Gut microbiome in endometriosis: a cohort study on 1000 individuals

Abstract

Background: Endometriosis, defined as the presence of endometrial-like tissue outside of the uterus, is one of the most prevalent gynecological disorders. Although different theories have been proposed, its pathogenesis is not clear. Novel studies indicate that the gut microbiome may be involved in the etiology of endometriosis; nevertheless, the connection between microbes, their dysbiosis, and the development of endometriosis is understudied. This case-control study analyzed the gut microbiome in women with and without endometriosis to identify microbial targets involved in the disease.

Methods: A subsample of 1000 women from the Estonian Microbiome cohort, including 136 women with endometriosis and 864 control women, was analyzed. Microbial composition was determined by shotgun metagenomics and microbial functional pathways were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Partitioning Around Medoids (PAM) algorithm was performed to cluster the microbial profile of the Estonian population. The alpha- and beta-diversity and differential abundance analyses were performed to assess the gut microbiome (species and KEGG orthologies (KO)) in both groups. Metagenomic reads were mapped to estrobolome-related enzymes' sequences to study potential microbiome-estrogen metabolism axis alterations in endometriosis.

Results: Diversity analyses did not detect significant differences between women with and without endometriosis (alpha-diversity: all p-values > 0.05; beta-diversity: PERMANOVA, both R ² < 0.0007, p-values > 0.05). No differential species or pathways were detected after multiple testing adjustment (all FDR p-values > 0.05). Sensitivity analysis excluding women at menopause (> 50 years) confirmed our results. Estrobolome-associated enzymes' sequence reads were not significantly different between groups (all FDR p-values > 0.05).

Conclusions: Our findings do not provide enough evidence to support the existence of a gut microbiome-dependent mechanism directly implicated in the pathogenesis of endometriosis. To the best of our knowledge, this is the largest metagenome study on endometriosis conducted to date.

Keywords: Endometriosis; Estrobolome; Gut microbiota; Metagenomics; Microbiome; Microbiota; Shotgun sequencing.

Fig. 1

Microbial landscape in the Estonian study population. Circular stacked barplots (“iris plots”) show the most relatively abundant phyla (A), genera (B), and species (C) in the study population. The outer bicolor rings indicate the endometriosis and control groups

Fig. 2

Enterotypes identified in the Estonian study population. A, B Relative abundance of Prevotella copri and Bacteroides spp. within the enterotypes on the principal coordinates analysis (PCoA) plot of the species-level microbiome profile based on the Bray–Curtis dissimilarity. C Distribution of women with and without endometriosis within the enterotypes. The dot’s shape indicates the cluster, while the colors highlight the relative abundances (A, B) or the endometriosis and control groups (C)

Fig. 3

Microbial diversity measures in endometriosis and control groups. A, B Alpha-diversity analysis (i.e., Shannon diversity index and observed richness). Groups comparisons indicate no significant differences (linear-mixed effects, all p-values > 0.05). C, D Beta-diversity analyses on the principal coordinates analysis (PCoA) of the species (C) and KOs (D) profile based on the Bray–Curtis dissimilarity (Adonis PERMANOVA, both R.² < 0.0007, both p-values > 0.05)

Fig. 4

Functional differences in the microbial pathways in endometriosis and control groups. Volcano plot displaying log fold change differences in the KEGG orthologs derived from the ANCOM-BC model. Points in blue and red represent KEGG orthologs which were decreased and increased in endometriosis and statistically significant (p < 0.05). Points in black represent KEGG orthologs that were not significantly different (p > 0.05). No KEGG orthologs remained statistically significant after Benjamini–Hochberg false discovery rate (FDR) correction (all FDR p-values > 0.05)