word count (limit 350 words): 314 28 29 Abstract 31 Background: Microbes and their metabolic products influence early-life immune and 32 microbiome development, yet remain understudied during pregnancy. Vaginal microbial 33 communities are typically dominated by one or a few well adapted microbes, which are able to 34 survive in a narrow pH range. In comparison to other human-associated microbes, vaginal 35 microbes are adapted to live on host-derived carbon sources, likely sourced from glycogen and 36 mucin present in the vaginal environment.37 Methods: Using 16S rRNA and ITS amplicon sequencing, we characterized the cervicovaginal 38 microbiomes of 18 healthy women throughout the three trimesters of pregnancy. Shotgun 39 metagenomic sequencing permitted refinement of the taxonomy established by amplicon 40 sequencing, and identification of functional genes. Additionally, we analyzed saliva and urine 41 metabolomes using GC-TOF and LC-MS/MS lipidomics approaches for samples from mothers 42 and their infants through the first year of life.
43Results: Amplicon sequencing revealed most women had either a simple community with one 44 highly abundant species of Lactobacillus or a more diverse community characterized by a high 45 abundance of Gardnerella, as has also been previously described in several independent 46 cohorts. Integrating GC-TOF and lipidomics data with amplicon sequencing, we found 47 metabolites that distinctly associate with particular communities. For example, cervicovaginal 48 microbial communities dominated by Lactobacillus crispatus also have high mannitol levels, 49 which contradicts the basic characterization of L. crispatus as a homofermentative Lactobacillus 50 species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal 51 microbiome are dictated by the availability of host sugars, such as fructose, which is the most 52 likely substrate being converted to mannitol. Furthermore, indole-3-lactate (ILA) was also 53 indicative of L. crispatus specifically. ILA has immunomodulatory properties through binding the 54 human aryl hydrocarbon receptor (AhR), which may maintain the especially low diversity of L. 55 crispatus dominated communities.
56Conclusions: Overall, using a multi-'omic approach, we begin to address the genetic and 57 molecular means by which a particular vaginal microbiome becomes vulnerable to large 58 changes in composition.Vaginal microbes sustain important physiologies and produce metabolites that can 62 directly or indirectly affect maternal health and infant development during pregnancy.
63Perturbations to early-life microbiomes and associated metabolic dysfunction have been linked 64 with allergy and auto-immune diseases such as asthma [1][2][3][4]. For example, regular pre-natal 65 and post-natal farm exposure, i.e., contact with a diversity of microbes during pregnancy and 66 infancy, have been shown to reduce the incidence of chronic health diseases such as asthma 67 and atopy [5]. Moreover, recent research has supported the idea of fetal ...