Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing
Microbiota research has received an increasing attention for its role in disease development and fungi are considered as one of the key players in the microbial niche. Various sequencing approaches have been applied to uncover the role of fungal community in health and disease; however, little is kn...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2022-12-01
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| Series: | Gut Microbes |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2022.2110638 |
| _version_ | 1811340892208889856 |
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| author | Crispin Wiesmann Konrad Lehr Juozas Kupcinskas Ramiro Vilchez-Vargas Alexander Link |
| author_facet | Crispin Wiesmann Konrad Lehr Juozas Kupcinskas Ramiro Vilchez-Vargas Alexander Link |
| author_sort | Crispin Wiesmann |
| collection | DOAJ |
| description | Microbiota research has received an increasing attention for its role in disease development and fungi are considered as one of the key players in the microbial niche. Various sequencing approaches have been applied to uncover the role of fungal community in health and disease; however, little is known on the performance of various primers and comparability between the studies. Motivated by the recent publications, we performed a systematic comparison of the 18S and ITS regions to identify the impact of various primers on the sequencing results. Using four pairs of primers extensively used in literature, fungal community was retrieve from 25 fecal samples, and applying high throughput sequencing; and the results were compared in order to select the most suitable primers for fungal detection in human fecal samples. Considering the high variability between samples, primers described in the Earth microbiome project detected the broadest fungal spectrum suggesting its superior performance in mycobiome research. |
| first_indexed | 2024-04-13T18:48:38Z |
| format | Article |
| id | doaj.art-f3330cf9573744c6b84eef2df2c2d3b7 |
| institution | Directory Open Access Journal |
| issn | 1949-0976 1949-0984 |
| language | English |
| last_indexed | 2024-04-13T18:48:38Z |
| publishDate | 2022-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj.art-f3330cf9573744c6b84eef2df2c2d3b72022-12-22T02:34:31ZengTaylor & Francis GroupGut Microbes1949-09761949-09842022-12-0114110.1080/19490976.2022.2110638Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencingCrispin Wiesmann0Konrad Lehr1Juozas Kupcinskas2Ramiro Vilchez-Vargas3Alexander Link4Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, GermanyDepartment of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, GermanyInstitute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, LithuaniaDepartment of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, GermanyDepartment of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, GermanyMicrobiota research has received an increasing attention for its role in disease development and fungi are considered as one of the key players in the microbial niche. Various sequencing approaches have been applied to uncover the role of fungal community in health and disease; however, little is known on the performance of various primers and comparability between the studies. Motivated by the recent publications, we performed a systematic comparison of the 18S and ITS regions to identify the impact of various primers on the sequencing results. Using four pairs of primers extensively used in literature, fungal community was retrieve from 25 fecal samples, and applying high throughput sequencing; and the results were compared in order to select the most suitable primers for fungal detection in human fecal samples. Considering the high variability between samples, primers described in the Earth microbiome project detected the broadest fungal spectrum suggesting its superior performance in mycobiome research.https://www.tandfonline.com/doi/10.1080/19490976.2022.2110638MycobiomeITS18Ssequencingfungi |
| spellingShingle | Crispin Wiesmann Konrad Lehr Juozas Kupcinskas Ramiro Vilchez-Vargas Alexander Link Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing Gut Microbes Mycobiome ITS 18S sequencing fungi |
| title | Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing |
| title_full | Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing |
| title_fullStr | Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing |
| title_full_unstemmed | Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing |
| title_short | Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing |
| title_sort | primers matter influence of the primer selection on human fungal detection using high throughput sequencing |
| topic | Mycobiome ITS 18S sequencing fungi |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2022.2110638 |
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