Fine-scale congruence in bacterial community structure from marine sediments sequenced by short-reads on Illumina and long-reads on Nanoporeuse asterix (*) to get italics

Alice Lemoinne, Guillaume Dirberg, Myriam Georges, Tony RobinetPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

2023

<p style="text-align: justify;">Following the development of high-throughput sequencers, environmental prokaryotic communities are usually described by metabarcoding with genetic markers on the 16S domain. However, short-read sequencing encounters a limitation in phylogenetic coverage and taxonomic resolution, due to the primers choice and read length. On these critical points, nanopore sequencing, a rising technology, suitable for long-read metabarcoding, was much undervalued because of its relatively higher error rate per read. Here we compared the prokaryotic community structure in a mock community and 52 sediment samples from two contrasted mangrove sites, described by short-reads on 16SV4-V5 marker (ca. 0.4kpb) analyzed by Illumina sequencing (MiSeq, V3), with those described by long-reads on bacterial nearly complete 16S (ca. 1.5 kpb) analyzed by Oxford Nanopore (MinION, R9.2). Short- and long-reads retrieved all the bacterial genera from the mock, although both showing similar deviations from the awaited proportions. From the sediment samples, with a coverage-based rarefaction of reads and after singletons filtering, co-inertia and Procrustean tests showed that bacterial community structures inferred from short- and long-reads were significantly similar, showing both a comparable contrast between sites and a coherent sea-land orientation within sites. In our dataset, 84.7 and 98.8% of the short-reads were assigned strictly to the same species and genus, respectively, than those detected by long-reads. Primer specificities of long-16S allowed it to detect 92.2% of the 309 families and 87.7% of the 448 genera that were detected by the short 16SV4-V5. Long-reads recorded 973 additional taxa not detected by short-reads, among which 91.7% were identified to the genus rank, some belonging to 11 exclusive phyla, albeit accounting for only 0.2% of total long-reads.</p>

https://github.com/tonyrobinet/nanopore_metabarcodingYou should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

https://github.com/tonyrobinet/nanopore_metabarcodingYou should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

microbial metabarcoding, environmental DNA, methods, primers, diversity

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Microbial ecology and environmental microbiology, Molecular microbiology

Rasmus Kirkegaard, Petra Pjevac, Craig Herbold, Kate Howell, Sebastien Massart, Nika Pende, Willem Stock, Vojtech Tlaskal, Olivier Gros, Mina Bizic, Aymé Spor, Konstantinos (Kostas) Kormas, A. Murat Eren, Graeme Nicol, Nadine Praeg No need for them to be recommenders of PCIMicrobiol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

2023-06-07 17:48:08

Aymé Spor