Metagenomics approaches in systems microbiology

Abstract

The world of microorganisms comprises a vast diversity of live organisms, each with its individual set of genes, cellular components and metabolic reactions that interact within the cell and communicate with the environment in many different ways. There is a strong imperative to gain a broader view of the wired and interconnected cellular and environmental processes as a whole via the systems microbiology approach in order to understand and predict ecosystem functioning. On the other hand, currently we experience a rise of metagenomics as an emerging tool to study communities of uncultured microorganisms. In this review, we conducted a survey of important methodologies in metagenomics and describe systems microbiology-like approaches for gaining a mechanistic understanding of complex microbial systems to interrogate compositional, evolutionary and metabolic properties. The review also discusses how metagenomics can be used as a holistic indicator for ecosystem response in terms of matter, nutrient and energy sources and functional networking.

Targeted metagenomics of active microbial populations with stable-isotope probing

“…For low-diversity microbial habitats [5,6], including engineered environments [7], metagenomics can achieve relatively complete genomic coverage in metagenomic libraries with available sequencing capacity. However, although a 40,000-fosmid library might capture 40 around 400 genomes of an average size of 4 Mbp [8], this falls short of capturing the majority of taxa in a species-rich environment, such as soil, which has potentially greater than 10 5 different genomes per g of material [8]. Because of the potential limitations associated with high diversity, metagenomic studies can be preceded by careful selection of environmental samples in order to target a particular set of microorganisms and enzymes with specific activity profiles that may be 45 enriched.…”

A Novel Cold Active Esterase from a Deep Sea Sponge Stelletta normani Metagenomic Library

“…Thus, microbial communities which have adapted to these extremes of temperature, salinity, pressure, and low levels of light are likely to possess novel biochemistry; and have enzymes that may be uniquely suited to many industrial processes (Alcaide et al, 2015a). In addition seawater samples are an extremely rich source of potential biocatalytic biodiversity when one considers that with bacteria capable of achieving densities of up to 10 6 per milliliter of seawater (Azam, 1998), and assuming that there are ∼3,000 genes in a single genome and that 40% of these genes have catalytic activity then there may be as many as 3 × 10 9 genes mediating up to 1·2 × 10 9 putative reactions in a milliliter of seawater (Dinsdale et al, 2008;Vieites et al, 2009). Thus, although the deep sea is likely to be a rich source of microbial biocatalytic biodiversity, very few studies have to date attempted to access or exploit this biodiversity; most likely due to both the technical difficulties and costs associated with sampling at lower depths.…”

Diversity of Glycosyl Hydrolases from Cellulose-Depleting Communities Enriched from Casts of Two Earthworm Species

“…The habitats of microorganisms with great GH diversity are the ruminant animal rumen, mouse bowel, and rabbit cecum (10,24,26,28,49,74). Microorganisms associated with soil invertebrates in general and with soil earthworms in particular carry out metabolic processes that contribute to element cycling and are essential in sustaining processes which their hosts are unable to perform (20,52,72,76). Although some species of earthworms produce cellulases (15,55), they generally rely on microbes inhabiting their gastrointestinal (GI) tracts to perform cellulose utilization processes (31,47,77).…”