Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics

Abstract

Innovations in next-generation sequencing technology have introduced new avenues in microbial studies through "omics" approaches. This technology has considerably augmented the knowledge of the microbial world without isolation prior to their identification. With an enormous volume of bacterial "omics" data, considerable attempts have been recently invested to improve an insight into virosphere. The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation. This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse microbial communities. Omics technologies illuminate the role of bacteriophage in an environment, the influences of phage proteins on the bacterial host and provide information about the genes important for interaction with bacteria. These investigations will reveal some of bio-molecules and biomarkers of the novel phage which demand to be unveiled.

Keywords: bacteriophage; genomics; next-generation sequencing; transcriptomics.

Figure 1

Significance of bacteriophages in regulating environment. In this figure, (A) depicts infection and insertion phage DNA into the host cell. After the phage infection, the host cell may get converted into a virocell (B), containing vAMGs that leading to an altered regulation or novel functions in bacterial host cell. The phage infection leading to lytic cycle (C) results into lysing host cell hence, controlling cell population. Infected cell leading to a lysogeny cycle (D) may contain phage genome into the bacterial genome, which can lead to an increased microbial diversity because of horizontal gene transfers- HGT (E). Also, the dead debris of bacteria as a result of phage lysis enters the food-web and biogeochemical cycles (F), as a result the nutrients get re-circulated in the ecosystem.

Figure 2

Different techniques to gain an insight into virosphere. Genomics includes concentration of phages, DNA isolation, quantification, and sequencing. Transcriptomics includes processing of RNA converting it to cDNA and sequencing. Proteomics encompasses protein extraction, separation and quantification using several tools like sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), electron spray ionization—mass spectroscopy (ESI-MS), liquid chromatography–mass spectrometry (LC-MS), matrix-assisted laser ionization and deionization (MALDI)-MS and nuclear magnetic resonance (NMR), and Whole phage shotgun analysis (WSA). Metabolomics refers to metabolite extraction separation and quantification in a given time and different metabolites can be analysis using different tools like nanostructure initiator MS (NIMS) and desorption electron spray ionization (DESI) for the understanding of bacteriophage and its interactions.

Figure 3

Workflow to study the genomic content of bacteriophages. Genomics of phages initiates by filtering phage particles from microbial community (A) through 0.22 μ filter which results in (B) virus particles containing residual DNA and RNA of other microbial communities. (C) Purification of virus particles from residual DNA and RNA are removed by CsCl density gradient method. (D) Phage particles are concentrated using polyethylene glycol or ultra-centrifugation. (E) Extraction of viral DNA uses kits or conventional methods. The DNA is amplified and libraries are prepared and subsequently sequenced them.

Figure 4

Understanding phage diversity, community interactions and chemical profiles using meta-omics approach. Genomics elucidates the phage diversity, abundance, probable functional features while transcriptomics gives an insight about the actively expressed genes in a community. Proteomics suggests the phage structural proteins, its functions and the proteins responsible for interaction between phage and host. Metabolomics advocates the metabolites produced by hosts in presence and absence of phage infection, alterations in regulation and metabolic profiles after infection. SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; ESI-MS, electron spray ionization–mass spectroscopy; LC-MS, liquid chromatography–mass spectrometry; MALDI-MS, matrix-assisted laser ionization and deionization; NMR, nuclear magnetic resonance; NIMS, nanostructure initiator MS.