Abstract
The study of mycobiota remains relatively unexplored due to the lack of sufficient available reference strains and databases compared to those of bacterial microbiome studies. Deep sequencing of Internal Transcribed Spacer (ITS) regions is the de facto standard for fungal diversity analysis. However, results are often biased because of the wide variety of sequence lengths in the ITS regions and the complexity of high-throughput sequencing (HTS) technologies. In this study, a curated ITS database, ntF-ITS1, was constructed. This database can be utilized for the taxonomic assignment of fungal community members. We evaluated the efficacy of strategies for mycobiome analysis by using this database and characterizing a mock fungal community consisting of 26 species representing 15 genera using ITS1 sequencing with three HTS platforms: Illumina MiSeq (MiSeq), Ion Torrent Personal Genome Machine (IonPGM), and Pacific Biosciences (PacBio). Our evaluation demonstrated that PacBio’s circular consensus sequencing with greater than 8 full-passes most accurately reconstructed the composition of the mock community. Using this strategy for deep-sequencing analysis of the gut mycobiota in healthy Japanese individuals revealed two major mycobiota types: a single-species type composed of Candida albicans or Saccharomyces cerevisiae and a multi-species type. In this study, we proposed the best possible processing strategies for the three sequencing platforms, of which, the PacBio platform allowed for the most accurate estimation of the fungal community. The database and methodology described here provide critical tools for the emerging field of mycobiome studies.
Highlights
Comprehensive analysis of bacterial communities has been made possible with the advent of high-throughput sequencing (HTS) technologies
The resulting sequences were converted into a format that was suitable for the Ribosomal Database Project (RDP) Classifier (Wang et al, 2007), and this was used as the database nt-Fungi-ITS1 for mycobiota analysis
Comparison of Ion Torrent Personal Genome Machine (IonPGM), MiSeq, and Pacific Biosciences (PacBio) ITS1 Sequencing for Characterization of a Fungal Community
Summary
Comprehensive analysis of bacterial communities (microbiota) has been made possible with the advent of high-throughput sequencing (HTS) technologies. This has led to understanding the composition of the gut microbiome as influenced by factors, such as genetic background, diet, and immune function. Various types of fungi are present in the intestines (Schulze and Sonnenborn, 2009; Chen et al, 2011; Dollive et al, 2012). Fungi in the intestines induce colitis through the activity of host Dectin-1, a C-type lectin receptor (Sonoyama et al, 2011; Iliev et al, 2012). Fungal communities (mycobiota) in the intestines clearly play an important role in the health of the host
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
