Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales
Summary: Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database a...
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Elsevier
2025-01-01
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| Series: | Cell Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124724015481 |
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| author | Polonca Stefanic Eva Stare Valentina A. Floccari Jasna Kovac Robert Hertel Ulisses Rocha Ákos T. Kovács Ines Mandić-Mulec Mikael Lenz Strube Anna Dragoš |
| author_facet | Polonca Stefanic Eva Stare Valentina A. Floccari Jasna Kovac Robert Hertel Ulisses Rocha Ákos T. Kovács Ines Mandić-Mulec Mikael Lenz Strube Anna Dragoš |
| author_sort | Polonca Stefanic |
| collection | DOAJ |
| description | Summary: Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B. subtilis, shedding light on bacterial genome evolution and phage-host dynamics. |
| format | Article |
| id | doaj-art-7b309ed957904eb3b30fe3857b241ac9 |
| institution | Kabale University |
| issn | 2211-1247 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj-art-7b309ed957904eb3b30fe3857b241ac92025-01-11T06:41:14ZengElsevierCell Reports2211-12472025-01-01441115197Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scalesPolonca Stefanic0Eva Stare1Valentina A. Floccari2Jasna Kovac3Robert Hertel4Ulisses Rocha5Ákos T. Kovács6Ines Mandić-Mulec7Mikael Lenz Strube8Anna Dragoš9Department of Microbiology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, SloveniaDepartment of Microbiology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, SloveniaDepartment of Microbiology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, SloveniaDepartment of Food Science, Pennsylvania State University, University Park, PA 16802, USADepartment of Genomic and Applied Microbiology, Georg-August-University of Göttingen, 37077 Göttingen, GermanyDepartment of Applied Microbial Ecology, Helmholtz Center for Environmental Research, 04318 Leipzig, GermanyInstitute of Biology, Leiden University, 2333 Leiden, the Netherlands; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby 2800, DenmarkDepartment of Microbiology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, SloveniaDepartment of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby 2800, DenmarkDepartment of Microbiology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; Corresponding authorSummary: Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B. subtilis, shedding light on bacterial genome evolution and phage-host dynamics.http://www.sciencedirect.com/science/article/pii/S2211124724015481CP: Microbiology |
| spellingShingle | Polonca Stefanic Eva Stare Valentina A. Floccari Jasna Kovac Robert Hertel Ulisses Rocha Ákos T. Kovács Ines Mandić-Mulec Mikael Lenz Strube Anna Dragoš Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales Cell Reports CP: Microbiology |
| title | Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales |
| title_full | Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales |
| title_fullStr | Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales |
| title_full_unstemmed | Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales |
| title_short | Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales |
| title_sort | ecology of prophage like elements in bacillus subtilis at global and local geographical scales |
| topic | CP: Microbiology |
| url | http://www.sciencedirect.com/science/article/pii/S2211124724015481 |
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