NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective

Claudia Colabella, Laura Corte, Luca Roscini, Matteo Bassetti, Joseph C Mellor, Wieland Meyer, Vincent Albert Romain Ghislain Robert, D. Vu, Gianluigi Cardinali

Research output: Contribution to journal/periodicalArticleScientificpeer-review

21 Citations (Scopus)

Abstract

Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.
Original languageEnglish
Pages (from-to)91-105
Number of pages15
JournalIMA Fungus
DOIs
Publication statusPublished - 09 Jun 2018

Fingerprint

Dive into the research topics of 'NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective'. Together they form a unique fingerprint.

Cite this