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© Carmen Buchrieser, Marie-Christine Prevost
Legionella pneumophila et son flagelle, bactérie responsable de pneumopathie aigue grave. Bactérie de l'environnement , l'émergence récente de cette maladie s'explique par son affinité pour les systèmes modernes d'alimentation en eau comme les tours de refroidissement. Image colorisée.
Publication : Microbial genomics

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Microbial genomics - 24 Jul 2020

Pérez-Cobas AE, Gomez-Valero L, Buchrieser C,

Link to Pubmed [PMID] – 32706331

Link to DOI [DOI] – 10.1099/mgen.0.000409

Microb Genom 2020 Jul; ():

Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.

https://pubmed.ncbi.nlm.nih.gov/32706331