If this “in utero colonization hypothesis” proves correct, there would be major repercussions on our understanding of the establishment of the pioneer human microbiome, its role in human health and the role of environmental, lifestyle, and clinical factors that affect its assembly and function. These studies propose that neither the fetus, the placenta, nor the amniotic fluid are sterile, and that acquisition and colonization of the human gastrointestinal tract begins in utero. However, there is now a multitude of recent studies employing modern sequencing technologies that have challenged the traditional view of human microbiome acquisition.
According to this concept, which has been referred to as the sterile womb paradigm, microbes are acquired both vertically (from the mother) and horizontally (from other humans or the environment) during and after birth. In the second half of the last century, the field reached a consensus that the fetus was maintained in a sterile state. The degree of sterility of the fetal environment and the possibility of in utero microbiome transfer have been debated for almost 150 years. Considering the importance of the pioneer infant microbiota for human development and biology, it is essential that we elucidate the exact mechanisms by which this community is acquired, the time-points when colonization events occur, and the endogenous and exogenous factors that influence these events. In contrast to these models of symbiosis, the modes of transmission for the more complex microbiomes of humans and other vertebrates are more intricate and incompletely understood. Symbiont transmission has been well-established in many host-microbial symbioses, especially in invertebrates (i.e., insects, nematodes, and the Hawaiian squid Euprymna scolopes) where it ranges from being strictly vertical (maternal) to horizontal (transmission between members of the same species or the environment). Given the importance of microbial symbionts to their host’s development and survival, mechanisms must be in place to facilitate their reliable transmission. Research in both animal models and humans suggests that the process of microbial colonization is especially significant during early life, as this period constitutes a critical window for immunological and physiological development. The host-microbiome interrelationship is therefore considered a mutualistic symbiosis, with the human body providing sustenance and an adequate physical environment for the microbial populations, while the microbes execute essential functions, such as aiding in immune system development and providing defense against enteric infections. The gastrointestinal tract of humans is colonized by a dense microbial community that has co-evolved with its host to become a vital component of our biology. 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. Most importantly, the ability to reliably derive axenic animals via cesarean sections strongly supports sterility of the fetal environment in mammals.
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.
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. 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. However, recent studies using molecular techniques suggest bacterial communities in the placenta, amniotic fluid, and meconium from healthy pregnancies. 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.