The longitudinal studies have found that the human gut microbiota is stable over time with some major bacterial lineages or even strains persisting for years. This was recently extended to gut bacteriophages using the metagenomic data. Here, we focused on cultivation of the major Bacteroidota of the human gut, the Bacteroides and Phocaeicola strains, and their bacteriophages from two healthy donors. The persistence of Bacteroides and Phocaeicola species and strains was confirmed. We have isolated 31 genetically different phages grouped into seven distinct clusters, two of which were new. Moreover, the bacteriophages from several groups, although being genetically quite homogeneous, had the ability to infect the strains belonging to different species isolated from several sampling time-points and different donors. We propose that the ability to infect several host species, which differ in their nutritional niches, may promote long-term persistence of dominant gut bacteriophage groups. Additionally, bacterial genomes were analyzed for the presence of potential prophages and their dynamics was observed between time points and donors. We identified 65 prophages, groupped into four clusters. Identified prophages were stable over the sampling period and could infect different bacterial species. The isolated phages were used in an in vitro system for the cultivation of fecal microbiota, where we studied their influence on the composition of the fecal microbiota and the stability and presence of phages in the metavirome.
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