Related Experiment Video
Updated: Aug 31, 2025
Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
Published on: March 19, 2018
Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing
Crispin Wiesmann1, Konrad Lehr1, Juozas Kupcinskas2,3
1Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
Abstract:
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.
Insights
This study compared fungal DNA sequencing primers for human fecal samples. Primers from the Earth Microbiome Project showed the best performance for detecting a wide range of fungi in mycobiome research.
Area of Science:
- Microbiology
- Genetics
- Bioinformatics
Background:
- Fungi are key players in the human microbiome and disease development.
- Understanding fungal communities requires reliable sequencing methods.
- Comparability between studies is limited by primer variability.
Purpose of the Study:
- To systematically compare the performance of different primers for fungal DNA sequencing.
- To identify the most suitable primers for detecting the fungal community in human fecal samples.
- To assess the impact of primer choice on sequencing results.
Main Methods:
- Sequencing of the 18S and ITS regions from 25 human fecal samples.
- Utilized four pairs of commonly used fungal primers.
- Applied high-throughput sequencing technology.
- Compared results to evaluate primer performance.
Main Results:
- Significant variability was observed between different primer sets.
- Primers described in the Earth Microbiome Project detected the broadest fungal spectrum.
- This suggests superior performance for mycobiome research.
Conclusions:
- Primer selection critically impacts the detection of fungal communities.
- Earth Microbiome Project primers are recommended for comprehensive human mycobiome studies.
- Standardizing primer use will improve comparability across research.
