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New Actinobacteriophage Clusters

Dear SEA-PHAGES Faculty,

Following the expansion of our collective phage interests beyond those of Mycobacterium smegmatis mc2 155, SEA-PHAGES has collected a number of new phages on different hosts within the phylum Actinobacteria---in no small part due to your efforts! We are excited about a major push to explore this much broader landscape of microbial terrain.

There are two key aspects we wanted to bring to your attention. First, Dan has done a major redesign and restructuring of http://phagesdb.org such that it is no longer the Mycobacteriophage Database, and is now the Actinobacteriophage Database. So there are no longer separate DB’s for phages of different hosts, and everything is at a single site. Most of the functionality is as before, although you will see some differences, including of course information about the isolation host. Please contact Dan at info@seaphages.org if you have any questions or suggestions.

Secondly, we have finally decided on a nomenclature for naming phage clusters, using input that you have sent us or communicated at prior symposia. In brief, we will organize all phages of Actinobacteria hosts within a series of clusters and subclusters with unique names, and avoiding duplication. A key advantage is that phages with related genomes can be grouped together regardless of the host on which they were isolated.

The names we previously used for “Mycobacteriophage” Clusters will remain as is; that is, Cluster A will contain the same phages, but we will now refer to it as “Actinobacteriophage Cluster A”. Colloquially we will probably refer to them still as Cluster A, Cluster B etc, except where it is necessary to distinguish them from Clusters in other Phyla (such as "Proteobacteria Cluster A”).

As phages of new hosts are sequenced that do not fall into existing clusters, new cluster designations will be given, that progress from Cluster Z to Cluster AA, AB, AC etc etc. In order to include some sense of order, we have blocked off groups of names for phages of the newer hosts, and can add more blocks as needed. For example:

Mycobacteriophages: A – AJ

Arthrobacteriophages: AK – AZ

Streptomyces phages: BA – BT

Propionibacterium phages BU – BZ

Rhodococcus phages: CA – CP

Gordonia phages: CQ – CZ.

You can check out these cluster assignments at

http://phagesdb.org/clusters/

We hope this is clear but please let us know if you have any questions. We look forward to discussing all this further at the symposium!

The SEA-PHAGES team

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