LAUSR

Human gastrointestinal tract harbors trillions of commensal microbes including bacteria, viruses, and fungi to form an ecological community, commonly known as the gut microbiome. Being the second most dominant taxonomic kingdom in the gut (5.8% of total microbiome DNA), enteric viruses are increasingly acknowledged for their roles in shaping the overall composition of the gut microbiome and maintaining human health. Recent advancements in metagenomic sequencing have brought breakthrough in deciphering the features and functions of the gut virome. Notably, there are several factors restricting the application of this technology in virome study. For instance, the amount of isolated viral DNA from human samples is usually insufficient for metagenomic sequencing. To solve this issue, amplification techniques such as polymerase chain reaction andmultiple displacement amplification are widely used to increase the amount of extracted viral DNAprior to sequencing, which in turn could introduce amplification bias, chimeric reads, and random mutations. Meanwhile, given that most studies analyzed metagenomic reads at low depth (from 0.0003 GB to 7.7 GB), there is currently lack of high quality assembled viral genomes, as well as failure in identifying viruses with low abundance in samples. In addition, Illumina sequencing that generates short reads, has been frequently used. However, short sequencing reads were reported to be inadequate for accurate assembly of viral genomes as they contain hypervariable sequences and repeating regions.