In a context of climate change, food security and population monitoring, DIAG4ZOO has carried out for an aquaculture production company, analyses by integrative approach of viral and bacterial communities (microbiomes) present in different samples such as eggs, larvae and fish (gills and fins by non-lethal sampling) as well as in the environment of the animal: water. The analysis of this microbiome plays a major role in the prevention of diseases or mortalities, but especially in the quality of life of the fish, and thus its growth and the quality of its flesh.
Microbiome analysis method
These metagenomic analyses are performed in several steps:
- extraction and purification of the DNAs present in the sample,
- qualification of the DNAs,
- PCR amplification and sequencing of the qualified DNAs on the latest generation of high-throughput platforms,
- bioinformatics and biostatistical analysis of the sequence data.
Depending on the expected results and their purpose (unannounced monitoring or implementation of a routine monitoring tool), DIAG4ZOO targets either a variable region of the 16S ribosomal RNA gene carried and encoded by the ribosomal DNA, or the entire ribosomal DNA.
In the present study, the first approach was implemented and the targeted metagenomic sequences from the microbiome were analyzed using the bioinformatics pipeline established by DIAG4ZOO.
This work has thus allowed to identify the structuring of prokaryotic communities, also called operational taxonomic units (OTUs), in the different samples.
The result is a classification of the reads at several taxonomic levels: phylum, class, order, family, genus and species.
More generally, the DIAG4ZOO scientific team has a significant experience in Barcoding and Metabarcoding approaches, techniques based on the extraction and the high throughput sequencing of DNA, that is contained in several samples, even heterogeneous, with multiple applications: detection of pathogens, invasive species, monitoring of taxonomic groups, study of diets…