Abstract
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.
Similar content being viewed by others
References
Asshauer KP, Wemheuer B, Daniel R, Meinicke P (2015) Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics 31:2882–2884
Berlemont R, Martiny AC (2015) Genomic potential for polysaccharide deconstruction in bacteria. Appl Environ Microbiol 81:1513–1519
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624
Chen L, Brookes PC, Xu JM, Zhang JB, Zhang CZ, Zhou XY, Luo Y (2016) Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass. Soil Biol Biochem 98:1–10
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998
Edgar RC (2018) Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics, bty113.
Estaki M, Pither J, Baumeister P, Little JP, Gill SK, Ghosh S et al (2016) Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions. Microbiome 4:13
Gilbert JA, Jansson JK, Knight R (2014) The earth microbiome project: successes and aspirations. BMC Biol 12:4
Goberna M, Verdu M (2016) Predicting microbial traits with phylogenies. ISME J 10:959–567
Hugerth LW, Andersson AF (2017) Analysing microbial community composition through amplicon sequencing: from sampling to hypothesis testing. Front Microbiol 8:1561
Jimenez DJ, Chaves-Moreno D, van Elsas JD (2015) Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw. Sci Rep 5:13845
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821
Lladó S, Lopez-Mondejar R, Baldrian P (2017) Forest soil bacteria: diversity, involvement in ecosystem processes, and response to global change. Microbiol Mol Biol Rev 81:e00063–e00016
López-Mondéjar R, Zühlke D, Becher D, Riedel K, Baldrian P (2016) Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Sci Rep 6:25279
Martiny AC, Treseder K, Pusch G (2013) Phylogenetic conservatism of functional traits in microorganisms. ISME J 7:830–838
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15:589–594
Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER et al (2016) Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 351:158–162
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386
Nguyen NP, Warnow T, Pop M, White B (2016) A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. Npj Biofilms Microbiomes 2:16004
Puigbo P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV (2014) Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Biol 12:66
Rosselló-Móra R, Amann R (2015) Past and future species definitions for bacteria and archaea. Syst Appl Microbiol 38:209–216
Schmidt TSB, Matias Rodrigues JF, von Mering C (2014) Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale. PLoS Comput Biol 10:e1003594
Tikhonov M, Leach RW, Wingreen NS (2015) Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J 9:68–80
VanInsberghe D, Maas KR, Cardenas E, Strachan CR, Hallam SJ, Mohn WW (2015) Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils. ISME J 9:2435–2441
Větrovský T, Baldrian P (2013) The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One 8:e0057923
Yin YB, Mao XZ, Yang JC, Chen X, Mao FL, Xu Y (2012) dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 40:W445–W451
Zimmerman AE, Martiny AC, Allison SD (2013) Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J 7:1187–1199
Funding
This work was supported by the Czech Science Foundation (18-25706S) and by the Ministry of Education, Youth and Sports of the Czech Republic (LTT17022).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Supplementary Table 1
List of bacterial genomes used in this paper. (XLSX 17 kb)
Rights and permissions
About this article
Cite this article
Lladó Fernández, S., Větrovský, T. & Baldrian, P. The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar. Folia Microbiol 64, 19–23 (2019). https://doi.org/10.1007/s12223-018-0627-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12223-018-0627-y