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

doi:10.1038/s41597-022-01762-z

Benchmarking second and third-generation sequencing platforms for microbial metagenomics

Journal Article · Thu Nov 10 23:00:00 EST 2022 · Scientific Data

DOI:https://doi.org/10.1038/s41597-022-01762-z· OSTI ID:1898987

^[1]; ^[1]; Da Silva, Kévin ^[1]; ^[1]; Pons, Nicolas ^[1]; Roume, Hugo ^[1]; ^[2]; ^[1]

Univ. Paris-Saclay, Gif-sur-Yvette (France); French National Research Institute for Agriculture, Food and Environment (INRAE), Champenoux (France)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); European Union (EU); Metagenopolis; National Institute of Dental and Craniofacial Research; National Institutes of Health (NIH)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1898987

Journal Information:: Scientific Data, Journal Name: Scientific Data Journal Issue: 1 Vol. 9; ISSN 2052-4463

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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