Extensive cultivation of human gut phages revealing undescribed Bacteroidaceae phages

The isolated and characterized gut phages remain rare. Most of the gut phages that have been isolated and propagated thus far are lytic phages, leaving significant gaps in the study of gut temperate phages. In this study, we successfully isolated a large-scale collection of gut bacteria and phages, containing 1,679 bacterial strains from 86 species and 79 phages that infect bacteria from 26 different species. Among the phage isolates, 32 are temperate phages and two of these temperate phages were directly isolated from faecal samples of healthy human donors. Sequence comparisons and analysis show that the isolated temperate phages are characterized with highly diverse genomes and significantly higher prevalence in the human gut when compared with these characterised lytic gut phages. Further analysis shows that most of these temperate phages contain unique diversity-generating retroelements (DGRs) and may have a broad host range. Additionally, by combining sequence and structural similarity we developed a pipeline that can significantly enhance the annotation rate of our gut phage genomes. The annotation pipeline helps to identify a candidate phage family, "Bacteroiduroviridae", that diverged from other bacteriophages early in the evolutionary process.