{"id":66,"date":"2022-02-04T09:47:23","date_gmt":"2022-02-04T08:47:23","guid":{"rendered":"https:\/\/pgtb.fr\/?page_id=66"},"modified":"2026-05-19T13:59:16","modified_gmt":"2026-05-19T11:59:16","slug":"la-metagenomique-ciblee","status":"publish","type":"page","link":"https:\/\/pgtb.fr\/en\/la-metagenomique-ciblee\/","title":{"rendered":"Targeted metagenomic (metabarcoding)"},"content":{"rendered":"

Targeted metagenomics (metabarcoding) enables the identification of organisms (bacteria, archaea, eukaryotes) present in complex environments (tissues, faeces, saliva, soil samples, water, air, food, etc.). This method, which is an alternative to culturing samples in the laboratory, is based on the analysis of environmental DNA using next-generation sequencing (NGS) of targeted DNA regions, which have been previously amplified by PCR.<\/p>\n\n\n\n

Metabarcoding analysis using next-generation sequencing (NGS) involves several steps. First, total DNA is extracted from the sample, after which a taxonomically informative marker common to a specific group of interest is amplified. It is also possible to analyse several markers of interest simultaneously using multiplexing. The resulting amplicons are sequenced and analysed using bioinformatics to determine which organisms are present in the sample and their relative abundance. <\/p>\n\n\n

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PGTB offers this analysis as short-read sequencing on Illumina\u2019s MiSeq i100 and NextSeq 2000 sequencers, and as long-read sequencing on Oxford Nanopore Technologies\u2019 PromethION 2 Solo sequencer:<\/p>\n\n\n\n

 <\/td>Short read<\/strong><\/td>Long read<\/strong><\/td><\/tr>
Maximum number of sequences per run<\/td>300 M (2×300 pb)<\/td>5 M<\/td><\/tr>
Maximum number of samples per run<\/td>1140<\/td>96<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

IMPORTANT <\/strong>: For targeted metagenomic analyses, Illumina recommends using 35% PhiX to avoid compromising the quality of the data produced due to the lack of diversity in this type of library. We follow these recommendations, which results in a proportional reduction in the number of usable reads.<\/p>\n\n\n\n

The PGTB also provides a dedicated DNA laboratory<\/a> for the extraction of DNA from environmental samples and the preparation of libraries under optimal conditions.<\/p>\n\n\n\n

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