Technical articles



Metagenomics is a method for studying the microbiome, i.e., all the microorganisms (bacteria, viruses, fungi, yeasts, plankton, etc.) present in a specific environment (skin, organs, maritime environments, soil, air, etc.).

This approach, based on new generation sequencing techniques, allows to describe the content of the sample, but also to give an insight into the functional potential of the microbiome under study.

  1. Background

Micro-organisms, although invisible to the naked eye, are present everywhere; from water (rainwater, river water, etc.) to soils and other surfaces, including living beings or even the air. These micro-organisms can have no effect on their host or on the contrary interact closely with it with either good or bad outcome (mutualism, parasitism).

For example, the human body harbors an average of 1 to 2 kg of bacteria, distributed in various places. For example, the intestinal, vaginal, or cutaneous microbiotas participate in the healthy functioning of the body and can lead to pathologies if disturbed. Soil microbiotas contribute notably to the fertility and regeneration of soils and interact with the plants that grow there, particularly at the root level. In the ocean, bacteria participate in many chemical processes and are a food source for many other complex organisms (such as phytoplankton). Finally, the aerial microbiota has notably been suspected of promoting the transmission of diseases, such as COVID19.

For these reasons, metagenomics, i.e., the study and analysis of these microbiota, has been a very active area of research in recent decades.

  • Technical aspects

High-throughput sequencing, which provides access to information related to the DNAs found in one or more samples, generates very large amounts of data that must then be analyzed using bioinformatics and statistical methods. In addition, while the analysis of genomics data can be like solving a puzzle of millions of pieces, metagenomics consists of solving a dozen puzzles whose pieces are mixed. The development of metagenomics therefore requires powerful computational resources and solid skills to develop and manage the constantly evolving tools and databases.

Two main approaches to metagenomics exist:

• Sequencing of one or more marker genes specific to the species of interest (such as 16S RNA for bacteria or ITS for fungi). This is called targeted metagenomics or metabarcoding.

• Sequencing the whole genomes of all organisms present in a sample without distinction. This approach is usually referred to as shotgun metagenomics.

These two approaches have of course their own advantages and disadvantages which are summarized in the following table:

MetabarcodingQuick and inexpensive
Identification of a wide variety of bacteria and eukaryotes
No information on genes other than the targeted one
Amplification biasUnable to identify viruses
Characterization at species level can be difficult
Shotgun metagenomicsNo amplification bias
Detection of all bacteria, archae, viruses and eukaryotes in the sample
De novo assembly of genomes of undescribed species
Identification at species or even strain level
Need of a high sequencing depth
Contamination by the host: necessary discrimination of host sequences vs sequences associated with the microbiota
Usually need to have access to reference genomes for classification
  • Applications

Metagenomics is therefore of major interest for many areas of industry. The potential applications are limited only by imagination. Some examples of current projects:

  • Health:
    • Characterization and study of the intestinal microbiota in order to find new therapeutic targets (inflammatory diseases, allergies, cancers, etc.) or treatments by fecal transplantation
    • Detection of microorganisms in aerosols to improve epidemic monitoring
  • Agrifood:
    • Development of products rich in probiotics and study of the impacts on the digestive system
    • Soil optimization for plant cultivation
  • Hygiene:
    • Assessment of the sterility of surfaces production facilities 
    • Evaluation of the effectiveness of sterilization or protection devices such as gloves and masks
  • Ecology:
    • Study of the metabolic capacities of the microbial flora present in the wastewater treatment plants
    • Assessment of the impact of climate change on marine and telluric microbiota
  • Cosmetics:
    • Study of the impact of products on the skin and scalp microbiome

And many other examples exist!


Metagenomics has successfully demonstrated its usefulness through various projects in several fields and in particular in human health, but its potential remains largely untapped as shown by numerous growth projections of the metagenomics market.

The drop in sequencing costs and the evolution of methods and databases open the way to a whole new range of applications providing important added values, whether in terms of innovation or research and development.

Efor, European leader in Life Sciences, supports you at every step of your metagenomics projects, from the setup of the experimental plan to the development of computational solutions and the obtention and analysis of the data.

Our experts can support you in the different stages of your project.

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