The endometrial microbiome of clinical miscarriage, ectopic pregnancy and during early pregnancy in a successful live-birth

Characterize taxonomically and functionally the endometrial microbiome in clinical miscarriage, ectopic pregnancy and successful live-birth. The endometrial microbiome was analyzed in patients undergoing ART. We describe the results of endometrial fluid samples analyzed prior to embryo transfer with euploid embryos resulting in 2 clinical miscarriages and 1 ectopic pregnancy (Patient 1), and a clinical miscarriage and a 4-week spontaneous successful pregnancy resulting in live birth (Patient 2). For taxonomic classification, 16S rRNA profiles were obtained using the Ion 16S metagenomics kit and sequenced on the Ion S5 XL system (ThermoFisher Scientific). Functional composition was assessed by Whole Metagenome Sequencing using the Nextera DNA Flex Library Preparation kit and sequenced on the NextSeq 500 system (Illumina). The 16S rRNA sequencing of the endometrial fluid collected prior to clinical miscarriages and ectopic pregnancy showed the existence of a pathologic microbiota profile, whereas at 4-weeks of pregnancy had reversed to a normal Lactobacillus-dominated profile.Tabled 1Patient 1Patient 2Ectopic (%)Miscarriage (%)Miscarriage (%)Miscarriage (%)Live birth (%)Lactobacillus12.10.84817.693.5Gardnerella32.828.832.80.00.1Pseudoalteromonas14.216.80.016.31.4Bifidobacterium8.85.06.20.00.0Rhodanobacter5.613.00.017.21.7Atopobium0.413.45.40.10.0Streptococcus1.00.20.03.30.1Pseudomonas3.22.70.13.70.5Enterobacteriaceae1.50.00.02.90.2Staphylococcus0.50.00.01.20.0 Open table in a new tab The functional metagenomics revealed different Lactobacillus species and associated functions between the clinical miscarriage and successful pregnancy. In clinical miscarriage, L. crispatus was detected with the indicated pathogens showing an unstable functional pattern with transposases and insertion elements. Whereas, in the same patient L. iners was the only bacteria present in the uterine cavity at the 4-week in the successful pregnancy, associated with defense mechanisms, energy production and cell division. Finally, since bacteria produce G protein-coupled receptors ligands to modulate the host’s physiology, we searched for sequences associated with N-acyl synthase protein family PFAM13444 detecting 44 sequences in the miscarriage versus 0 in the early successful pregnancy. This is the first demonstration that the uterine microbiome in an early successful pregnancy is completely different from clinical miscarriages and ectopic pregnancy, revealing the different uterine microbial environment encountered by the embryo at implantation in these clinical outcomes. The potential of these new findings remains to be proven in larger series.