Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages
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...
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2025-02-01
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| Online Access: | https://doi.org/10.1186/s12866-025-03827-6 |
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| author | Nejc Stopnisek Stina Hedžet Tomaž Accetto Maja Rupnik |
| author_facet | Nejc Stopnisek Stina Hedžet Tomaž Accetto Maja Rupnik |
| author_sort | Nejc Stopnisek |
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| description | 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. |
| format | Article |
| id | doaj-art-bd85512be7c8459a94e58e8918e6d78d |
| institution | DOAJ |
| issn | 1471-2180 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj-art-bd85512be7c8459a94e58e8918e6d78d2025-08-20T02:59:35ZengBMCBMC Microbiology1471-21802025-02-0125111010.1186/s12866-025-03827-6Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophagesNejc Stopnisek0Stina Hedžet1Tomaž Accetto2Maja Rupnik3Department for Microbiological Research, Centre for Medical Microbiology, National Laboratory of Health, Environment and FoodDepartment for Microbiological Research, Centre for Medical Microbiology, National Laboratory of Health, Environment and FoodBiotechnical Faculty, University of LjubljanaDepartment for Microbiological Research, Centre for Medical Microbiology, National Laboratory of Health, Environment and FoodAbstract 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.https://doi.org/10.1186/s12866-025-03827-6Prophage detectionBacteroidesPhocaeicolaGut microbiomeProphage diversityCaudoviricetes |
| spellingShingle | Nejc Stopnisek Stina Hedžet Tomaž Accetto Maja Rupnik Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages BMC Microbiology Prophage detection Bacteroides Phocaeicola Gut microbiome Prophage diversity Caudoviricetes |
| title | Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages |
| title_full | Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages |
| title_fullStr | Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages |
| title_full_unstemmed | Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages |
| title_short | Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages |
| title_sort | insights into diversity host range and temporal stability of bacteroides and phocaeicola prophages |
| topic | Prophage detection Bacteroides Phocaeicola Gut microbiome Prophage diversity Caudoviricetes |
| url | https://doi.org/10.1186/s12866-025-03827-6 |
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