Hominids and hominins serve as remarkable hosts to microbes, and we have co-evolved over the
past 4.5 million years as highly plethoric communities. Human-associated microorganisms (the
"microbiome") are present in numbers exceeding the quantities of human cells by at least
10-fold beginning in the neonatal period. The collective genome (the "metagenome") exceeds
our human genome in terms of gene content by more than 150-fold. With respect to microbiota
and preterm birth, it has generally assumed that the majority of intrauterine infections
originate in the lower genital tract, with microbiota ascending into the otherwise sterile
intrauterine environment to infect the placenta (preterm birth), fetal membranes
(chorioamnionitis), umbilical cord (funisitis), and the fetus (sepsis). However, we and
others have recently demonstrated that the vaginal and gut microbiome communities are
distinctly structured in pregnancy, and the placenta is in fact not sterile, but rather
harbors a low-abundance microbiome which is likely acquired through hematogenous transmission
of the oral microbiome.
Based on our prior studies and preliminary data, our central hypothesis is that a distinct
and largely commensal resident microbiome in pregnancy renders risk for preterm birth. By
utilizing our state-of-the-science technology and analysis tools in a longitudinal
case-cohort of preterm birth subjects, we will be able to transform "discovery based"
metagenomics and multi'omics science into readily translatable mechanistic studies at a
previously unparalleled level.
Specific Aim 1. Longitudinal maternal (vaginal, oral, skin, gut), fetal (oral, skin, gut) and
placental (basal plate and parenchyma) 16S-based metagenomic profiling with inferred
metagenomics will reveal distinct microbial communities in association with preterm birth.
Methods: We will enroll 526 at-risk gravidae to yield an approximated 135 preterm births with
401 at-risk term controls. Starting in the first/early second trimester, we will sample
multiple body sites (vagina, oral, stool, placenta) at multiple time points (antenatal
through delivery), isolate microbial DNA, and perform 16S-based determination of
niche-specific microbial communities found in association with preterm birth. With our
case-cohort longitudinal design, we will be able to apply our well-developed supervised
learning approaches to reveal which taxa contribute to risk of preterm birth, and at what
body sites and gestational ages they are predictive of preterm birth.
Specific Aim 2. Whole-genome shotgun (WGS) metagenomics from selected subjects and body sites
will enable species identification, generation of microbial gene catalogues, and metabolic
reconstructions to determine the structure, function and diversity of the preterm birth
microbiome. Methods: To probe metabolic functionality and describe pathogen-related
mechanisms, we will analyze changes in total gene content using shotgun metagenomics on a
subset of samples. We will build on our functional computational pipelines to fully
characterize targeted subjects' metagenomic signatures.
Specific Aim 3. Integrated host genomics, metatranscriptomics and metabonomics data will
reveal molecular mechanisms and networks underlying preterm birth in a limited subset of
samples. Methods: We will interrogate and integrate our concomitantly acquired clinical
metadata, microbial and host gene expression data (RNA-Seq metatranscriptomics), and
metabonomics profiling with advanced computational and biostatistical approaches. We will be
guided in our choice of subjects by our data from Aims 1 and 2.
- Gravidae at risk for preterm birth, defined as: History of prior spontaneous preterm
birth at 16w0d-36w6d gestational age confirmed by review of medical records. If
efforts to retrieve medical records are unsuccessful, eligibility will depend upon the
events surrounding the prior birth and birthweight under 2 kg; Documented shortened
cervix <2.5 cm by transvaginal ultrasound performed by experienced sonographer at <24
weeks gestational age; Documented and culture-proven complicated lower or upper
urinary tract infection defined as a urinary tract infection requiring hospitalization
(e.g., pyelonephritis); Documented periodontal disease, treated or untreated;
Documented recurrent lower genital infection; Smoking or other chemical dependency
that would convey an increased risk of preterm birth; Other clinical concern for high
risk of preterm birth (and cleared by PI Dr. Aagaard at BCM or Dr. Saade at UTMB)
- Enrollment at less than or equal to 20 weeks gestation by best obstetrical estimate
- Able to speak English or work with an interpreter
- Cognitively aware enough to be able to participate in the study
- Gravidae with viable pregnancy >10 weeks gestational age
- Willingness to consent to all required aspects of protocol - There will be additional
non-required aspects that we will recruit 20% of subjects to participate in. These
will be voluntary opt-in aspects
- 16 years of age or older
- Multifetal gestation at any time during the pregnancy
- Known HIV or Hepatitis C infection
- Known immunosuppressive disease
- Use of any of the following drugs within the last 6 months; Cytokines; Methotrexate or
immunosuppressive cytotoxic agents
- History of cancer except for squamous or basal cell carcinomas of the skin or thyroid
cancer that have been managed and fully treated.
- Major surgery of the GI tract (including gastric bypass), with the exception of
cholecystectomy and appendectomy in the past five years. Any major bowel resection at
any time. If conditions arise that require such surgeries during participation in the
study, subjects will not be excluded after enrollment. If patient develops need for
such surgery after enrollment, they will not be excluded.
- Documented chronic GI disorders, (e.g., Crohn's diseae)
- Chronic conditions with GI symptoms, (e.g. cystic fibrosis)
- Autism spectrum disorder or significant developmental delay, psychosis, major
depressive disorder, or a history of bipolar disorder if there is concern about
ability to consent
- Treatment for or suspicion of ever having had toxic shock syndrome.
- Fatal fetal anomaly. Will exclude after enrollment if not previously identified