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Benchmarking second and third-generation sequencing platforms for microbial metagenomics.
Meslier, Victoria; Quinquis, Benoit; Da Silva, Kévin; Plaza Oñate, Florian; Pons, Nicolas; Roume, Hugo; Podar, Mircea; Almeida, Mathieu.
Afiliação
  • Meslier V; Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France.
  • Quinquis B; Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France.
  • Da Silva K; Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France.
  • Plaza Oñate F; Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France.
  • Pons N; Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France.
  • Roume H; Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France.
  • Podar M; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. podarm@ornl.gov.
  • Almeida M; Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France. mathieu.almeida@inrae.fr.
Sci Data ; 9(1): 694, 2022 11 11.
Article em En | MEDLINE | ID: mdl-36369227
Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Metagenômica / Microbiota Idioma: En Ano de publicação: 2022 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Metagenômica / Microbiota Idioma: En Ano de publicação: 2022 Tipo de documento: Article