Agrawal, Shelesh and Kinh, Co Thi and Schwartz, Thomas and Hosomi, Masaaki and Terada, Akihiko and Lackner, Susanne (2019):
Determining uncertainties in PICRUSt analysis – An easy approach for autotrophic nitrogen removal.
In: Biochemical Engineering Journal, 152, p. 107328. Elsevier, ISSN 1369-703X, e-ISSN 1873-295X,
DOI: 10.1016/j.bej.2019.107328,
[Article]
Abstract
The diversity and dynamics of microorganisms in engineered ecosystems have a high impact on performance and operational stability. Nitrogen removal from wastewater is one example of such complex and dynamic ecosystems. Following the microbial community composition and its functional potential is highly valuable information for optimizing performance. Molecular methods and data analysis tools have become more and more popular in recent years. PICRUSt, a bioinformatics tool to predict the functional potential of a sample from 16S rRNA amplicon sequencing, was tested in the context of autotrophic nitrogen removal for its accuracy. Two experimental studies were extended by qPCR to demonstrate how qPCR can be used to deliver information about the accuracy of PICRUSt predictions. Two main points were discovered: (1) the correlation between qPCR data and PICRUSt predictions depends on the relative abundance of the target gene. With higher abundance, better correlations are achievable; (2) the more genome information available, the stronger the correlation.
| Item Type: | Article |
|---|---|
| Erschienen: | 2019 |
| Creators: | Agrawal, Shelesh and Kinh, Co Thi and Schwartz, Thomas and Hosomi, Masaaki and Terada, Akihiko and Lackner, Susanne |
| Title: | Determining uncertainties in PICRUSt analysis – An easy approach for autotrophic nitrogen removal |
| Language: | English |
| Abstract: | The diversity and dynamics of microorganisms in engineered ecosystems have a high impact on performance and operational stability. Nitrogen removal from wastewater is one example of such complex and dynamic ecosystems. Following the microbial community composition and its functional potential is highly valuable information for optimizing performance. Molecular methods and data analysis tools have become more and more popular in recent years. PICRUSt, a bioinformatics tool to predict the functional potential of a sample from 16S rRNA amplicon sequencing, was tested in the context of autotrophic nitrogen removal for its accuracy. Two experimental studies were extended by qPCR to demonstrate how qPCR can be used to deliver information about the accuracy of PICRUSt predictions. Two main points were discovered: (1) the correlation between qPCR data and PICRUSt predictions depends on the relative abundance of the target gene. With higher abundance, better correlations are achievable; (2) the more genome information available, the stronger the correlation. |
| Journal or Publication Title: | Biochemical Engineering Journal |
| Journal volume: | 152 |
| Publisher: | Elsevier |
| Uncontrolled Keywords: | Nitrogen removal Wastewater treatment (q)PCR Next-generation sequencing Data analysis Uncertainty |
| Divisions: | 13 Department of Civil and Environmental Engineering Sciences 13 Department of Civil and Environmental Engineering Sciences > Institute IWAR 13 Department of Civil and Environmental Engineering Sciences > Institute IWAR > Wastewater Engineering |
| Date Deposited: | 02 Apr 2020 10:17 |
| DOI: | 10.1016/j.bej.2019.107328 |
| Official URL: | http://www.sciencedirect.com/science/article/pii/S1369703X19... |
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