Metagenomic Analyses: Past and Future Trends

Abstract

Metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. Metagenomics comprising construction and screening of metagenomic DNA libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. So far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. Recently, metagenomes of extreme environments have also been used as sources of novel biocatalysts. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body, and ocean water. Analyses of these data sets opened a window into the enormous taxonomic and functional diversity of environmental microbial communities. To assess the functional dynamics of microbial communities, metatranscriptomics and metaproteomics have been developed. The combination of DNA-based, mRNA-based, and protein-based analyses of microbial communities present in different environments is a way to elucidate the compositions, functions, and interactions of microbial communities and to link these to environmental processes.

Rumen microbial (meta)genomics and its application to ruminant production

“…Other potential targets include the biotransformation of compounds of interest for the animal or the consumer, such as antioxidants and conjugated linoleic acids or the detoxification of plant toxins, mycotoxins and xenobiotics. Other strategies used in functional metagenomic screening are the heterologous complementation of host strains and mutants and induction of reporter genes (Simon and Daniel, 2011). A drawback of this technique is that expression microbial hosts do not always express the proteins from other taxonomic groups in a functional form.…”

Poster abstracts of GCB 2015

“…In contrast to metagenomic sequences which just indicate the functional potential of the community, metatranscriptomic RNA-Seq data provides evidence for gene functions and metabolic activities that are actually performed by the community [SD11]. The experimental data consists of a large number of short sequencing reads which have to be classified according to the phylogenetic origin and putative functions.…”

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

“…Some natural habitats have extreme physicochemical conditions similar to those used in industrial processes (Antunes, Ngugi et al 2011). It has been determined that there are 10 6 -10 8 different genospecies of prokaryotes (Simon and Daniel 2011), surpassing the number of isolated microbial species by a factor of about 10 4 . Almost three decades ago, the well-known phrase in microbial ecology of the "great plate count anomaly" was coined to describe this mismatch in numbers (Staley and Konopka 1985).…”