A philosophical perspective on the prenatal in utero microbiome debate

Within the last 6years, a research field has emerged that focuses on the characterization of microbial communities in the prenatal intrauterine environment of humans and their putative role in human health. However, there is considerable controversy around the existence of such microbial populations. The often contentious debate is primarily focused on technical aspects of the research, such as difficulties to assure aseptic sampling and to differentiate legitimate signals in the data from contamination. Although such discussions are clearly important, we feel that the problems with the prenatal microbiome field go deeper. In this commentary, we apply a philosophical framework to evaluate the foundations, experimental approaches, and interpretations used by scientists on both sides of the debate. We argue that the evidence for a sterile womb is based on a scientific approach that aligns well with important principles of the philosophy of science as genuine tests of the hypothesis and multiple angles of explanatory considerations were applied. In contrast, research in support of the in utero colonization hypothesis is solely based on descriptive verifications that do not provide explanatory insight, which weakens the evidence for a prenatal intrauterine microbiome. We propose that a reflection on philosophical principles can inform not only the debate on the prenatal intrauterine microbiome but also other disciplines that attempt to study low-biomass microbial communities.

Automated summary

The emergence of a new research field focusing on the characterization of microbial communities in the prenatal intrauterine environment of humans and their potential impact on human health has led to significant controversy over the existence of such microbial populations. The debate revolves mainly around technical aspects and difficulties in ensuring sterile sampling and distinguishing legitimate signals from contamination in data. Arguments in favor of a sterile womb are based on scientific principles aligning well with philosophy of science, while research supporting in utero colonization hypothesis lacks explanatory insight, weakening evidence for a prenatal intrauterine microbiome. Reflection on philosophical principles can inform debates on this topic and other disciplines studying low-biomass microbial communities.