Microbiological diagnosis

points microbia environnement  Genetic inventory of the microbial community by next-generation sequencing

A sudden change or a recurrent problem in your site? You are wondering how ‘healthy’ is your ecosystem? 

We propose to make a check-up by inventorying the whole of microbial populations present in water by metabarcoding.

This approach relies on high-throughput sequencing and bioinformatics processing. We basically target a broad spectrum of microorganisms using the genetic material directly extracted from water samples.

An exhaustive semi-quantitative list of species is generated giving a comprehensive overview of the microbial community.

Metabarcoding represents a cutting-edge technology in the field of applied ecology since microorganisms are largely disregarded in traditionnal visual inventories due to the the poor accuracy of taxonomic identification by microscopy.

When used repetitively (monitoring programs) and/or at key moments, relying metabacoding data with field observations makes possible to evaluate and to follow-up with the state of health of an ecosystem, thanks to organisms identified as bioindicators.

Identification and Monitoring of bioindicators and/or toxic microorganisms


Microbia Environnement proposes metabarcoding services, consisting of :

  • Customized water sampling strategy
  • Genetic and environmental data acquisition
  • Detailed reporting of microbiological status of the ecosystem (health status)
  • Tech support and recommendations to optimize management of your site, with option of deploying an early-warning system for toxic blooms using our specific genetic biosensors.

points microbia environnement  Complete diagnosis of toxic species-associated risk with M.A.R.T.A.

Is there any toxin-producing microorganisms in your water? Is it possible to identify them, to estimate their number, to follow their activity within time? To answer these questions, we perform a high-sensitivity molecular diagnosis and we provide you with clear guidelines to engage actions in case of risk.

M.A.R.T.A. =  MicroArray for RNA detection of Toxic Algae is a lab-on-chip detection platform enabling:

  • Identification of toxic microalgae the most commonly observed in marine environments, i.e. an overview of 30 genera/species
  • Estimation of the respective cellular activities 
  • Simultaneous monitoring of the different populations within time
A technology under the patent N° WO2015008011


Based on site characteristics and environmental parameters (e.g. pH, temperature, wind), the Microbia Environnement team sets up a specific workflow to follow the algal community overtime, focusing on critical periods to adjust alarm thresholds for toxic blooms.

The complete list of targeted microalgae is available on request.

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