AUTHOR=Waechter Christian , Fehse Leon , Welzel Marius , Heider Dominik , Babalija Lek , Cheko Juan , Mueller Julian , Pöling Jochen , Braun Thomas , Pankuweit Sabine , Weihe Eberhard , Kinscherf Ralf , Schieffer Bernhard , Luesebrink Ulrich , Soufi Muhidien , Ruppert Volker TITLE=Comparative analysis of full-length 16s ribosomal RNA genome sequencing in human fecal samples using primer sets with different degrees of degeneracy JOURNAL=Frontiers in Genetics VOLUME=14 YEAR=2023 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1213829 DOI=10.3389/fgene.2023.1213829 ISSN=1664-8021 ABSTRACT=
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