Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

Abstract

Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral ‘dark matter’ of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research.

Abundance and diversity of phages, microbial taxa and antibiotic resistance genes in the sediments of the river Ganges through metagenomic approach

“…There are various studies, which advocate the importance and focused on the exploration of virome and phages from diverse sources [3, 14, 82-87]. However, to best of our knowledge, there is no metagenomic study reported that explore phage diversity from the Ganges River since the discovery of phages.…”

“…Phages also have evolutionary impact as they can facilitate recombination event, integration as prophages etc. [10, 14]. Furthermore, they are also effective alternative to antibiotics and can be utilized as therapy [15, 16].…”

“…To overcome these limitations, viral metagenomics approach using high throughput sequencing platforms (454, Illumina, PacBio, Nanopore etc.) provided a great hand and instrumental for understanding viral (microbial) world [3, 14, 18]. Various studies have supported the application of metagenomics to investigate the viral ecology, pathogen surveillance and to elucidate viral evolution and diversity [3, 21-27].…”

“…Various studies have supported the application of metagenomics to investigate the viral ecology, pathogen surveillance and to elucidate viral evolution and diversity [3, 21-27]. Moreover, it is of prime interest to get insight into the viromes specifically phage communities from different environments as it may affect the microbial diversity of the area and could assist in the future research of phage based therapeutics to combat bacterial pathogens [14, 28-34]. We still have inadequate knowledge and understanding of phage diversity in different ecosystems, which remains to be fully explored.…”

Identifying microbial species by single-molecule DNA optical mapping and resampling statistics

“…And finally, it leaves viruses invisible because of the absence of a universally conserved marker gene in their genome. (10) A second approach is to sequence the whole genome of all the species in the microbiome. (9) While whole-genome sequencing does not suffer from the same problems such as amplification bias and intrinsic preclusion of viruses, the most common sequencing techniques are unable to deliver both long sequence-reads and high-throughput.…”