labs. And because the risk of labs working on the same thing is lower in new communities, people tend to be more open to sharing resources and expertise.

Potential for Highly Cited Papers

You have the potential to establish a useful new model! The extra work you have to put in will lay the foundations for others. In addition, most of what you find will carry an intrinsic degree of novelty. Both factors are likely to result in highly cited papers. If you are lucky, you can open new research avenues or capsize entire thinking paradigms in biology.

Final Considerations

Working with a non-model organism, as with all challenges, is both rewarding and frustrating. Consider if you can tackle the same research question in a well-characterized model first. If you are sure that the best way to go is to establish a new model, be ready to reach out to others who are trying to do the same and prepare to be surprised by your findings.

Do you have experience working with non-model or emerging model organisms? Leave a comment below and share your tips!


  1. Brenner, S. In the Beginning Was the Worm… Genetics 182, 413–415 (2009). doi: 10.1534/genetics.109.104976
  2. Oren, A. A hundred years of Dunaliella research: 1905-2005. Saline Systems 1, 2 (2005). doi: 10.1186/1746-1448-1-2

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