109 Is the equine gut colonised in utero by amniotic bacteria?

Abstract

Until very recently it was believed that the uterus was sterile, with microbial colonisation of the foal's gastrointestinal tract (GIT) commencing at birth. GIT colonisation is an integral developmental process, critical for an optimal functioning immune system and ongoing health of the foal. The in utero colonisation paradigm has now challenged this concept, indicating that the amniotic fluid (AF) composition contains non-pathogenic microbiota that potentially commence colonisation of the GIT during the process of fetal swallowing. In turn, preparing the foal for life outside the womb. This study examined the presence of microbiota in the AF of healthy pregnant mares, identifying microorganisms that have the potential to colonise the fetal GIT in utero. AF samples were obtained from 14 healthy mares in the second stage of parturition, before the rupture of the amnion. When the amnion was clearly visible, the surface was seared with a sterile spatula and AF extracted with a sterile needle and syringe. The sample had no contact with any other surface of the mare and was immediately snap-frozen and stored at −80°C for microbiota analysis. Genomic DNA was extracted and processed for 16S rRNA gene amplicon sequencing, followed by bioinformatic analysis of the results using QIIME2 and CalypsoV8.84 software packages. Microbiota was detected in all AF samples. Communities were of low diversity, as indicated by the α diversity parameters Chao1, Evenness, Richness and Simpson's Index. Operational Taxonomic Units (OTUs) of the top 20 taxa showed some host variation. The most abundant OTUs across the majority of samples were classified to the phyla Opisthokonta (100% of samples), Bacteroidetes (79%), Actinobacteria (57%) and Firmicutes (57%). At the family level, Staphylococcacea (79%) and Microbacteriaceae (71%) were the most abundant. These microbes have been previously detected across other locations of the equine microbiome, including the oral, esophageal, distal GIT and vaginal ecosystems. Our results have demonstrated the presence of a complex microbial ecosystem of low diversity in the AF of healthy equine pregnancies, likely of maternal origin. The environmental and gastrointestinal microbes detected in the AF displayed similarities to other equine ecosystems, suggesting microbial translocation from the mare to the AF. Further research would be required to determine if these AF microbes are being ingested by the fetus, thus commencing GIT colonisation in utero . Deciphering microbial colonisation of the foal's GIT has important implications for maternal management before parturition and could lead to the development of strategies to enhance foal health outcomes.