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## Introduction ## Introduction
Bacteria and their phages have co-existed for billions of years. The pressure of phage infection is thought to be a major driver of bacterial evolution and has led them to develop a diversity of anti-phage weapons. These weapons, namely anti-phage defense systems can be defined as defined as single genes or groups of genes that partially or fully inhibit phage infection. For reviews on anti-phage systems, see : :ref{doi=10.1038/s41586-019-1894-8}, :ref{doi=10.1146/annurev-micro-020722-013730}, :ref{doi=10.1016/j.mib.2005.06.006}, :ref{doi=10.1038/s41579-023-00934-x}. Bacteria and their phages have co-existed for billions of years. The pressure of phage infection is thought to be a major driver of bacterial evolution and has favored the development of a diversity of anti-phage weapons. These weapons, namely anti-phage defense systems can be defined as single genes or groups of genes that partially or fully inhibit phage infection. For reviews on anti-phage systems, see : :ref{doi=10.1038/s41586-019-1894-8, 10.1146/annurev-micro-020722-013730, 10.1016/j.mib.2005.06.006, 10.1038/s41579-023-00934-x}.
## A brief history of anti-phage systems ## A brief history of anti-phage systems
The first discovered anti-phage system, a Restriction-Modification (RM) system,was described in the early 1950s ref{doi=10.1128/jb.64.4.557-569.1952}, :ref{doi=10.1128/jb.65.2.113-121.1953}. In the following decades, a handful of other systems were discovered :ref{doi=10.1016/j.mib.2005.06.006}. In 2007, CRISPR-Cas systems were discovered to be anti-phage systems :ref{doi=10.1126/science.1138140}. As CRISPR-Cas systems and RM systems are extremely prevalent in bacteria, it was thought for some years that the antiviral immune system of bacteria had been mostly elucidated.
Yet, a paradigm shift occurred following the discovery that anti-phage defense systems tend to colocalize on the bacterial genome in defense-islands :ref{doi=10.1128/JB.05535-11} . In the last decade this phenomenon has been leveraged to discover over a hundred new types of defense systems. The first discovered anti-phage system, a Restriction-Modification (RM) system, was described in the early 1950s ref{doi=10.1128/jb.64.4.557-569.1952, 10.1128/jb.65.2.113-121.1953}. In the following decades, a handful of other systems were discovered :ref{doi=10.1016/j.mib.2005.06.006}. In 2007, CRISPR-Cas systems were discovered to be anti-phage systems :ref{doi=10.1126/science.1138140}. As CRISPR-Cas systems and RM systems are extremely prevalent in bacteria, it was thought for some years that the antiviral immune system of bacteria had been mostly elucidated.
Yet, a paradigm shift occurred following the discovery that anti-phage defense systems tend to colocalize on the bacterial genome in defense-islands :ref{doi=10.1128/JB.05535-11}. In the last decade this phenomenon has been leveraged to discover over a hundred new types of defense systems.
To date over 150 types of defense systems have been described, unveiling an unsuspected diversity of molecular mechanisms. The antiviral immune systems of bacteria therefore appear much more complex than previously envisioned, and new discoveries do not seem to be slowing down. To date over 150 types of defense systems have been described, unveiling an unsuspected diversity of molecular mechanisms. The antiviral immune systems of bacteria therefore appear much more complex than previously envisioned, and new discoveries do not seem to be slowing down.
## Introducing the defense finder wiki ## Introducing the defense finder wiki
The fast pace of discoveries in the field can be intimidating to newcomers and can make it difficult for all to keep track of new discoveries. For this reason, we decided to implement a collaborative knowledge base for the community. This wiki is divided in two sections: The fast pace of discoveries in the field can be intimidating to newcomers and can make it difficult for all to keep track of new discoveries. For this reason, we decided to implement a collaborative knowledge base for the community. This wiki is divided in two sections:
1. A “general concepts” section, introducing key notions and ideas to study anti-phage defense 1. A “general concepts” section, introducing key notions and ideas to understand anti-phage defense
2. A section introducing succinctly each of the defense systems currently known. 2. A section introducing succinctly each of the defense systems currently known.
This wiki is only a first version, and is intended to evolve based on the ideas and needs of the people using it. Whether it is to suggest new pages or to edit existing ones, all contributions are more than welcomed: please do not hesitate to contact us to participate! This wiki is only a first version, and is intended to evolve based on the ideas and needs of the people using it. Whether it is to suggest new pages or to edit existing ones, all contributions are more than welcomed: please do not hesitate to contact us to participate!
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