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Outside the Lab Microbiology and immunology, Training and education

Classifying the Unclassifiable

About 20 years ago, I was investigating amoeba and the Legionella bacteria living within them, in a collection from Timothy Rowbotham. We identified five new species of Legionella and also made a surprising discovery – Gram-positive chlamydia-like bacteria living in amoeba. We tried and tried to amplify the newly discovered microbe, but all our attempts came to nothing, until eventually we started to question if it was a bacterium at all. We inspected the amoeba under an electronic microscope before and after extraction, and saw something that wasn’t bacteria-like at all, but instead looked very much like a virus. What we originally thought was a Legionella-like bacteria turned out to be mimivirus, a giant 0.4–0.8 µm virus with a 1.2 megabase genome.

Mimivirus is a very unusual virus. In fact, it’s debatable whether it is a virus at all.  It bears more resemblance to bacteria, archaea, and eukarya. When we investigated mimivirus further, we found that the structural motif of its DNA and RNA polymerases are very old – we suspect that their origins may date back to before the operation of ribosomes. Mimiviruses can also be infected by viruses (virophages) themselves.

A recently published study from my lab showed once more that mimiviruses don’t adhere to the typical properties of a virus (1). In this study, we discovered that mimiviruses have a defense mechanism against virophages, which we called MIMIVIRE, and it operates similarly to the CRISPR–Cas system in bacteria, representing a nucleic-acid-based immunity.

The classification system needs to shift and adapt to new discoveries.

I believe that there should be a fourth branch to accommodate microbes such as mimivirus. The classification system needs to shift and adapt to new discoveries just as the rest of the scientific field does. Right now, I’m arbitrarily referring to this fourth branch as “truc” which means “thing” in French. I’m not the only one with this belief about classification – there are other scientists who agree that it’s time to update our system (2), and I think if we keep relying on this outdated classification standard then we’ll miss out on so many discoveries, just like my collaborators and I almost missed out on discovering mimivirus.

Going forward, whether the classification system changes or not, we need to encourage young, upcoming researchers to think outside the box and to treat theories as theories, not the ultimate truth. They have to be prepared to break theories apart and find out the truth for themselves. If we want future scientists to discover new things, we need to teach them how to fish. I often tell young scientists that they need to try something new – they can either use a new type of fishing rod (new tools) or fish where nobody else is fishing (new theories).

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  1. A Levasseur et al., “MIMIVIRE is a defence system in mimivirus that confers resistance to virophage”, Nature, 531, 249-252 (2016).
  2. A Nasir et al., “Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya”, BMC Evolutionary Biology, 12 (2012). PMID: 22920653.
About the Author
Didier Raoult

Didier Raoult is the Director of Research Unit in Infectious and Tropical Emerging Diseases.

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