20.500.12556/DiRROS-21575 Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages 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. prophage detection Bacteroides Phocaeicola gut microbiome prophage diversity Caudoviricetes antibiotic resistance phage-bacteria interactions temporal stability odkrivanje profagov črevesni mikrobiom raznolikost profagov odpornost na antibiotike interakcije med fagi in bakterijami časovna stabilnost true false true Angleški jezik Slovenski jezik Neznano 2025-02-28 03:44:16 2025-03-06 09:03:35 2025-03-11 03:37:21 0000-00-00 00:00:00 2025 0 0 str. 1-10 št. članka 92 Letn. 25 Feb. 2025 0000-00-00 Zaloznikova Objavljeno NiDoloceno 2025-09-05 2025-02-13 2025-02-26 579 1471-2180 10.1186/s12866-025-03827-6 227497475 Insights_into_diversity_Stopnisek_et_al._2025.pdf Insights_into_diversity_Stopnisek_et_al._2025.pdf 1 E21DD146A874883BF1406B10E8904DA9 65b4945e75cc35a321b6712e4c65365df24e5fea52edeb14c63aaa982020f630 e2c867c1-fd78-11ef-88ed-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=31029 https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-03827-6 0 e75cf15a-f57d-11ef-9f1e-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=30873 https://github.com /NLZOHomr/prophages_2024 1 e75ed68a-f57d-11ef-9f1e-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=30874 Nacionalni laboratorij za zdravje, okolje in hrano 0 0 0