Extended Data Figure 1: Method used for OTU consolidation.
From: Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice
a, OTU consolidation was performed to limit pseudo-duplication of taxa. ‘Counts’ on the y axis refer to the number of OTU–OTU correlations falling within a given range of Spearman’s correlation values shown on the x axis (n = 341,640 OTU–OTU comparisons; see Methods for details). b, A subset of the matrix used to derive the distribution shown in a illustrates how OTUs within a single family-level taxon are consolidated. In this example, three clusters composed of OTUs with Spearman’s correlation coefficients of >0.7 are identified and the abundances of their constituent OTUs are summed. Each OTU cluster is assigned an identifier number with the prefix ‘C.’ and given a consensus taxonomic assignment (see Supplementary Table 5). Note that the OTUs used to generate a given ‘consolidated OTU’ shared 99.3 ± 0.4% (mean ± s.d.) nucleotide sequence identity in their V4-16S rRNA nucleotide sequences.
