Based on the diminishing slope found in our rate-of-discovery
analysis (Fig. 2C), we propose that there may be a relatively limited
pool of common phages present in many individuals along with
a much larger set of rarer phages that will require significantly
more sequencing to reach saturation. However, we note that it is
difficult to compare these results with predictions on global phage
diversity (Rohwer 2003) since our method can only detect phages
targeted by the bacterial CRISPR immune system and is tilted toward
discovery of phages associated with the more abundant gut
bacterial species. Furthermore, our method excludes both smallersized
phage genomes, such as Microviridae whose presence in the
human gut has been repeatedly demonstrated (Breitbart et al. 2003;
Krupovic and Forterre 2011; Minot et al. 2011), and RNA phages,
which are absent from the DNA-based MetaHIT data. The latter
concern is mitigated by the finding that the majority of RNA viruses
in the human gut are not bacteriophages (