N2N seminar: Construction of operational taxonomic units from environmental sequences - Robustness and Reproducibility

Mar/05 11:00 - Mar/05 12:00
Jozef Schell seminar room Technologiepark 927 B-9052 Gent

Professor Christian von Mering
University of Zurich, Institute of Molecular Life Sciences, Zurich, Switzerland

Thursday, March 5, 2015 - 11:00 to 12:00

Jozef Schell seminar room
Technologiepark 927
B-9052 Gent

The demarcation of operational taxonomic units (OTUs) from complex sequence data sets is a key step in contemporary studies of microbial ecology. However, as biologically motivated ‘optimal’ OTU-binning algorithms remain elusive, many conceptually distinct approaches continue to be used. We set out systematically to test which of the methods provides more robust OTU delineations, and to find out to what extent different methods are in agreement. Using a global data set of 887 870 bacterial 16S rRNA gene sequences, we objectively quantified biases and disagreements over a wide range of parameters and methods. We found that OTU-binning methods often provided surprisingly non-equivalent partitions of identical data sets, notably when clustering to the same nominal similarity thresholds; and we quantified the resulting impact on ecological data description for a well-defined human skin microbiome data set. We observed that some methods were very robust to varying clustering thresholds, while others were found to be highly susceptible even to slight threshold variations. Lastly, we developed external tests for OTU quality, using as arbiters meta-information that is not based on sequences. Our findings may contribute to an enhanced comparability of results across sequence-processing pipelines, and we arrive at recommendations towards higher levels of standardization in established workflows.

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