Fig. 1

Identification of the large phage scaffolds and definition of pOTU. a The pipeline used three strategies to identify the large phage scaffolds (≥ 10 k) (see also supplementary Materials and Methods for details). In strategy I, the scaffolds were probed by CRISPR spacer(s). In strategy II, the scaffolds were mapped by reads from the VLP metagenome with a high breadth of coverage (≥ 40%). In strategy III, the scaffolds encoding genes homologous to those of ENA phages were identified. The Bacteria and Phage Gene Database (BPGDB) was constructed. The assigned scaffolds were manually checked by comparing them against the BPGDB and GenBank nr database. The scaffolds with ambiguous assignments were discarded in the next analysis steps. b Definition of pOTUs to profile the phageome on the read level (see also supplementary Materials and Methods for details). The Expanded Phage-Specific Gene database (EPSGDB) was constructed according to the Phage Orthologous Groups (POGs). The phage taxonomical classification was performed based on the International Committee on Taxonomy of Viruses (ICTV) [17, 30]. The relative number of a pOTU in a sample was calculated by summing the numbers of all phage genomes belonging to the pOTU and dividing by the number of 16S rRNA gene reads in the sample