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

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

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.
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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.

Mentions: A typical genomic experiment begins with isolation of genomic DNA of virus particles (Figure 3). The primary step is filtration of the sample through 0.22 μm filters for elimination of bacterial constituents and other contaminations. Samples are then concentrated by ultracentrifugation or polyethylene glycol precipitation (Helms et al., 1985) and subjected to DNase and RNase treatments to exclude residual genomic material from any contaminant bacteria that may pass through 0.22 μm filter. This treated sample would include only virus particles which can be cleaved and their genome can be extracted using kits or standard methods (Adhikary et al., 2014). In order to examine with NGS platforms, DNA is fragmented, ends are repaired and are ligated with adaptors (Holmfeldt et al., 2013). Finally, fragmented DNA library is cleaned and amplified through PCR as well as is quantified and sequenced. Several sequencing platforms are available such as Ion Torrent, Illumina, PacBio which are preferred as per the requirement of their read length, coverage, paired reads, insert size, accuracy, error rates, sequencing yield, run time and sequencing cost (Quail et al., 2012). To reduce chances of bacterial contamination in the library, a section of DNA is PCR amplified for 16S rRNA genes, and if bands are detected, it conveys the presence of host contamination. In the instance of lesser viral DNA yields, amplification using multiple displacement amplification (MDA) can be performed, but it may generate chimeras (Yilmaz et al., 2010). Apparently, amplifications using linkers may depict impartial viromes (Duhaime et al., 2012; Hurwitz et al., 2015). The sequences acquired by sequencing are developed for data filtering and the sequence reads that passes quality check, is mapped to reference genomes or assembled de novo. If the sequence of contaminating host is furthermore present in reads even after purifying the sample, it can be distinguished by comparing reads to reference bacterial genome or 16S rRNA database (Hurwitz et al., 2013). For annotation of viral genomes, a database such as NCBI non-redundant nucleotides can be used. ORFs can be determined and annotated using CyVerse (Goff et al., 2011) in the PCPipe application through the iVirus project (Hurwitz et al., 2014).


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

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getmorefigures.php?uid=PMC5383658&req=5

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.
Mentions: A typical genomic experiment begins with isolation of genomic DNA of virus particles (Figure 3). The primary step is filtration of the sample through 0.22 μm filters for elimination of bacterial constituents and other contaminations. Samples are then concentrated by ultracentrifugation or polyethylene glycol precipitation (Helms et al., 1985) and subjected to DNase and RNase treatments to exclude residual genomic material from any contaminant bacteria that may pass through 0.22 μm filter. This treated sample would include only virus particles which can be cleaved and their genome can be extracted using kits or standard methods (Adhikary et al., 2014). In order to examine with NGS platforms, DNA is fragmented, ends are repaired and are ligated with adaptors (Holmfeldt et al., 2013). Finally, fragmented DNA library is cleaned and amplified through PCR as well as is quantified and sequenced. Several sequencing platforms are available such as Ion Torrent, Illumina, PacBio which are preferred as per the requirement of their read length, coverage, paired reads, insert size, accuracy, error rates, sequencing yield, run time and sequencing cost (Quail et al., 2012). To reduce chances of bacterial contamination in the library, a section of DNA is PCR amplified for 16S rRNA genes, and if bands are detected, it conveys the presence of host contamination. In the instance of lesser viral DNA yields, amplification using multiple displacement amplification (MDA) can be performed, but it may generate chimeras (Yilmaz et al., 2010). Apparently, amplifications using linkers may depict impartial viromes (Duhaime et al., 2012; Hurwitz et al., 2015). The sequences acquired by sequencing are developed for data filtering and the sequence reads that passes quality check, is mapped to reference genomes or assembled de novo. If the sequence of contaminating host is furthermore present in reads even after purifying the sample, it can be distinguished by comparing reads to reference bacterial genome or 16S rRNA database (Hurwitz et al., 2013). For annotation of viral genomes, a database such as NCBI non-redundant nucleotides can be used. ORFs can be determined and annotated using CyVerse (Goff et al., 2011) in the PCPipe application through the iVirus project (Hurwitz et al., 2014).

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