**5. Conclusions**

This study allowed the changes in fecal microbial communities caused by isoflavone supplementation for one month to be monitored in a group of menopausal women. Isoflavone consumption was associated with a significant increase in the relative abundance of the genus *Slackia*, to which strains that metabolise isoflavones and produce equol are the most studied in this respect. Moreover, the taxa *Pseudoflavonifractor*, *Dorea*, and *Lachnospiraceae incertae sedis* were found in greater proportions in equol-producing women. Fecal microbial communities of equol producers were more similar to each other after isoflavone treatment, a fact that was not observed among those of equol non-producers. However, distinctive differences in the excretion of fatty acids associated with the equol status (which might be related to inflammation) were not observed.

**Author Contributions:** S.D. and B.M. contributed with the conception and design of the study. L.G. performed bacterial DNA extraction, sequence data analysis, and statistics. S.D. performed library construction. R.T. carried out the recruitment and diagnoses of the women. M.A.A.-P. contributed with the high-throughput sequencing and analysis of the samples. S.D. and B.M. planned the experimental design of the study and contributed to the interpretation of the data. L.G. drafted the manuscript. B.M. and S.D. performed a critical revision of the manuscript. All authors have read and agreed to the published version of the manuscript.

**Funding:** The research was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) (AGL-2014-57820-R) and Asturias Principality (GRUPIN14-137). The Microbiome Core Facility is supported in part by the NIH/National Institute of Diabetes and Digestive and Kidney Diseases gran<sup>t</sup> P30 DK34987. L.G. was supported by a research contract of the FPI Program from MINECO (BES-2012-062502). S.D. was supported by a research contract from MINECO (RYC-2016- 19726).

**Institutional Review Board Statement:** The study was conducted according to the guidelines of the Declaration of Helsinki, and approved by the Bioethics Subcommittee of the Spanish Research Council (Consejo Superior de Investigaciones Científicas or CSIC) and the Regional Ethics Committee for Clinical Research of the Health Service of Asturias (Servicio de Salud del Principado de Asturias) (approval number: 15/2011).

**Informed Consent Statement:** Informed consent was obtained from all subjects involved in the study.

**Data Availability Statement:** The raw data generated in this study can be found in the Sequence Read Archive (SRA) of the NCBI database. under accession numbers: SRR9855012-25, SRR6656999, and SRR6657000.

**Acknowledgments:** We would like to thank Ana Hernández and Jorge Rodríguez from IPLA-CSIC for their technical assistance in the chromatographic analysis of fecal acids.

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.
