Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

Abstract

Advancement in the next generation sequencing technologies has led to evolution of the field of genomics and metagenomics in a slim duration with nominal cost at precipitous higher rate. While metagenomics and genomics can be separately used to reveal the culture-independent and culture-based microbial evolution, respectively, (meta)genomics together can be used to demonstrate results at population level revealing in-depth complex community interactions for specific ecotypes. The field of metagenomics which started with answering ''who is out there?'' based on 16S rRNA gene has evolved immensely with the precise organismal reconstruction at species/strain level from the deeply covered metagenome data outweighing the need to isolate bacteria of which 99% are de facto non-cultivable. In this review we have underlined the appeal of metagenomic-derived genomes in providing insights into the evolutionary patterns, growth dynamics, genome/gene-specific sweeps, and durability of environmental pressures. We have demonstrated the use of culturebased genomics and environmental shotgun metagenome data together to elucidate environment specific genome modulations via metagenomic recruitments in terms of gene loss/gain, accessory and core-genome extent. We further illustrated the benefit of (meta)genomics in the understanding of infectious diseases by deducing the relationship between human microbiota and clinical microbiology. This review summarizes the technological advances in the (meta)genomic strategies using the genome and metagenome datasets together to increase the resolution of microbial population studies.

Diversity of fungi from mangrove sediments of Goa, India, obtained by metagenomic analysis using Illumina sequencing

“…Till date, examination of fungal diversity and activities from mangroves of Goa relied on culture-based studies on individual and/or specific groups of fungi (Verma et al 2010;Nazareth et al 2011Nazareth et al , 2012Dastager et al 2012;Devi et al 2012;Nayak et al 2012;Bicholkar and Nazareth 2015). However, in the modern era of scientific advancements, 'omic' technologies are emerging as potential tools to ensure holistic insight into environmental systems, thereby leading to in-depth understanding of the complex mechanisms in an ecosystem (Sharma and Lal 2017). It forms a radical tool that helps to detect microbes and to decipher their full biological activities within the environmental niche which otherwise would have remained unnoticed due to our inability of mimicking their growth conditions under laboratory set-ups.…”

16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

“…The few microbial diversity studies that have been conducted were mainly culture-dependent [12]. Considering that about 98% of microbes are uncultivable, the 'omic' technologies are emerging as potential tools to ensure holistic insight into environmental systems [14] and this has led to the increasing application of high-throughput sequencing in studying microbial communities [10,15]. In this study, the vertical profiles of bacteria communities in the rhizospheres of four mangrove species namely, Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina, were determined and compared.…”

Taxonomic diversity of bacteria from mangrove sediments of Goa: metagenomic and functional analysis

“…Though there is an upsurge in interest on bacterial diversity of mangrove sediment in recent years, most of the studies on mangroves of Goa relied on the study of individual microorganisms through culture-based assays (Poharkar et al 2016;Kharangate and;Bhosle 2016). In modern era of scientific advancements, 'omic' technologies are emerging as potential tools to ensure holistic insight into environmental systems, thereby leading to in-depth understanding of the complex mechanisms in an ecosystem (Sharma and Lal 2017). It is a revolutionary tool that helps to detect microbes and to decipher their full biological activities within the environmental niche which, otherwise, would have remained unnoticed due to our inability of mimicking their growth conditions under laboratory set-ups.…”