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

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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.

No MeSH data available.


Related in: MedlinePlus

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.
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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.

Mentions: The interplay between host and phage particle initiates as soon as the phage recognizes specific receptors on the bacterial cell wall. The tail proteins of phage particle recognize the receptor protein(s) of bacteria and inject own DNA into host cytoplasm choosing either lytic or lysogenic lifecycle. Once the phage DNA is inserted into the bacterial cell, the cell is termed as a “virocell” carrying virus auxiliary metabolic genes (vAMGs), which are believed to augment the metabolic potential of the host during infection process as shown in Figure 1 (Rosenwasser et al., 2016). The phages acquire new genes into their genomes by interactions with the host genome in order to replicates in the host cells. The bacterial genes that attach near to the prophage attachment site, suggests the genes were acquired by inaccurate prophage excision. Some novel genes can similarly be transmitted into the interior part of the genome by some unexplained mechanism (Juhala et al., 2000). However, these genes may be autonomous transcripts or repressed prophages that provide benefit to hosts (Brüssow et al., 2004). Horizontal gene transfer (HGT) by these phage particles from one host to another host genomes, results in an increased microbial diversity (Dutta and Pan, 2002; Weinbauer and Rassoulzadegan, 2004). Thus, the interaction between phage and host chiefly emphasizes the structure of microbial communities (Rohwer and Thurber, 2009). Some genes derived by phage also aid in nutrient cycling and gear up the biogeochemical cycles on Earth. Furthermore, phages have a crucial aspect in host mortality, carbon cycling (Breitbart et al., 2004) and nutrient cycling (Suttle, 2007). Also, microbial lysis by phage infection has significance in bacterial population control and the debris of these dead microbes act as a food source in the food web of the environment (Sime-Ngando and Colombet, 2009), thus involved the cycling nutrients (Figure 1). Phages are thus accounted as an application to limit bacterial pathogens and multi-drug resistant organisms in the environment by the mechanism of specifically lysing the bacterial hosts (Parmar et al., 2017). Despite an immense abundance and diversity of phages and their reimbursement in the global webs, molecular knowledge of phage-host interactions is missing. In the era of NGS, employing genomics, single cell genomics, transcriptomics, proteomics, and metabolomics can be a smart attempt to understand the interaction among the phages and their bacterial hosts (Figure 2). A review of the literature has been solicited to confer the claims of omics approach in phage research (Table 1).


Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics
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.
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Related In: Results  -  Collection

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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.
Mentions: The interplay between host and phage particle initiates as soon as the phage recognizes specific receptors on the bacterial cell wall. The tail proteins of phage particle recognize the receptor protein(s) of bacteria and inject own DNA into host cytoplasm choosing either lytic or lysogenic lifecycle. Once the phage DNA is inserted into the bacterial cell, the cell is termed as a “virocell” carrying virus auxiliary metabolic genes (vAMGs), which are believed to augment the metabolic potential of the host during infection process as shown in Figure 1 (Rosenwasser et al., 2016). The phages acquire new genes into their genomes by interactions with the host genome in order to replicates in the host cells. The bacterial genes that attach near to the prophage attachment site, suggests the genes were acquired by inaccurate prophage excision. Some novel genes can similarly be transmitted into the interior part of the genome by some unexplained mechanism (Juhala et al., 2000). However, these genes may be autonomous transcripts or repressed prophages that provide benefit to hosts (Brüssow et al., 2004). Horizontal gene transfer (HGT) by these phage particles from one host to another host genomes, results in an increased microbial diversity (Dutta and Pan, 2002; Weinbauer and Rassoulzadegan, 2004). Thus, the interaction between phage and host chiefly emphasizes the structure of microbial communities (Rohwer and Thurber, 2009). Some genes derived by phage also aid in nutrient cycling and gear up the biogeochemical cycles on Earth. Furthermore, phages have a crucial aspect in host mortality, carbon cycling (Breitbart et al., 2004) and nutrient cycling (Suttle, 2007). Also, microbial lysis by phage infection has significance in bacterial population control and the debris of these dead microbes act as a food source in the food web of the environment (Sime-Ngando and Colombet, 2009), thus involved the cycling nutrients (Figure 1). Phages are thus accounted as an application to limit bacterial pathogens and multi-drug resistant organisms in the environment by the mechanism of specifically lysing the bacterial hosts (Parmar et al., 2017). Despite an immense abundance and diversity of phages and their reimbursement in the global webs, molecular knowledge of phage-host interactions is missing. In the era of NGS, employing genomics, single cell genomics, transcriptomics, proteomics, and metabolomics can be a smart attempt to understand the interaction among the phages and their bacterial hosts (Figure 2). A review of the literature has been solicited to confer the claims of omics approach in phage research (Table 1).

View Article: PubMed Central - PubMed

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.

No MeSH data available.


Related in: MedlinePlus