Number of the records: 1
The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar
- 1.
SYSNO ASEP 0518049 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar Author(s) Lladó, Salvador (MBU-M) ORCID
Větrovský, Tomáš (MBU-M) ORCID, RID
Baldrian, Petr (MBU-M) RID, ORCIDSource Title Folia Microbiologica. - : Springer - ISSN 0015-5632
Roč. 64, č. 1 (2019), s. 19-23Number of pages 5 s. Language eng - English Country NL - Netherlands Keywords operational taxonomic units ; bacterial communities ; 16S rRNA gene Subject RIV EE - Microbiology, Virology OECD category Microbiology R&D Projects GA18-25706S GA ČR - Czech Science Foundation (CSF) LTT17022 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Method of publishing Limited access Institutional support MBU-M - RVO:61388971 UT WOS 000455916000003 EID SCOPUS 85048790907 DOI 10.1007/s12223-018-0627-y Annotation The concept of operational taxonomic units (OTUs), which constructs mathematically defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between molecular taxa, real taxa, and OTUs seems to be much more complicated. Strains of the same bacterial species (ideally belonging to the same OTU) typically only share some genes (the core genome), while other genes are strain-specific and unique. It is thus unclear to what extent are important functional traits homogeneous within an OTU and how correctly can functional traits be inferred for individual OTU members. Here, we have tested in silico the similarity of all genes and, more specifically, the set of genes encoding for glycoside hydrolases (GH) in bacterial genomes that belong to the same OTU. Genome similarity varied among OTUs, but as many as 5-78% of genes were not shared between the two bacterial genomes in the pair. The complement of GH families (the presence of gene families and the number of genes per family) differed in 95% of OTUs. In average, 43% of GH families either differed in gene counts or were present in one genome and absent in the other. These results show a serious limitation of the OTU-based approaches when used to infer the functional traits of bacterial communities and open the questions how to link environmental sequencing data and microbial functions. Workplace Institute of Microbiology Contact Eliška Spurná, eliska.spurna@biomed.cas.cz, Tel.: 241 062 231 Year of Publishing 2020 Electronic address https://link.springer.com/article/10.1007%2Fs12223-018-0627-y
Number of the records: 1