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Search: AMNE:(NATURAL SCIENCES) AMNE:(Biological Sciences) AMNE:(Genetics) > (2010-2019) > Critical Issues in ...

LIBRIS Formathandbok  (Information om MARC21)
FältnamnIndikatorerMetadata
00004789naa a2200685 4500
001oai:gup.ub.gu.se/250506
003SwePub
008240528s2017 | |||||||||||000 ||eng|
0247 a https://gup.ub.gu.se/publication/2505062 URI
0247 a https://doi.org/10.3389/fmicb.2017.001802 DOI
040 a (SwePub)gu
041 a eng
042 9 SwePub
072 7a ref2 swepub-contenttype
072 7a art2 swepub-publicationtype
1001 a Halwachs, Bettina4 aut
2451 0a Critical Issues in mycobiota analysis
264 c 2017-02-14
264 1b Frontiers Media SA,c 2017
338 a electronic2 rdacarrier
520 a 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.
650 7a NATURVETENSKAPx Biologix Biologisk systematik0 (SwePub)106122 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Biological Systematics0 (SwePub)106122 hsv//eng
650 7a NATURVETENSKAPx Biologix Mikrobiologi0 (SwePub)106062 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Microbiology0 (SwePub)106062 hsv//eng
650 7a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Mikrobiologi inom det medicinska området0 (SwePub)301092 hsv//swe
650 7a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Microbiology in the medical area0 (SwePub)301092 hsv//eng
650 7a NATURVETENSKAPx Biologi0 (SwePub)1062 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciences0 (SwePub)1062 hsv//eng
650 7a NATURVETENSKAPx Biologix Botanik0 (SwePub)106072 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Botany0 (SwePub)106072 hsv//eng
650 7a NATURVETENSKAPx Biologix Genetik0 (SwePub)106092 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Genetics0 (SwePub)106092 hsv//eng
650 7a MEDICIN OCH HÄLSOVETENSKAPx Klinisk medicinx Infektionsmedicin0 (SwePub)302092 hsv//swe
650 7a MEDICAL AND HEALTH SCIENCESx Clinical Medicinex Infectious Medicine0 (SwePub)302092 hsv//eng
650 7a NATURVETENSKAPx Biologix Ekologi0 (SwePub)106112 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Ecology0 (SwePub)106112 hsv//eng
650 7a NATURVETENSKAPx Biologix Bioinformatik och systembiologi0 (SwePub)106102 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Bioinformatics and Systems Biology0 (SwePub)106102 hsv//eng
653 a microbiota
653 a mycobiota
653 a internal transcribed spacer (ITS)
653 a 16S rRNA gene
653 a multiple sequence alignment (MSA)
653 a OTU picking
653 a formalin-fixed paraffin-embedded tissue (FFPE)
653 a DNA isolation
7001 a Madhusudhan, N4 aut
7001 a Krause, R4 aut
7001 a Nilsson, R. Henrik,d 1976u Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences4 aut0 (Swepub:gu)xnihen
7001 a Moissl-Eichinger, C4 aut
7001 a Hoegenauer, C4 aut
7001 a Thallinger, GG4 aut
7001 a Gorkiewicz, G4 aut
7102 a Göteborgs universitetb Institutionen för biologi och miljövetenskap4 org
7730 t Frontiers in Microbiologyd : Frontiers Media SAg 8q 8x 1664-302X
8564 u https://gup.ub.gu.se/publication/250506x primaryx freey FULLTEXT
8564 u https://www.frontiersin.org/articles/10.3389/fmicb.2017.00180/pdf
8564 8u https://gup.ub.gu.se/publication/250506
8564 8u https://doi.org/10.3389/fmicb.2017.00180

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