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16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys
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SYSNO ASEP 0541306 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název 16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys Tvůrce(i) Starke, Robert (MBU-M) ORCID, RID
Pylro, V. S. (BR)
Morais, Daniel (MBU-M) ORCIDZdroj.dok. Microbial Ecology. - : Springer - ISSN 0095-3628
Roč. 81, č. 2 (2021), s. 535-539Poč.str. 5 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova 16S rRNA ; Gene ; Metataxonomic surveys Vědní obor RIV EE - Mikrobiologie, virologie Obor OECD Microbiology CEP GA18-25706S GA ČR - Grantová agentura ČR GJ20-02022Y GA ČR - Grantová agentura ČR Způsob publikování Open access Institucionální podpora MBU-M - RVO:61388971 UT WOS 000563713400001 EID SCOPUS 85089975354 DOI 10.1007/s00248-020-01586-7 Anotace 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. Pracoviště Mikrobiologický ústav Kontakt Eliška Spurná, eliska.spurna@biomed.cas.cz, Tel.: 241 062 231 Rok sběru 2021 Elektronická adresa https://link.springer.com/article/10.1007%2Fs00248-020-01586-7
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