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Semin Reprod Med 2023; 41(05): 125-143
DOI: 10.1055/s-0044-1779025
Review Article

Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms

Eduardo Salas-Espejo    *
1   Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
,
Laura C. Terrón-Camero    *
2   Bioinformatics Unit, Institute of Parasitology and Biomedicine “López-Neyra” (IPBLN), CSIC, Granada, Spain
,
José L. Ruiz 
2   Bioinformatics Unit, Institute of Parasitology and Biomedicine “López-Neyra” (IPBLN), CSIC, Granada, Spain
,
Nerea M. Molina 
1   Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
,
Eduardo Andrés-León 
2   Bioinformatics Unit, Institute of Parasitology and Biomedicine “López-Neyra” (IPBLN), CSIC, Granada, Spain
› Author Affiliations Funding This study was funded by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and the European Regional Development Fund (FEDER) through MCIN/AEI/10.13039/501100011033 and ERFD's “A way of making Europe projects”. Endo-Map (PID2021-127280OB-I00) and ROSY (CNS2022-135999). L.C.T.-C. was also recipient of a postdoctoral fellowship from the Regional Government of Andalusian (POSTDOC_21_00394). J.L.R. was recipient of a technical support staff grant from the Ministry of Science and Innovation of the Spanish Government (PTA2021-019864-I). N.M.M. was also recipient of FPU19/01638 funded by MCIN/AEI/10.13039/501100011033 and by ESF Investing in your future. E.A.-L. was recipient of a postdoctoral fellowship from the Regional Government of Andalusian (POSTDOC_20_00541).
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Abstract

Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.

Keywords

metagenomics - microbiome - reproduction - fertility - vagina - semen

* Both authors contributed equally to this work.




Publication History

Article published online:
06 February 2024

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