Metagenomics – Definition, origin and uses

What is metagenomics?
“Metagenome” used by Handelsman et al., in 1998 to describe “collective genomes of soil microflora”

Metagenomics is the study of genetic material recovered directly from environmental samples.

“Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification”

The broad field may also be referred to as environmental genomics, ecogenomics or community genomics.

origin of metagenomics
The term metagenomics is derived and coined from the statistical concept of meta-analysis (the process of statistically combining separate analyses) and genomics (the comprehensive analysis of an organism’s genetic material) to capture the notion of analysis of a collection of similar but not identical items as in a meta-analysis which is an analysis of analyses.

The field initially started with the cloning of environmental DNA, followed by functional expression screening, and was then quickly complemented by direct random shotgun sequencing of environmental DNA. These initial projects not only showed proof of principle of the metagenomic approach, but also uncovered an enormous functional gene diversity in the microbial world around us

This approach has already opened new avenues of research by enabling unprecedented analyses of genome heterogeneity and evolution in environmental contexts and providing access to far more microbial diversity than that has been viewed in the petri dish.

Uses of metagenomics
Microbes of earth
Microbes are essential for all life on earth because they are involved with processes in the biosphere to convert key elements of life (e.g. carbon, nitrogen, oxygen, sulfur) into biologically accessible forms. These chemical cycles are dependent on microbes to continue and maintain environmental stability.

metagenomics-microbes on earth

Human life is hence intricately linked with microbial communities, which are responsible for the supply of nutrients, metals and vitamins. Microbes are directly involved in the process of fermentation, remediation of toxins, nutrient extraction and food digestion.

Microbial communities and human health
Given the essential role that microbes play in the health of humans and animals on earth, it may come as a surprise that the overwhelming majority of the microbial population that resides within humans has not been observed and researched significantly in the past.This opens up a new playing field for research in the field of metagenomics. If we are able to deepen our understanding of the microbial communities that regularly interact with humans, such as those that reside inside the gastrointestinal tract, this may shed some light on the interplay between microbes and human health. Microbes may encode metabolic pathways that are essential for survival of human life, even though they do not exist in the genome of humans.

Changes in the levels of microbes that regularly interact with humans may be associated with causing some health conditions, such as inflammatory bowel disease (IBD), cardiovascular disease, eczema or cancer

Limitations and pitfalls
Data used for analysis can have limitations:
• 16S rRNA genes has limited resolving power and subject to copy number variation.
• For Viral sequences, currently no gold-standard reference database.
• For Protist sequences,little experimentally-derived annotation of protein function in public databases different functional and taxonomic analysis tools can give different results.
• The same tools can give different results depending on the version and underlying algorithm (e.g., HMMER2 vs HMMER3)
• The same version of the same tools can give different results depending on the reference database used.

Metagenomic portals
EBI metagenomics: https://www.ebi.ac.uk/metagenomics/
MG-RAST: http://www.mg-rast.org/
IMG: https://img.jgi.doe.gov/
imicrobe:https://www.imicrobe.us/