Albert C Vill, Véronique A Delesalle, Brianne E Tomko, Katherine B Lichty, Madison S Strine, Alexandra A Guffey, Elizabeth A Burton, Natalie T Tanke, Greg P Krukonis
{"title":"美国西南部6种枯草芽孢杆菌噬菌体的比较基因组学研究。","authors":"Albert C Vill, Véronique A Delesalle, Brianne E Tomko, Katherine B Lichty, Madison S Strine, Alexandra A Guffey, Elizabeth A Burton, Natalie T Tanke, Greg P Krukonis","doi":"10.1089/phage.2022.0030","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Despite their importance to microbial dynamics involving <i>Bacillus subtilis</i>, we have a limited understanding of the diversity of phages that can lyse this model organism.</p><p><strong>Materials and methods: </strong>Phages were isolated from soil samples collected from various sites in the southwest U.S. deserts on a wild <i>B. subtilis</i> strain. Their genomes were assembled, characterized, and bioinformatically compared.</p><p><strong>Results: </strong>Six Siphoviruses with high nucleotide and amino acid similarity to each other (>80%) but very limited similarity to phages currently in GenBank were isolated. These phages have double-stranded DNA genomes (55,312 to 56,127 bp) with 86-91 putative protein coding genes, and a low GC content. Comparative genomics reveal differences in loci encoding proteins that are putatively involved in bacterial adsorption with evidence for genomic mosaicism and a possible role for small genes.</p><p><strong>Conclusions: </strong>A comparative approach provides insights into phage evolution, including the role of indels in protein folding.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 3","pages":"171-178"},"PeriodicalIF":0.0000,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917325/pdf/phage.2022.0030.pdf","citationCount":"1","resultStr":"{\"title\":\"Comparative Genomics of Six Lytic <i>Bacillus subtilis</i> Phages from the Southwest United States.\",\"authors\":\"Albert C Vill, Véronique A Delesalle, Brianne E Tomko, Katherine B Lichty, Madison S Strine, Alexandra A Guffey, Elizabeth A Burton, Natalie T Tanke, Greg P Krukonis\",\"doi\":\"10.1089/phage.2022.0030\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Despite their importance to microbial dynamics involving <i>Bacillus subtilis</i>, we have a limited understanding of the diversity of phages that can lyse this model organism.</p><p><strong>Materials and methods: </strong>Phages were isolated from soil samples collected from various sites in the southwest U.S. deserts on a wild <i>B. subtilis</i> strain. Their genomes were assembled, characterized, and bioinformatically compared.</p><p><strong>Results: </strong>Six Siphoviruses with high nucleotide and amino acid similarity to each other (>80%) but very limited similarity to phages currently in GenBank were isolated. These phages have double-stranded DNA genomes (55,312 to 56,127 bp) with 86-91 putative protein coding genes, and a low GC content. Comparative genomics reveal differences in loci encoding proteins that are putatively involved in bacterial adsorption with evidence for genomic mosaicism and a possible role for small genes.</p><p><strong>Conclusions: </strong>A comparative approach provides insights into phage evolution, including the role of indels in protein folding.</p>\",\"PeriodicalId\":74428,\"journal\":{\"name\":\"PHAGE (New Rochelle, N.Y.)\",\"volume\":\"3 3\",\"pages\":\"171-178\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2022-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917325/pdf/phage.2022.0030.pdf\",\"citationCount\":\"1\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"PHAGE (New Rochelle, N.Y.)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1089/phage.2022.0030\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"PHAGE (New Rochelle, N.Y.)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1089/phage.2022.0030","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States.
Background: Despite their importance to microbial dynamics involving Bacillus subtilis, we have a limited understanding of the diversity of phages that can lyse this model organism.
Materials and methods: Phages were isolated from soil samples collected from various sites in the southwest U.S. deserts on a wild B. subtilis strain. Their genomes were assembled, characterized, and bioinformatically compared.
Results: Six Siphoviruses with high nucleotide and amino acid similarity to each other (>80%) but very limited similarity to phages currently in GenBank were isolated. These phages have double-stranded DNA genomes (55,312 to 56,127 bp) with 86-91 putative protein coding genes, and a low GC content. Comparative genomics reveal differences in loci encoding proteins that are putatively involved in bacterial adsorption with evidence for genomic mosaicism and a possible role for small genes.
Conclusions: A comparative approach provides insights into phage evolution, including the role of indels in protein folding.
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