Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing

Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from approximate to 500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained approximate to 35% (7675) complete genomes, which is approximate to nine times more than those in the Gut Virome Database (GVD, approximate to 4%, 1,443). Interestingly, the majority (approximate to 60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications. The CHGV, a human gut virome database, comprises 21,499 non-redundant phage genomes obtaine through viral-like particle enrichment and combined short- and long-read sequencing. The long-reads facilitate the identification of more complete viral genomes and surprisingly favor lowly abundant ones. The CHGV features novel genomes, prevalent phages exceeding crAssphages/Gubaphages, and enables functional analysis and viral-host interaction network construction. This enhances gut virome research and applications significantly.image