Customization of a DADA2-based pipeline for fungal internal transcribed spacer 1 (ITS1) amplicon data sets

Identification and analysis of fungal communities commonly rely on internal transcribed spacer-based (ITS-based) amplicon sequencing. There is no gold standard used to infer and classify fungal constituents since methodologies have been adapted from analyses of bacterial communities. To achieve high...

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Vydáno v:JCI insight Ročník 7; číslo 1
Hlavní autoři: Rolling, Thierry, Zhai, Bing, Frame, John, Hohl, Tobias M., Taur, Ying
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States American Society for Clinical Investigation 11.01.2022
American Society for Clinical investigation
Témata:
Annotations
Bayesian analysis
Biological variation
Datasets
Discrimination
Infectious disease
Microbiology
Microbiota
Resource and Technical Advance
Ribosomal DNA
Saccharomyces cerevisiae
Taxonomy
Yeast
Microbiology
Infectious disease
Fungal infections
ISSN:2379-3708, 2379-3708
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Shrnutí:Identification and analysis of fungal communities commonly rely on internal transcribed spacer-based (ITS-based) amplicon sequencing. There is no gold standard used to infer and classify fungal constituents since methodologies have been adapted from analyses of bacterial communities. To achieve high-resolution inference of fungal constituents, we customized a DADA2-based pipeline using a mix of 11 medically relevant fungi. While DADA2 allowed the discrimination of ITS1 sequences differing by single nucleotides, quality filtering, sequencing bias, and database selection were identified as key variables determining the accuracy of sample inference. Due to species-specific differences in sequencing quality, default filtering settings removed most reads that originated from Aspergillus species, Saccharomyces cerevisiae, and Candida glabrata. By fine-tuning the quality filtering process, we achieved an improved representation of the fungal communities. By adapting a wobble nucleotide in the ITS1 forward primer region, we further increased the yield of S. cerevisiae and C. glabrata sequences. Finally, we showed that a BLAST-based algorithm based on the UNITE+INSD or the NCBI NT database achieved a higher reliability in species-level taxonomic annotation compared with the naive Bayesian classifier implemented in DADA2. These steps optimized a robust fungal ITS1 sequencing pipeline that, in most instances, enabled species-level assignment of community members.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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Authorship note: TMH and YT are co–senior authors.
ISSN:2379-3708
2379-3708
DOI:10.1172/jci.insight.151663