16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys

0541306 - MBÚ 2021 RIV US eng J - Journal Article
Starke, Robert - Pylro, V. S. - Morais, Daniel
16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.
Microbial Ecology. Roč. 81, č. 2 (2021), s. 535-539. ISSN 0095-3628. E-ISSN 1432-184X
R&D Projects: GA ČR(CZ) GA18-25706S; GA ČR(CZ) GJ20-02022Y
Institutional support: RVO:61388971
Keywords : 16S rRNA * Gene * Metataxonomic surveys
OECD category: Microbiology
Impact factor: 4.192, year: 2021
Method of publishing: Open access
https://link.springer.com/article/10.1007%2Fs00248-020-01586-7

Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.
Permanent Link: http://hdl.handle.net/11104/0318884