RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

Abstract

The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

“…Genomics and metagenomics are powerful tools for analyzing microbial communities at the genomic level from various contaminated environments. This technology gives a new array to environmental microbiologists for understanding unculturable microbiota with a genetic variability of microbial communities (Devarapalli and Kumavnath, 2015 ; Zhu et al, 2018 ; Awasthi et al, 2020 ). It gives more details about the particular degradation potential of microbial communities, as it directly entails the whole-genome sequence from environmental samples ( Table 1 ).…”

Omics-Driven Biotechnology for Industrial Applications

“…Metagenomics studies the structure and function of genetic material in complex samples of multi-organisms as well as of entire microbial communities without a cultivation step and can offer a solution for such challenges and facilitate the discovery of novel genes, enzymes, and metabolic pathways. Metagenomics analyses are classified as sequence-based and function-based screening, which are used to discover and identify, respectively, novel natural genes and compounds from environmental samples (Chistoserdova, 2010 ; Gilbert and Heiner, 2015 ; Kumar Awasthi et al, 2020 ). For example, metagenomics is actively used in agricultural research to understand the microbial communities in the soil system (Durot et al, 2009 ), to examine various microbes that can stimulate the cycling of macro- and micro-nutrients, and the release of essential enzymes, which enhance crop production (Cupples, 2005 ).…”

Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches

“…The metagenomic information will enable researchers to integrate pure culture study with genomics (Hodkinson and Grice, 2015). It uses the pool of environmental genomes of microorganisms which increases the probability to discover unique genes and diverse pathways with new enzymes containing highly specific catalytic properties (Scholz et al, 2012;Yergeau et al, 2017;Awasthi et al, 2020). Due to the dearth of high-throughput sequencing technologies and software early metagenomic studies were focused on environments like acid mine drainage and the human gut microbiome.…”

“…have been studied using metagenomics which provides infinite chances for bioprospecting and exploring of novel biomolecules like proteins, enzymes, etc. (Oulas et al, 2015;Awasthi et al, 2020).…”

“…The method to access the microbial world remains immensely perplexing, as the majority of microbes in the environment are non-culturable under in-vitro conditions (Handelsman, 2004). Only a petite percent of microorganisms from diverse environment samples are actively culturable effortlessly and thus not accessible for fundamental research (Dickson et al, 2014;Bursle and Robson, 2016;Awasthi et al, 2020).…”