Profiling of human gut virome with Oxford Nanopore technology

The human gut virome plays critical roles in maintaining gut microbial composition and functionality, as well as host physiology and immunology. Yet, there are insufficient amount of studies on this topic mainly due to methodological limitations, including enrichment of viruses (phages and host viruses) as well as short read-length from current sequencing technology.

Here we developed a full working protocol for analyzing the human gut virome using physical enrichment, reverse transcription and random amplification, and eventually the state-of-art single-molecule real-time sequencing (SMRT) platform of Oxford Nanopore Technology (ONT).

We demonstrate that sequencing viral DNA directly, or viral DNA/cDNA after amplification, using ONT, achieves much longer reads and provides more information regarding virome diversity - many of the virome sequences do not have a match in current databases. Moreover, direct DNA sequencing of the virome provides a first insight into the epigenetic modifications in phage genomes, where signals of methylation can be directly detected.

Our study demonstrates that progressing sequencing technology and bioinformatic improvements will bring more knowledge into the virome composition, diversity and potentially its important function.