We agree with the reviewer that we have not stressed this fact enough and have added more sentences explaining why OTUs are used and the problem: “Enormous progress happened in prokaryote taxonomy in the recent years [8,12,24]. However, the data produced with novel methodologies, such as next generation sequencing, often requires a high throughput taxonomic classification of sequences such as fixed threshold to identify OTUs. This kind of fixed numeric classifications can always only be a vague approximation to the actual structure of relatedness of organisms.”
It is necessary to stress the fact that the numerical criteria (e.g., exactly limited percentage similarity) never are valid uniformly for large groups of organisms and cannot be applied as one main criterion in large groups.