Hiergeist, Andreas and Ruelle, Jean and Emler, Stefan and Gessner, Andre (2023) Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach. PLOS ONE, 18 (2): e0280870. ISSN 1932-6203,
Full text not available from this repository. (Request a copy)Abstract
The use of NGS-based testing of the bacterial microbiota is often impeded by inconsistent or non-reproducible results, especially when applying different analysis pipelines and reference databases. We investigated five frequently used software packages by submitting the same monobacterial datasets to them, representing the V1-2 and the V3-4 regions of the 16S-rRNA gene of 26 well characterized strains, which were sequenced by the Ion Torrent (TM) GeneStudio S5 system. The results obtained were divergent and calculations of relative abundance did not yield the expected 100%. We investigated these inconsistencies and were able to attribute them to failures either of the pipelines themselves or of the reference databases they rely on. On the basis of these findings, we recommend certain standards which should help to render microbiome testing more consistent and reproducible, and thus useful in clinical practice.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | RNA GENE-SEQUENCES; QUALITY; GREENGENES; DATABASE; PRIMERS; SILVA; |
| Subjects: | 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Lehrstuhl für Medizinische Mikrobiologie und Hygiene |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 09 Mar 2024 09:02 |
| Last Modified: | 09 Mar 2024 09:02 |
| URI: | https://pred.uni-regensburg.de/id/eprint/59250 |
Actions (login required)
 |
View Item |
