ONT long-read sequencing and Illumina short-read sequencing of 16S rDNA amplicons give comparable results in terms of bacterial community structure in marine sediments
Fine-scale congruence in bacterial community structure from marine sediments sequenced by short-reads on Illumina and long-reads on Nanopore
Recommendation: posted 12 October 2023, validated 13 October 2023
Spor, A. (2023) ONT long-read sequencing and Illumina short-read sequencing of 16S rDNA amplicons give comparable results in terms of bacterial community structure in marine sediments. Peer Community in Microbiology, 100014. 10.24072/pci.microbiol.100014
ONT long-read high-throughput sequencing is not routinely used for metabarcoding studies of microbial communities. Even though this technology is supposed to considerably improve phylogenetic coverage and taxonomic resolution, it initially suffered from relatively poor read accuracy. Assessment of the performance of this new approach in comparison with routinely used 16S rDNA short-read sequencing is therefore needed to validate its use.
The study by Lemoinne et al. (2023) offers a comprehensive comparison of two 16S rDNA metabarcoding approaches on marine sediment samples. By comparing Illumina short-read sequencing with ONT long-read sequencing, the authors conclude that bacterial community structures inferred from both technologies were similar. They also found that differences observed between sampling sites and along the sea-land orientation were comparable between the two technologies. However, the choice of technology still has an impact on the obtained results, notably in terms of bacterial diversity retrieved, taxonomic resolution, and replicability between biological replicates.
Altogether, these results validate the use of ONT long-read sequencing for 16S metabarcoding approaches in marine sediments. Comparisons of such kinds targeting other remote environments are needed, as they might offer new opportunities for field scientists with no access to sequencing platforms to study the structure and composition of microbial communities.
Lemoinne, A., Dirberg, G., Georges, M., & Robinet, T. (2023). Fine-scale congruence in bacterial community structure from marine sediments sequenced by short-reads on Illumina and long-reads on Nanopore. biorXiv, version 3 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.06.06.541006
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Office Français de la Biodiversité (OFB) and BOREA lab (MNHN)
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2023.06.06.541006
Version of the preprint: 1
Author's Reply, 12 Sep 2023
Decision by Aymé Spor, posted 17 Jul 2023, validated 18 Jul 2023
Two reviewers have now evaluated your manuscript and given useful comments for improving its quality.
I suggest you take all the reviewers' comments into account for providing a revised version of the manuscript. More specifically, I would ask you to particularly take into account reviewer 2's comments regarding your experimental design (confounding factors between technologies and primers choice) and elaborate upon this in the revised version.