دورية أكاديمية
Exploring the diversity and evolutionary strategies of prophages in Hyphomicrobiales, comparing animal-associated with non-animal-associated bacteria.
| العنوان: | Exploring the diversity and evolutionary strategies of prophages in Hyphomicrobiales, comparing animal-associated with non-animal-associated bacteria. |
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| المؤلفون: | Gonçalves-Oliveira J; Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel., Pattenden T; School of Management, Economics and Mathematics, King's University College, Western University, London, ON, Canada., Nachum-Biala Y; Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel., de Sousa KCM; Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel., Wahl L; Department of Applied Mathematics, Western University, London, ON, Canada., Harrus S; Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel. shimon.harrus@mail.huji.ac.il. |
| المصدر: | BMC microbiology [BMC Microbiol] 2024 May 09; Vol. 24 (1), pp. 159. Date of Electronic Publication: 2024 May 09. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't; Comparative Study |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : BioMed Central, [2001- |
| مواضيع طبية MeSH: | Prophages*/genetics , Evolution, Molecular* , Genome, Bacterial*/genetics, Animals ; Phylogeny ; Genome, Viral/genetics ; Bacteria/virology ; Bacteria/genetics ; Bacteria/classification ; Genetic Variation |
| مستخلص: | The Hyphomicrobiales bacterial order (previously Rhizobiales) exhibits a wide range of lifestyle characteristics, including free-living, plant-association, nitrogen-fixing, and association with animals (Bartonella and Brucella). This study explores the diversity and evolutionary strategies of bacteriophages within the Hyphomicrobiales order, comparing animal-associated (AAB) with non-animal-associated bacteria (NAAB). We curated 560 high-quality complete genomes of 58 genera from this order and used the PHASTER server for prophage annotation and classification. For 19 genera with representative genomes, we curated 96 genomes and used the Defense-Finder server to summarize the type of anti-phage systems (APS) found in this order. We analyzed the genetic repertoire and length distributions of prophages, estimating evolutionary rates and comparing intact, questionable, and incomplete prophages in both groups. Analyses of best-fit parameters and bootstrap sensitivity were used to understand the evolutionary processes driving prophage gene content. A total of 1860 prophages distributed in Hyphomicrobiales were found, 695 in AAB and 1165 in the NAAB genera. The results revealed a similar number of prophages per genome in AAB and NAAB and a similar length distribution, suggesting shared mechanisms of genetic acquisition of prophage genes. Changes in the frequency of specific gene classes were observed between incomplete and intact prophages, indicating preferential loss or enrichment in both groups. The analysis of best-fit parameters and bootstrap sensitivity tests indicated a higher selection coefficient, induction rate, and turnover in NAAB genomes. We found 68 types of APS in Hyphomicrobiales; restriction modification (RM) and abortive infection (Abi) were the most frequent APS found for all Hyphomicrobiales, and within the AAB group. This classification of APS showed that NAAB genomes have a greater diversity of defense systems compared to AAB, which could be related to the higher rates of prophage induction and turnover in the latter group. Our study provides insights into the distributions of both prophages and APS in Hyphomicrobiales genomes, demonstrating that NAAB carry more defense systems against phages, while AAB show increased prophage stability and an increased number of incomplete prophages. These results suggest a greater role for domesticated prophages within animal-associated bacteria in Hyphomicrobiales. (© 2024. The Author(s).) |
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| معلومات مُعتمدة: | RGPIN-2019-06294 Natural Sciences and Engineering Research Council of Canada; No. 688/17 Israel Science Foundation |
| فهرسة مساهمة: | Keywords: Bartonella; Brucella; Bacteriophages; Defense systems; Genetic repertoire; Hyphomicrobiales; Prophage genes |
| تواريخ الأحداث: | Date Created: 20240509 Date Completed: 20240510 Latest Revision: 20240512 |
| رمز التحديث: | 20240512 |
| مُعرف محوري في PubMed: | PMC11080155 |
| DOI: | 10.1186/s12866-024-03315-3 |
| PMID: | 38724926 |
| قاعدة البيانات: | MEDLINE |
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Full Text Finder | تدمد: | 1471-2180 |
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| DOI: | 10.1186/s12866-024-03315-3 |