Are there active microorganisms in the uterus? RNA analysis changes our understanding of the uterine microbiome

A study by the Granada Institute for Biomedical Research (ibs.GRANADA) and the University of Granada reveals that detecting bacterial DNA in the endometrium does not necessarily mean that the microorganisms are active and questions whether lactobacilli form a stable community in this tissue

Identifying the microorganisms present in the uterine cavity and determining their biological activity is one of the main challenges in reproductive health research. This information could contribute to the development of more accurate diagnoses and personalized treatments for fertility problems and certain pregnancy complications.

For a long time, the human uterus was considered a completely sterile environment. The advent of molecular sequencing techniques made it possible to detect microbial genetic material and opened the debate about the existence of a possible uterine microbiome. However, because it is an environment of very low biomass, it is difficult to distinguish between active microorganisms, inactive cells, DNA fragments, or signals originating from other areas of the reproductive tract.

A recent investigation, led by Dr. Signe Altmäe, a researcher in the group TEC14-Human Reproduction and Hereditary and Complex Diseases Researchers from ibs.GRANADA and the Department of Biochemistry and Molecular Biology I of the University of Granada have compared conventional DNA-based methods with an RNA metatranscriptomic analysis aimed at identifying functional microbial activity.

The results call into question that bacteria of the genus LactobacillusThese bacteria, which are predominant and beneficial in the vaginal microbiota, form an active and stable community in the uterus. Although their DNA can be detected in uterine samples, RNA analysis did not find equivalent signs of biological activity.

DNA indicates presence, but not necessarily activity

DNA sequencing allows the identification of genetic material present in a sample, but it does not determine whether it comes from live, active microorganisms or from residual fragments. To overcome this limitation, the Repro-UGR team analyzed vaginal swabs, samples obtained by uterine brushing, and tissue biopsies in parallel using DNA and RNA techniques.

While DNA provides a picture of the microorganisms whose genetic material is present, RNA allows us to approximate the genes being expressed at the time of sampling. The comparison showed low concordance between the two profiles, especially relevant in organs with low microbial biomass.

DNA tests detected a high presence of Lactobacillus in some uterine samples. However, RNA analysis did not show equivalent activity.

"Our results indicate that Lactobacillus "It doesn't appear to actively colonize the uterus. One possible explanation is that the detected DNA signals correspond to dormant cells or genetic debris ascending from the vagina," explains Dr. Altmäe.

This interpretation does not necessarily imply that the uterus is sterile, but rather requires differentiating between the detection of microbial material and the existence of a functionally active community.

A greater capacity to identify active alterations

RNA analysis also showed a greater capacity to identify potentially pathogenic microorganisms when an imbalance existed in uterine tissue. In these cases, metatranscriptomics detected signs of activity that DNA-based methods had missed or underestimated.

The study also found that the collection procedure influences the results. Uterine brushing detected a greater richness of microbial signals than deep tissue biopsies, highlighting the need to standardize both sampling and analysis techniques.

Towards more accurate fertility diagnoses

The results have implications for the study of fertility and for the design of interventions aimed at modifying the uterine environment. The vagina presents conditions, including an acidic pH, that favor the predominance of certain species of LactobacillusThe uterus has a different microenvironment, so it cannot be assumed that these bacteria perform the same function in both organs.

"Treatments aimed at introducing lactobacilli into the uterus may not produce the expected effects if these bacteria do not find the necessary conditions there to remain active," the researcher points out.

The study also urges caution when using broad-spectrum antibiotics based solely on DNA detection, as finding genetic material from a bacterium does not necessarily mean there is an active infection.

The team proposes moving towards diagnostic tools that integrate DNA and RNA analysis. This approach would allow for the simultaneous evaluation of which microorganisms or microbial fragments are present and which show biological activity, leading to more specific fertility diagnoses tailored to each patient's characteristics.

About the group

El grupo TEC-14 of Human Reproduction and Hereditary and Complex Diseases The ibs.GRANADA research group conducts multidisciplinary and translational research aimed at improving the safety and efficacy of assisted reproductive technologies. Its main lines of research encompass uterine receptivity, spermatogenesis disorders, and the prevention and treatment of premature birth. The group also investigates complex hereditary diseases, such as certain kidney pathologies and hereditary cancers, by studying their genetic basis and developing prevention strategies and reproductive counseling.

More information:   https://www.ibsgranada.es/grupos-de-investigacion/tec14-reproduccion-humana-y-enfermedades-hereditarias-y-complejas/