Microbiota of the pregnant mouse: characterization of the bacterial communities in the oral cavity, lung, intestine, and vagina through culture and DNA sequencing

Abstract

Mice are frequently used as animal models for mechanistic studies of infection and obstetrical disease, yet characterization of the murine microbiota during pregnancy is lacking. The objective of this study was to therefore characterize the microbiotas of distinct body sites of the pregnant mouse that harbor microorganisms that could potentially invade the murine amniotic cavity leading to adverse pregnancy outcomes: vagina, oral cavity, intestine, and lung. The microbiotas of these body sites were characterized through anoxic, hypoxic, and oxic culture, as well as through 16S rRNA gene sequencing. With the exception of the vagina, the cultured microbiotas of each body site varied with atmosphere, with the greatest diversity in the cultured microbiota appearing under anoxic conditions. Only cultures of the vagina were able to recapitulate the microbiota observed from direct DNA sequencing of body site samples, primarily due to the dominance of two Rodentibacter strains. Identified as R. pneumotropicus and R. heylii, these isolates exhibited dominance patterns similar to those of Lactobacillus crispatus and L. iners in the human vagina. Whole genome sequencing of these Rodentibacter strains revealed shared genomic features, including the ability to degrade glycogen, an abundant polysaccharide in the vagina. In summary, we report body site specific microbiotas in the pregnant mouse with potential ecological parallels to those of humans. Importantly, our findings indicate that the vaginal microbiota of pregnant mice can be readily cultured, suggesting that mock vaginal microbiotas can be tractably generated and maintained for experimental manipulation in future mechanistic studies of host vaginal-microbiome interactions. IMPORTANCEMice are widely utilized as animal models of obstetrical complications; however, the characterization of the murine microbiota has been neglected during pregnancy. Microorganisms from the vagina, oral cavity, intestine, and lung have been found in the intra-amniotic space, where their presence threatens the progression of gestation. Herein, we characterize the microbiotas of pregnant mice and establish the appropriateness of culture in capturing the microbiota at each site. The high relative abundance of Rodentibacter observed in the vagina is similar to that of Lactobacillus in humans, suggesting potential ecological parallels. Importantly, we report that the vaginal microbiota of the pregnant mouse can be readily cultured under hypoxic conditions, demonstrating that mock microbial communities can be utilized to test the potential ecological parallels between microbiotas in human and murine pregnancy, and to evaluate the relevance of the structure of these microbiotas for adverse pregnancy outcomes, especially intra-amniotic infection and spontaneous preterm birth.