Profiling of Human Gut Virome with Oxford Nanopore Technology

Highlights

• Virus-like particles were enriched from human stool samples.

• Viral nucleotides were sequenced with Oxford Nanopore Technology with and without amplification.

• Gut virome in humans showed highly individualized composition.

• Novel sequences and contigs were found to be the majority in the resulted sequences.

• Epigenetic modifications were detected directly on virus genomes.

Abstract

Human gut virome play 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 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 cDNA/DNA after amplification using ONT achieves much longer reads and provides more information regarding virome diversity, many of the virome sequences do not have match in current databases. Moreover, direct DNA sequencing of virome provides first insights into the epigenetic modifications on phages, where signals of methylations can be directly detected. Our study demonstrates that progressing sequencing technology and bioinformatic improvements will bring more knowledge into virome composition, diversity and potentially their important functions.