Next-generation sequencing (NGS): a revolution in the era of microbial ecology

Though above-mentioned culture-independent techniques provide a comprehensive overview of microbial community structure in various environments, all methods are very laborious, erroneous and hampered with various other limitations such as identification of only dominant (abundant) microorganisms, not rare taxa. Advent of NGS technology has tremendously revolutionized the field of microbial ecology and broadened the scientific vision towards complex community composition. The term NGS refers to massively parallel sequencing technologies that include various commercialized platforms such as 454/Roclie, Illumina/Solexa, Ion Torrent and ABI/SOLiD. In this section, the details of each NGS platforms are not described, although interested readers are directed to Chapter 9 by Sushmitha et al., where the sequencing chemistries and applications of NGS platforms in relation to bacterial diversity assessment are explained.

The main characteristics of these technologies, such as generating millions of reads (high throughput) at a relatively rapid rate and lesser costs, have greatly transformed the field of microbial ecology. In the field of microbial ecology, these high-throughput technologies are useful in various environmental studies that deal with metageuomics, metatranscriptomics, proteogenomics, amplicons sequencing and whole-genome shotgun sequencing.

Concluding remarks and future directions

Advent of molecular genomic tools has gr eatly revolutionized the field of microbial ecology. The frequency of studies earned out to study microbial diversity and their unique role in various ecosystems uncover that we have only explored the superficial surface of the huge genetic diversity present on the Earth. Several fundamental questions, viz.: “How many number of microbial species are there on the Earth?”, “Which factors shape the community structure?”, “To what extend their metabolic activities are diverse?” are still of great ecological concern. Assessment of microbial community composition in an environmental sample is a great challenge due to the chances of error at various levels such as extraction of metagenomic DNA from environmental sample, number of samples for analysis, influence of other environmental factors that are not under consideration. PCR amplification, technical issues and limited tools for result analysis and interpretation.

All of the molecular tools available for community structure analysis are hampered with limitations, and none of the method provides a comprehensive and overall picture of complex microbial community. However, it has been highly recommended that any investigation should deal with both culture-dependent and -independent methods, particularly in the studies that deal with effect of anthropogenic activities on microbial diversity.

Advancements in NGS has already surpassed the use of molecular finger-printing methods and significantly contributed towards the understating of microbial ecology. The launch of frugal innovative technology such as Oxford’s Nauopore is expected to be a superior culture-independent approach in analysing microbial community. Integrated technologies of different meta-omic approaches, viz., metagenomics, metatranscriptomics and metaproteomics with in situ geochemistry could afford a more comprehensive data on host microbiome and indigenous microbial diversity along with theh potential functions. Moreover, single cell genomics is reaching its peak with its ability to define microbial community at species level. Considering the fast leap of recent advancements, microbial diversity associated with any organism and/or habitat has become an attainable scientific goal.


The authors sincerely acknowledge the computational and bioinformatics facility provided by the Alagappa University Bioinformatics Infrastructure Facility (funded by DBT, GOI; File No. BT/BI/25/012/2012, BIF). The authors also thankfully acknowledge DST-FIST (Giant No. SR/FST/LSI-639/2015(C)), UGC-SAP (Grant No. F.5-1/2018/DRS-II (SAP-II)) and DST-PURSE (Grant No. SRPURSE Phase 2/38 (G)) for providing instrumentation facilities. Financial support provided to MR by RUSAPhase 2.0 [F.24-51/2014-U, Policy (TN Multi-Gen), Dept, ofEdn, Gol] in the form of Pli.D. Fellowship is also thankfully acknowledged.

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