They could also correspond to transient species, which are accidentally passing,

although a recent metagenomic analysis found a very low rate of sequences from putative transient species [35]. We found that most OTUs have been observed once (Additional file 9, Table S4). We have deliberately omitted these OTUs from the analyses of SIS3 cosmopolitanism and specificity, because their low abundance does not allow to extract conclusions about their environmental distributions. Nevertheless, their inclusion does not affect significantly the conclusions extracted for all taxonomic ranks, except that of species (Additional file 10, Figure S6). Further study is required to understand why the majority of OTUs are rare, and some work has already been done by Sogin and colleagues to address this point [31]. As commented above, BMS-907351 chemical structure they could correspond to specialist species with a very limited niche. But it is also likely that PR-171 cell line the limited size of

samplings cannot recover low-abundance OTUs from the environments and samples where they actually exist. After all, it is virtually impossible to conclusively show that a microbial taxon is absent from a given location by the current sequencing methods [6]. Also the heterogeneous size of the samples can introduce a bias in the results, because big samples are likely to recover more species than small ones. Also rare OTUs are more likely to be detected in larger samples. Information about the abundance of each taxa in each sample could provide relevant information to correct this size effect. But unfortunately, this information is not present in the original source of data. Therefore, the patterns described here could be affected because samples of different size are being considered. To exclude this possibility, we created smaller datasets composed uniquely of samples of comparable size. The results of cosmopolitanism and ubiquity for two such datasets are shown in Additional file 2, Figure S1. It can be seen that the patterns are very similar to the ones obtained

with the full dataset. Also in the correspondence analysis we transformed the data dividing frequencies by the number of samples instead, as a proxy for the number of sequences, thus assuming that larger Doxorubicin price samples tend to have more sequences. Finally, in the Bayesian model of affinities, we included random effects to partially account for the variation of the unknown number of sequences. It is also necessary to consider that most data have been obtained by the standard sequencing procedures which involve PCR amplification steps using “”universal”" primers, a procedure that is known to be biased [36, 37]. Universal primers are designed according to current knowledge and could perform poorly or even miss species or taxa that remain unknown. Another source of potential biases is that in clone library sampling, often just some few clones of interest are sequenced or submitted, discarding the rest.