| Title: | Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages |
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| Authors: | ID Stopnišek, Nejc (Author)
ID Hedžet, Stina (Author)
ID Accetto, Tomaž (Author)
ID Rupnik, Maja (Author) |
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| Files: |  PDF - Presentation file, download (1,73 MB)
MD5: E21DD146A874883BF1406B10E8904DA9
 URL - Source URL, visit https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-03827-6
URL - Source URL, visit https://github.com /NLZOHomr/prophages_2024
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| Language: | English |
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| Typology: | 1.01 - Original Scientific Article |
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| Organization: |  NLZOH - National Laboratory of Health, Environment and Food
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| Abstract: | Background Phages are critical components of the gut microbiome, influencing bacterial composition and function as predators, parasites, and modulators of bacterial phenotypes. Prophages, integrated forms of these phages, are prevalent in many bacterial genomes and play a role in bacterial adaptation and evolution. However, the diversity and stability of prophages within gut commensals, particularly in the genera Bacteroides and Phocaeicola, remain underexplored. This study aims to screen and characterize prophages in these genera, providing insights into their diversity, host range, and temporal dynamics in the human gut. Results Using a combination of three bioinformatic tools—Cenote-Taker 3, Vibrant, and PHASTER—we conducted a comprehensive analysis of prophages in Bacteroides and Phocaeicola. Cenote-Taker 3 identified the most diverse set of prophages, with significant overlaps observed between the tools. After clustering high-quality prophages, we identified 22 unique viral operational taxonomic units (vOTUs). Notably, comparisons between prophages identified in isolated bacterial genomes, metaviromes, and large public gut virome databases revealed a broader host range than initially observed in single isolates. Certain prophages were consistent across time points and individuals, suggesting temporal stability. All identified prophages belonged to the Caudoviricetes class and contained genes related to antibiotic resistance, toxin production, and metabolic processes. Conclusions The combined use of multiple prophage detection tools allowed for a more comprehensive assessment of prophage diversity in Bacteroides and Phocaeicola. The identified prophages were not only prevalent but also exhibited broad host ranges and temporal stability. The presence of antibiotic resistance and toxin genes suggests that these prophages may significantly influence bacterial community structure and function in the gut, with potential implications for human health. These findings highlight the importance of using diverse detection tools to accurately assess prophage diversity and dynamics. |
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| Keywords: | prophage detection, Bacteroides, Phocaeicola, gut microbiome, prophage diversity, Caudoviricetes, antibiotic resistance, phage-bacteria interactions, temporal stability |
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| Publication status: | Published |
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| Publication version: | Version of Record |
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| Submitted for review: | 05.09.2025 |
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| Article acceptance date: | 13.02.2025 |
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| Publication date: | 26.02.2025 |
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| Year of publishing: | 2025 |
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| Number of pages: | str. 1-10 |
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| Numbering: | Letn. 25, št. članka 92 |
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| PID: | 20.500.12556/DiRROS-21575  |
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| UDC: | 579 |
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| ISSN on article: | 1471-2180 |
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| DOI: | 10.1186/s12866-025-03827-6 |
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| COBISS.SI-ID: | 227497475 |
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| Note: |
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| Publication date in DiRROS: | 06.03.2025 |
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| Views: | 218 |
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| Downloads: | 184 |
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