38
(De Bourcy et al. 2014; Gawad et al. 2016). Whole-genome analysis of a single cell
or an entire sample is a prominent methodology helping in identification of variations in single nucleotide and copy number (SNVs and CNVs) via reducing the
exome- related errors. Furthermore, WGS can explore the intronic region and insertion and deletion of translocated gene segments actively involved in most biological
systems (Gawad et al. 2016).
4.1.4 Overview of Single-Cell Sequencing Errors
Single-cell sequencing is a highly precise technique having less chance of errors
whereas sometimes errors happen during isolation of a single cell from the complex
tissues of the bulk sample, genome amplification, and copy number estimation.
Characteristics of the cells such as size and phases of cell division also mark the
cause of deviations in the final output (Hou et al. 2012). Single-cell sequencing of a
microbial cell can be done only when precise and sensitive techniques for cell disruption followed by combined and efficient amplification and copy number estimation strategies are considered for the study (Zong et al. 2012; Deleye et al. 2017).
Apart from the in-depth picture of single-cell phases, single-cell genomics also provides detailed information to users about the cell transition phases, although the
field is still new and requires various experimental and computational advances for
complete exploration of the potential (Trapnell 2015). Single-cell genomics studies
need new algorithms and software for identification of differentially expressed
genes. Continuous development of single molecule-based strategies via singlemolecule real-time sequencing and nanopore-mediated single-molecule sequence
analysis may avoid the need to amplify an individual cell genome and ultimately
allow direct sequencing of the DNA present in an individual environmental cell,
including its epigenome, representing a major breakthrough in this area (Woyke and
Jarett 2015).
4.2 Metagenomics
Each microbe in any environment has its specific set of gene pool and genome.
Metagenomics study covers the entire genome of all microbes inhabiting any habitat including soil and water without in vitro culturing, prior individual identification,
or amplification (Abulencia et al. 2006; Kunin et al. 2008). Recently, it has been
used as a prominent tool for the analysis of interacting soil microbes and their specific and interlinking functions. Remarkable developments were observed in
metagenome sequencing using NGS technologies, which have generated enormous
amounts of data. The technique comprises isolation of metagenomics DNA directly
from environmental sample, fragmentation, generation of sequence clone library,
and high-throughput sequencing to acquire detailed information. Function- and
sequence-driven screening can lead to functionality of the metagenome. Later on,
4 Single-Cell Genomics and Metagenomics for Microbial Diversity Analysis
(De Bourcy et al. 2014; Gawad et al. 2016). Whole-genome analysis of a single cell
or an entire sample is a prominent methodology helping in identification of variations in single nucleotide and copy number (SNVs and CNVs) via reducing the
exome- related errors. Furthermore, WGS can explore the intronic region and insertion and deletion of translocated gene segments actively involved in most biological
systems (Gawad et al. 2016).
4.1.4 Overview of Single-Cell Sequencing Errors
Single-cell sequencing is a highly precise technique having less chance of errors
whereas sometimes errors happen during isolation of a single cell from the complex
tissues of the bulk sample, genome amplification, and copy number estimation.
Characteristics of the cells such as size and phases of cell division also mark the
cause of deviations in the final output (Hou et al. 2012). Single-cell sequencing of a
microbial cell can be done only when precise and sensitive techniques for cell disruption followed by combined and efficient amplification and copy number estimation strategies are considered for the study (Zong et al. 2012; Deleye et al. 2017).
Apart from the in-depth picture of single-cell phases, single-cell genomics also provides detailed information to users about the cell transition phases, although the
field is still new and requires various experimental and computational advances for
complete exploration of the potential (Trapnell 2015). Single-cell genomics studies
need new algorithms and software for identification of differentially expressed
genes. Continuous development of single molecule-based strategies via singlemolecule real-time sequencing and nanopore-mediated single-molecule sequence
analysis may avoid the need to amplify an individual cell genome and ultimately
allow direct sequencing of the DNA present in an individual environmental cell,
including its epigenome, representing a major breakthrough in this area (Woyke and
Jarett 2015).
4.2 Metagenomics
Each microbe in any environment has its specific set of gene pool and genome.
Metagenomics study covers the entire genome of all microbes inhabiting any habitat including soil and water without in vitro culturing, prior individual identification,
or amplification (Abulencia et al. 2006; Kunin et al. 2008). Recently, it has been
used as a prominent tool for the analysis of interacting soil microbes and their specific and interlinking functions. Remarkable developments were observed in
metagenome sequencing using NGS technologies, which have generated enormous
amounts of data. The technique comprises isolation of metagenomics DNA directly
from environmental sample, fragmentation, generation of sequence clone library,
and high-throughput sequencing to acquire detailed information. Function- and
sequence-driven screening can lead to functionality of the metagenome. Later on,
4 Single-Cell Genomics and Metagenomics for Microbial Diversity Analysis