Alili R. auteur aut IRD Belda E. auteur aut IRD Le P. auteur aut IRD Wirth T. auteur aut IRD Zucker Jean-Daniel auteur aut IRD Prifti Edi auteur aut IRD Clement K. auteur aut IRD text journalArticle eng text/pdf reformatted digital access The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed for characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenge. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Here, we propose a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatics protocol to analyze ONT sequences taxonomically and functionally and optimized preanalytic protocols, including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence alignment and classification. Our protocol was evaluated using simulations of metagenomic communities, which reflect naturally occurring compositional variations. Next, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with ONT, Illumina, and SOLiD technologies. Results revealed similar diversity and microbial composition profiles. This protocol can be implemented in a clinical or research setting, bringing rapid personalized whole-genome profiling of target microbiome species. specialized semi-quantitative metagenomics microbiome obesity gut microbiota microbial DNA extraction sequencing simulation Oxford Nanopore Technologies MinION 054 084 020 12 10 1496 [21 p.] 2021 https://www.documentation.ird.fr/hor/fdi:010083309 10.3390/genes12101496 [F B010083309] https://www.documentation.ird.fr/hor/fdi:010083309 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2021-12/010083309.pdf IRD - Base Horizon / Pleins textes 2021-12-03 2025-02-24 fdi:010083309 fre