New Viruses Infecting Hyperthermophilic Bacterium Thermus thermophilus
, Constantine Pavlov 1, Alina Demkina 1, Aleksei Samolygo 1, Karyna Karneyeva 1, Anna Trofimova 1, Olga S. Sokolova 2,3, Andrei V. Moiseenko 3, Maria Kirsanova 1 and Konstantin Severinov 1,4,*
Paul Kirchberger
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe authors isolate and sequence several novel phages from Thermus thermophilus bacteria and compare them to the known diversity of phages from this genus.
The authors should try to taxonomically place their phages using a program such as https://github.com/amillard/tax_myPHAGE or ClassiPhage (https://www.mdpi.com/1999-4915/11/2/195). What I would appreciate is a table of all isolated phages, host, sample source and taxonomy.
Other than that, the work is solid, represents a welcome addition to our knowledge of phages, and I have only minor comments for fixes before publication.
Line-by-line:
29 (and several other instance) – double spaces should be replaced by single spaces (nitpick)
39: I don’t doubt that Thermus phages are undersamples (most phages are), but an abundance of CRISPR-spacers that don’t match known phages is not evidence for that – it could be plasmids or other mobile genetic elements.
97: What’s the MGI platform?
110: Could they only be extracted with plasmid miniprep kits? It should be noted and not just implied that these phages have ssDNA genomes in their virions, but (extractable) dsDNA replicative forms in host cells.
135: It might be worth noting here that inoviruses do not lyse their hosts but produce “plaques” for (pseudo)lysogens by reducing the growth of infected hosts.
136-139: A supplementary figure showing the alignments of the attachment proteins would be appreciated here
174: Do the authors actually mean similarity or identity? These terms have different meanings, and I suspect they mean identity.
304: Nitpick, but IN93 is not technically a sphaerolipovirus anymore as far as I can tell, in the sense that they are not in the Sphaerolipoviridae family – It’s a Matsushitoviridae (who can really keep track of all these changes?)
352: It is never described how prophages were detected in Thermus genomes – add this to the methods
364: Again what do the authors mean with similarity? Homology? Similar annotation? I do not see evidence in figure 6 or the text that these restriction endonucleases are shared between unrelated phages
395: Which Thermus strains? They’re mentioned in the text, but should also be here
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThis is a well-written paper that significantly expands our knowledge of the occurrence, morphology and genetics of phages infecting the Thermus genus. It is rare that I read a paper without suggesting improvements.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
