@article{fdi:010083309,
  title = {{E}xploring semi-quantitative metagenomic studies using {O}xford nanopore sequencing : a computational and experimental protocol},
  author = {{A}lili, {R}. and {B}elda, {E}. and {L}e, {P}. and {W}irth, {T}. and {Z}ucker, {J}ean-{D}aniel and {P}rifti, {E}di and {C}lement, {K}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. {L}arge-scale sequencing projects allowed for characterizing the perturbations of these communities. {H}owever, translating these discoveries into clinical applications remains a challenge. {T}o facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. {H}ere, we propose a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of human gut microbiome with {O}xford {N}anopore sequencing technology ({ONT}) that could be applied to other microbial ecosystems. {W}e 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. {T}his is a critical parameter for the sequence alignment and classification. {O}ur protocol was evaluated using simulations of metagenomic communities, which reflect naturally occurring compositional variations. {N}ext, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with {ONT}, {I}llumina, and {SOL}i{D} technologies. {R}esults revealed similar diversity and microbial composition profiles. {T}his protocol can be implemented in a clinical or research setting, bringing rapid personalized whole-genome profiling of target microbiome species.},
  keywords = {semi-quantitative metagenomics ; microbiome ; obesity ; gut microbiota ; microbial {DNA} extraction ; sequencing ; simulation ; {O}xford {N}anopore ; {T}echnologies ; {M}in{ION}},
  booktitle = {},
  journal = {{G}enes},
  volume = {12},
  numero = {10},
  pages = {1496 [21 p.]},
  year = {2021},
  DOI = {10.3390/genes12101496},
  URL = {https://www.documentation.ird.fr/hor/fdi:010083309},
}