Cited by 1,096Gut microbiota and healthInfant Nutrition and HealthMicrobial Community Ecology and Physiology

A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome

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Perez-Muñoz, Maria Elisa, Arrieta, Marie-Claire, Ramer-Tait, Amanda E., Walter, Jens·2017·Microbiome

Abstract

After more than a century of active research, the notion that the human fetal environment is sterile and that the neonate's microbiome is acquired during and after birth was an accepted dogma. However, recent studies using molecular techniques suggest bacterial communities in the placenta, amniotic fluid, and meconium from healthy pregnancies. These findings have led many scientists to challenge the "sterile womb paradigm" and propose that microbiome acquisition instead begins in utero, an idea that would fundamentally change our understanding of gut microbiota acquisition and its role in human development. In this review, we provide a critical assessment of the evidence supporting these two opposing hypotheses, specifically as it relates to (i) anatomical, immunological, and physiological characteristics of the placenta and fetus; (ii) the research methods currently used to study microbial populations in the intrauterine environment; (iii) the fecal microbiome during the first days of life; and (iv) the generation of axenic animals and humans. Based on this analysis, we argue that the evidence in support of the "in utero colonization hypothesis" is extremely weak as it is founded almost entirely on studies that (i) used molecular approaches with an insufficient detection limit to study "low-biomass" microbial populations, (ii) lacked appropriate controls for contamination, and (iii) failed to provide evidence of bacterial viability. Most importantly, the ability to reliably derive axenic animals via cesarean sections strongly supports sterility of the fetal environment in mammals. We conclude that current scientific evidence does not support the existence of microbiomes within the healthy fetal milieu, which has implications for the development of clinical practices that prevent microbiome perturbations after birth and the establishment of future research priorities.

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  • The infant gut is largely thought to be sterile in utero and colonized during birth and postnatally, with a trajectory toward adult-like complexity taking approximately 3 years.

    “Conversely, but equally important, the infant gut is largely thought to be sterile in utero and colonized during birth and postnatally with a trajectory toward an adult-like complexity taking approximately 3 years (Clarke et al., 2014a;Perez-Munoz et al., 2017).”

    From Gut reactions: Breaking down xenobiotic–microbiome interactions (2019) · cites this paper as Perez-Munoz et al., 2017

  • Current research findings suggest that the prenatal oral cavity is sterile until birth, after which colonization with microorganisms occurs upon exposure to the external environment.

    “Current research findings suggest that the prenatal oral cavity is sterile until birth after which colonization with microorganisms occurs upon exposure to the external environment.110”
  • Oral bacteria have been detected at various sites within the uterus.

    “However, oral bacteria have been detected at various sites within the uterus.110, 111”

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Authors
Perez-Muñoz, M. E., Arrieta, M.-C., Ramer-Tait, A. E., & Walter, J.
Affiliations
  • University of Calgary (CA)
  • University of Alberta (CA)
Corresponding author
Walter, Jens
Venue
Microbiome
Published
2017-04-28
Volume
5
Issue
1
Pages
48-48
ISSN
2049-2618 (ISSN-L)
OpenAlex
W2609646274
Cited by
1,096
References
154
Citations by year
2026: 56 · 2025: 81 · 2024: 108 · 2023: 116 · 2022: 140 · 2021: 154 · 2020: 167 · 2019: 117 · 2018: 104 · 2017: 52 · 2016: 1
FWCI
11.25
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Microbiome (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Lincoln (University of Nebraska) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Libraries and Cultural Resources (University of Calgary) (submittedVersion)
Funders
  • Crohn's and Colitis Foundation of America
  • University of Nebraska-Lincoln
  • University of Calgary
  • Crohn's and Colitis Foundation
  • Nebraska Corn Board
  • University of Alberta
  • Alberta Innovates
  • National Institutes of Health
  • Directorate for Biological Sciences
  • National Institute of General Medical Sciences (P20GM104320, R01GM099525)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
neonatal gut microbiota, placenta, amniotic fluid, meconium, cesarean section, contamination control, bacterial viability
MeSH terms
Gastrointestinal Microbiome, Animals, Female, Fetus, Humans, Infant, Infant, Newborn, Pregnancy, Uterus, Microbiota

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