Group therapy on in utero colonization: seeking common truths and a way forward

Silverstein, Rachel B.; Mysorekar, Indira U.

doi:10.1186/s40168-020-00968-w

Cited by 24 publications

(18 citation statements)

References 49 publications

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“…However, recent investigations have posited that the placenta (70)(71)(72)(73)(74)(75)(76)(77)(78)(79)(80)(81)(82), the amniotic fluid (75,(83)(84)(85), and the developing fetus (86)(87)(88) harbor resident microbiotas, and that the amniotic fluid microbiota functions as a primary source of microorganisms for initial colonization of the offspring in utero (75,83,85,89,90). These juxtaposed views have sparked much debate (69,84,(91)(92)(93)(94)(95).…”

Section: Introductionmentioning

confidence: 99%

Does the Amniotic Fluid of Mice Contain a Viable Microbiota?

et al. 2022

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The existence of an amniotic fluid microbiota (i.e., a viable microbial community) in mammals is controversial. Its existence would require a fundamental reconsideration of fetal in utero exposure to and colonization by microorganisms and the role of intra-amniotic microorganisms in fetal immune development as well as in pregnancy outcomes. In this study, we determined whether the amniotic fluid of mice harbors a microbiota in late gestation. The profiles of the amniotic fluids of pups located proximally or distally to the cervix were characterized through quantitative real-time PCR, 16S rRNA gene sequencing, and culture (N = 21 dams). These profiles were compared to those of technical controls for bacterial and DNA contamination. The load of 16S rRNA genes in the amniotic fluid exceeded that in controls. Additionally, the 16S rRNA gene profiles of the amniotic fluid differed from those of controls, with Corynebacterium tuberculostearicum being differentially more abundant in amniotic fluid profiles; however, this bacterium was not cultured from amniotic fluid. Of the 42 attempted bacterial cultures of amniotic fluids, only one yielded bacterial growth – Lactobacillus murinus. The 16S rRNA gene of this common murine-associated bacterium was not detected in any amniotic fluid sample, suggesting it did not originate from the amniotic fluid. No differences in the 16S rRNA gene load, 16S rRNA gene profile, or bacterial culture were observed between the amniotic fluids located Proximally and distally to the cervix. Collectively, these data indicate that, although there is a modest DNA signal of bacteria in murine amniotic fluid, there is no evidence that this signal represents a viable microbiota. While this means that amniotic fluid is not a source of microorganisms for in utero colonization in mice, it may nevertheless contribute to fetal exposure to microbial components. The developmental consequences of this observation warrant further investigation.

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Section: Introductionmentioning

confidence: 99%

Does the Amniotic Fluid of Mice Contain a Viable Microbiota?

et al. 2022

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“…The attempt to detect and describe a possible human placental microbiome has generated several studies and investigations [76, 46, 61, 77]. Leiby et al [78] published a detailed and well designed study contributing to the subject.…”

Section: Resultsmentioning

confidence: 99%

Contamination detection and microbiome exploration with GRIMER

2021

Preprint

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Exploring microbiome data is a time-consuming task that can be only partially automated due to the specific requirements and goals of each project. Visualizations and analysis platforms are crucial to better guide this step. Best practices in the field are constantly evolving and many pitfalls can lead to biased outcomes. Compositionality of data and sample contamination are two important points that should be carefully considered in early stages of microbiome studies. Detecting contamination can be a challenging task, especially in low-biomass samples or in studies lacking proper controls by design. However, external evidences and commonly identified contaminant taxa can be used to discover and mitigate contamination. We propose GRIMER, a tool that automates analysis, generates plots and runs external tools to create a portable dashboard integrating annotation, taxonomy and metadata. It unifies several sources of evidence towards contamination detection. GRIMER is independent of quantification methods and directly analyses contingency tables to create an interactive and offline report. GRIMER reports can be created in seconds and are accessible for non-specialists, providing an intuitive set of charts to explore data distribution among observations and samples and its connections with external sources. Further, we compiled an extensive list of common contaminants and possible external contaminant taxa reported in the literature and use it to annotate data. GRIMER is open-source and available at: https://gitlab.com/dacs-hpi/grimer

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“…These populations have been shown to be critical determinants of our health and well-being (2,3) and are founded early in life (4). Initial colonization of newborn infants primarily occurs during and immediately following birth (5,6), although there is an active debate on whether in utero seeding plays a role in this early colonization (7)(8)(9)(10)(11)(12)(13). Establishment of the microbiota is theorized to be critical to the programming of the neonatal immune system (14)(15)(16)(17).…”

Section: Introductionmentioning

confidence: 99%

Identification of shared bacterial strains in the vaginal microbiota of reproductive-age mothers and daughters using genome-resolved metagenomics

Brown

Rompalo

Brotman

2021

Preprint

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It has been suggested that the human microbiome might be vertically transmitted from mother to offspring and that early colonizers may play a critical role in development of the immune system. Studies have shown limited support for the vertical transmission of the intestinal microbiota but the derivation of the vaginal microbiota remains largely unknown. Although the vaginal microbiota of children and reproductive age cis women differ in composition, the vaginal microbiota could be vertically transmitted. To determine whether there was any support for this hypothesis, we examined the vaginal microbiota of daughter-mother pairs from the Baltimore metropolitan area (ages 14-27, 32-51; n=39). We assessed whether the daughter’s microbiota was similar in composition to their mother’s using metataxonomics. Permutation tests revealed that while some pairs did have similar vaginal microbiota, the degree of similarity did not exceed that expected by chance. Genome-resolved metagenomics was used to identify shared bacterial strains in a subset of the families (n=22). We found a small number of bacterial strains that were shared between mother-daughter pairs but identified more shared strains between individuals from different families, indicating that vaginal bacteria may display biogeographic patterns. Earlier-in-life studies are needed to demonstrate vertical transmission of the vaginal microbiota.ImportanceEarly colonizers of our microbiota are theorized to play an important role in the development of our immune system, yet we know little about how these communities are established. Vertical transmission from mother to offspring at the time of birth is theorized to be a major source of early colonizers but limited evidence supporting this process has only been shown for the intestinal tract microbiota. The provenance of the vaginal microbiota is largely unknown, although some have posited it is similarly vertically transmitted. We examined the vaginal microbiota of mother-daughter pairs and found limited evidence in support of this hypothesis. However, our analysis also revealed putative biogeographic patterns in the distribution of the strains which comprise the vaginal microbiota. Our results give insight into the role of vertical transmission for the vaginal microbiota and motivate future studies on the biogeography of these bacteria.

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Group therapy on in utero colonization: seeking common truths and a way forward

Cited by 24 publications

References 49 publications

Does the Amniotic Fluid of Mice Contain a Viable Microbiota?

Does the Amniotic Fluid of Mice Contain a Viable Microbiota?

Contamination detection and microbiome exploration with GRIMER

Identification of shared bacterial strains in the vaginal microbiota of reproductive-age mothers and daughters using genome-resolved metagenomics

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