Challenges of Studying the Human Virome – Relevant Emerging Technologies

• Published in: Trends in microbiology (Regular ed.) 2021-02, Vol.29 (2), p.171-181
• Main Authors: Khan Mirzaei, Mohammadali, Xue, Jinling, Costa, Rita, Ru, Jinlong, Schulz, Sarah, Taranu, Zofia E., Deng, Li
• Format: Article
• Language: English
• Subjects: bacteriophages; Biodiversity; computational tools; Computer applications; Deoxyribonucleic acid; DNA; host range; human virome; Metagenomics; Microorganisms; multi-omics; New technology; phage de novo discoveries; Phages; Reviews; Ribonucleic acid; RNA
• ISSN: 0966-842X; 1878-4380
• DOI: 10.1016/j.tim.2020.05.021

In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, and interactions with both the microbial community and the human body. We expect that these recent and future advances in the field of viromics will have a strong impact on how we develop phage-based therapeutic approaches. Shotgun sequencing bypasses the need for metabarcoding in viromics, although it is prone to high background noises and biases towards double-stranded DNA viruses.Protein-level assembly can be a better tool to use on virome data as they predict more protein sequences from complex unknown metagenomes.Using viral discovery methods can help to resolve the full diversity of viral fraction of microbiome data.Culture-independent methods such as viral-tagging can be used to measure the phage host range in the human body.