Critical Issues in Mycobiota Analysis

Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G Thallinger, Gregor Gorkiewicz

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Fungi constitute an important part of the human microbiota and they play a significant role for health and disease development. Advancements made in the culture-independent analysis of microbial communities have broadened our understanding of the mycobiota, however, microbiota analysis tools have been mainly developed for bacteria (e.g., targeting the 16S rRNA gene) and they often fall short if applied to fungal marker-gene based investigations (i.e., internal transcribed spacers, ITS). In the current paper we discuss all major steps of a fungal amplicon analysis starting with DNA extraction from specimens up to bioinformatics analyses of next-generation sequencing data. Specific points are discussed at each step and special emphasis is placed on the bioinformatics challenges emerging during operational taxonomic unit (OTU) picking, a critical step in mycobiota analysis. By using an in silico ITS1 mock community we demonstrate that standard analysis pipelines fall short if used with default settings showing erroneous fungal community representations. We highlight that switching OTU picking to a closed reference approach greatly enhances performance. Finally, recommendations are given on how to perform ITS based mycobiota analysis with the currently available measures.

Original languageEnglish
Article number180
JournalFrontiers in Microbiology
Volume8
DOIs
Publication statusPublished - 2017

Fingerprint

Microbiota
Computational Biology
Fungal Genes
rRNA Genes
Computer Simulation
Fungi
Bacteria
DNA
Health

Keywords

  • Journal Article

Cite this

Halwachs, B., Madhusudhan, N., Krause, R., Nilsson, R. H., Moissl-Eichinger, C., Högenauer, C., ... Gorkiewicz, G. (2017). Critical Issues in Mycobiota Analysis. Frontiers in Microbiology , 8, [180]. https://doi.org/10.3389/fmicb.2017.00180

Critical Issues in Mycobiota Analysis. / Halwachs, Bettina; Madhusudhan, Nandhitha; Krause, Robert; Nilsson, R Henrik; Moissl-Eichinger, Christine; Högenauer, Christoph; Thallinger, Gerhard G; Gorkiewicz, Gregor.

In: Frontiers in Microbiology , Vol. 8, 180, 2017.

Research output: Contribution to journalArticleResearchpeer-review

Halwachs, B, Madhusudhan, N, Krause, R, Nilsson, RH, Moissl-Eichinger, C, Högenauer, C, Thallinger, GG & Gorkiewicz, G 2017, 'Critical Issues in Mycobiota Analysis' Frontiers in Microbiology , vol. 8, 180. https://doi.org/10.3389/fmicb.2017.00180
Halwachs B, Madhusudhan N, Krause R, Nilsson RH, Moissl-Eichinger C, Högenauer C et al. Critical Issues in Mycobiota Analysis. Frontiers in Microbiology . 2017;8. 180. https://doi.org/10.3389/fmicb.2017.00180
Halwachs, Bettina ; Madhusudhan, Nandhitha ; Krause, Robert ; Nilsson, R Henrik ; Moissl-Eichinger, Christine ; Högenauer, Christoph ; Thallinger, Gerhard G ; Gorkiewicz, Gregor. / Critical Issues in Mycobiota Analysis. In: Frontiers in Microbiology . 2017 ; Vol. 8.
@article{5c29f998786e4431afc1d272a999684b,
title = "Critical Issues in Mycobiota Analysis",
abstract = "Fungi constitute an important part of the human microbiota and they play a significant role for health and disease development. Advancements made in the culture-independent analysis of microbial communities have broadened our understanding of the mycobiota, however, microbiota analysis tools have been mainly developed for bacteria (e.g., targeting the 16S rRNA gene) and they often fall short if applied to fungal marker-gene based investigations (i.e., internal transcribed spacers, ITS). In the current paper we discuss all major steps of a fungal amplicon analysis starting with DNA extraction from specimens up to bioinformatics analyses of next-generation sequencing data. Specific points are discussed at each step and special emphasis is placed on the bioinformatics challenges emerging during operational taxonomic unit (OTU) picking, a critical step in mycobiota analysis. By using an in silico ITS1 mock community we demonstrate that standard analysis pipelines fall short if used with default settings showing erroneous fungal community representations. We highlight that switching OTU picking to a closed reference approach greatly enhances performance. Finally, recommendations are given on how to perform ITS based mycobiota analysis with the currently available measures.",
keywords = "Journal Article",
author = "Bettina Halwachs and Nandhitha Madhusudhan and Robert Krause and Nilsson, {R Henrik} and Christine Moissl-Eichinger and Christoph H{\"o}genauer and Thallinger, {Gerhard G} and Gregor Gorkiewicz",
year = "2017",
doi = "10.3389/fmicb.2017.00180",
language = "English",
volume = "8",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media S. A.",

}

TY - JOUR

T1 - Critical Issues in Mycobiota Analysis

AU - Halwachs, Bettina

AU - Madhusudhan, Nandhitha

AU - Krause, Robert

AU - Nilsson, R Henrik

AU - Moissl-Eichinger, Christine

AU - Högenauer, Christoph

AU - Thallinger, Gerhard G

AU - Gorkiewicz, Gregor

PY - 2017

Y1 - 2017

N2 - Fungi constitute an important part of the human microbiota and they play a significant role for health and disease development. Advancements made in the culture-independent analysis of microbial communities have broadened our understanding of the mycobiota, however, microbiota analysis tools have been mainly developed for bacteria (e.g., targeting the 16S rRNA gene) and they often fall short if applied to fungal marker-gene based investigations (i.e., internal transcribed spacers, ITS). In the current paper we discuss all major steps of a fungal amplicon analysis starting with DNA extraction from specimens up to bioinformatics analyses of next-generation sequencing data. Specific points are discussed at each step and special emphasis is placed on the bioinformatics challenges emerging during operational taxonomic unit (OTU) picking, a critical step in mycobiota analysis. By using an in silico ITS1 mock community we demonstrate that standard analysis pipelines fall short if used with default settings showing erroneous fungal community representations. We highlight that switching OTU picking to a closed reference approach greatly enhances performance. Finally, recommendations are given on how to perform ITS based mycobiota analysis with the currently available measures.

AB - Fungi constitute an important part of the human microbiota and they play a significant role for health and disease development. Advancements made in the culture-independent analysis of microbial communities have broadened our understanding of the mycobiota, however, microbiota analysis tools have been mainly developed for bacteria (e.g., targeting the 16S rRNA gene) and they often fall short if applied to fungal marker-gene based investigations (i.e., internal transcribed spacers, ITS). In the current paper we discuss all major steps of a fungal amplicon analysis starting with DNA extraction from specimens up to bioinformatics analyses of next-generation sequencing data. Specific points are discussed at each step and special emphasis is placed on the bioinformatics challenges emerging during operational taxonomic unit (OTU) picking, a critical step in mycobiota analysis. By using an in silico ITS1 mock community we demonstrate that standard analysis pipelines fall short if used with default settings showing erroneous fungal community representations. We highlight that switching OTU picking to a closed reference approach greatly enhances performance. Finally, recommendations are given on how to perform ITS based mycobiota analysis with the currently available measures.

KW - Journal Article

U2 - 10.3389/fmicb.2017.00180

DO - 10.3389/fmicb.2017.00180

M3 - Article

VL - 8

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

M1 - 180

ER -