Comparative analysis of full-length 16s ribosomal RNA genome sequencing in human fecal samples using primer sets with different degrees of degeneracy.
16S rRNA
MinION Mk1C
gut microbiome
human fecal microbiome
nanopore sequencing
next-generation sequencing (NGS)
oxford nanopore technologies (ONT)
primer degeneracy
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2023
2023
Historique:
received:
28
04
2023
accepted:
10
07
2023
medline:
11
8
2023
pubmed:
11
8
2023
entrez:
11
8
2023
Statut:
epublish
Résumé
Next-generation sequencing has revolutionized the field of microbiology research and greatly expanded our knowledge of complex bacterial communities. Nanopore sequencing provides distinct advantages, combining cost-effectiveness, ease of use, high throughput, and high taxonomic resolution through its ability to process long amplicons, such as the entire 16s rRNA genome. We examine the performance of the conventional 27F primer (27F-I) included in the 16S Barcoding Kit distributed by Oxford Nanopore Technologies (ONT) and that of a more degenerate 27F primer (27F-II) in the context of highly complex bacterial communities in 73 human fecal samples. The results show striking differences in both taxonomic diversity and relative abundance of a substantial number of taxa between the two primer sets. Primer 27F-I reveals a significantly lower biodiversity and, for example, at the taxonomic level of the phyla, a dominance of
Identifiants
pubmed: 37564874
doi: 10.3389/fgene.2023.1213829
pii: 1213829
pmc: PMC10411958
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1213829Informations de copyright
Copyright © 2023 Waechter, Fehse, Welzel, Heider, Babalija, Cheko, Mueller, Pöling, Braun, Pankuweit, Weihe, Kinscherf, Schieffer, Luesebrink, Soufi and Ruppert.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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