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.
| Original language | English |
|---|---|
| Article number | 238 |
| Journal | Frontiers in Microbiology |
| Volume | 8 |
| Issue number | FEB |
| DOIs | |
| Publication status | Published - Feb 15 2017 |
Fingerprint
Keywords
- Fungi
- High-throughtput sequencing (HTS)
- Internal transcribed spacer (ITS)
- Mycobiota
- The gut mycobiota in Japanese
ASJC Scopus subject areas
- Microbiology
- Microbiology (medical)
Cite this
Fungal ITS1 deep-sequencing strategies to reconstruct the composition of a 26-species community and evaluation of the gut mycobiota of healthy Japanese individuals. / Motooka, Daisuke; Fujimoto, Kosuke; Tanaka, Reiko; Yaguchi, Takashi; Goto, Kazuyoshi; Maeda, Yuichi; Furuta, Yoki; Kurakawa, Takashi; Goto, Naohisa; Yasunaga, Teruo; Narazaki, Masashi; Kumanogoh, Atsushi; Horii, Toshihiro; Iida, Tetsuya; Takeda, Kiyoshi; Nakamura, Shota.
In: Frontiers in Microbiology, Vol. 8, No. FEB, 238, 15.02.2017.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Fungal ITS1 deep-sequencing strategies to reconstruct the composition of a 26-species community and evaluation of the gut mycobiota of healthy Japanese individuals
AU - Motooka, Daisuke
AU - Fujimoto, Kosuke
AU - Tanaka, Reiko
AU - Yaguchi, Takashi
AU - Goto, Kazuyoshi
AU - Maeda, Yuichi
AU - Furuta, Yoki
AU - Kurakawa, Takashi
AU - Goto, Naohisa
AU - Yasunaga, Teruo
AU - Narazaki, Masashi
AU - Kumanogoh, Atsushi
AU - Horii, Toshihiro
AU - Iida, Tetsuya
AU - Takeda, Kiyoshi
AU - Nakamura, Shota
PY - 2017/2/15
Y1 - 2017/2/15
N2 - 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.
AB - 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.
KW - Fungi
KW - High-throughtput sequencing (HTS)
KW - Internal transcribed spacer (ITS)
KW - Mycobiota
KW - The gut mycobiota in Japanese
UR - http://www.scopus.com/inward/record.url?scp=85014487797&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85014487797&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2017.00238
DO - 10.3389/fmicb.2017.00238
M3 - Article
AN - SCOPUS:85014487797
VL - 8
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
SN - 1664-302X
IS - FEB
M1 - 238
ER -