Equol producers and non-producers
Among the isoflavones and isoflavone-derived metabolites, equol, which in the human gut is synthesized from daidzein by minority bacterial populations, shows the strongest estrogenic and antioxidant activity.  The beneficial effects on human health of isoflavone consumption might be partially or indeed totally attributable to this equol. Although some of the bacterial strains involved in its formation have been identified, the interplay between the composition and functionality of the gut microbiota and equol producer phenotype has hardly been studied. In this study, three analytical pipelines for the taxonomic and functional annotation of shotgun sequencing data were used in the search for similarities and differences in the faecal metagenome of equol producer (n=3) and non-producer (n=2) women, with special focus on equol-producing taxa and their equol-associated genes. The taxonomic profiles of the faecal samples differed significantly depending on the analytical method followed, although the microbial diversity detected by each tool was very similar at the phylum, genus and species levels. In addition, equol-producing taxa were detected in both equol producer and non-producer women, but no correlation between the abundance of equol-producing taxa and the equol producer/non-producer phenotype was found. Indeed, functional metagenomic analysis was unable to identify the pathways and genes involved in equol production, even in samples from equol producers. By aligning the reductase-encoding genes involved in equol production with the collected metagenomics data, only two reads mapping to daidzein- and tetrahydrodaidzein-reductase sequences were recognized in a sample from an equol producer. In conclusion, the taxonomic analysis of metagenomic data might not be suitable for detecting and quantifying equol-producing microbes in human faeces. Functional analysis of the data might provide an alternative. However, to detect the genetic makeup of the minority gut populations, more extensive sequencing than that contemplated in the present study might be required.