Early Neonatal Meconium Does Not Have a Demonstrable Microbiota Determined through Use of Robust Negative Controls with
            <i>cpn</i>
            60-Based Microbiome Profiling

Santos, Scott J Dos; Pakzad, Zahra; Elwood, Chelsea; Albert, Arianne; Gantt, Soren; Manges, Amee R.; Dumonceaux, Tim J.; Maan, Evelyn J.; Hill, Janet E.; Money, Deborah

doi:10.1128/spectrum.00067-21

Cited by 15 publications

(12 citation statements)

References 55 publications

(94 reference statements)

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“…We profiled the microbiomes of 623 maternal vaginal swabs taken on admission to labour and delivery, 142 meconium samples, 581 stool samples from 10-day-old infants and 462 stool samples from 3-month-old infants. Data for LEGACY meconium samples have been described elsewhere, demonstrating lack of a detectable microbiome signature that could be differentiated from background signal and no evidence of an in-utero stool microbiome ( Dos Santos et al., 2021 ). Following quality control, 71,826,602 reads were retained from 621 vaginal microbiomes, 570 10-day stool microbiomes, 460 3-month stool microbiomes and 176 controls.…”

Section: Resultsmentioning

confidence: 99%

Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life

Santos

Pakzad

Albert

et al. 2023

Front. Cell. Infect. Microbiol.

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Birth mode has been implicated as a major factor influencing neonatal gut microbiome development, and it has been assumed that lack of exposure to the maternal vaginal microbiome is responsible for gut dysbiosis among caesarean-delivered infants. Consequently, practices to correct dysbiotic gut microbiomes, such as vaginal seeding, have arisen while the effect of the maternal vaginal microbiome on that of the infant gut remains unknown. We conducted a longitudinal, prospective cohort study of 621 Canadian pregnant women and their newborn infants and collected pre-delivery maternal vaginal swabs and infant stool samples at 10-days and 3-months of life. Using cpn60-based amplicon sequencing, we defined vaginal and stool microbiome profiles and evaluated the effect of maternal vaginal microbiome composition and various clinical variables on the development of the infant stool microbiome. Infant stool microbiomes showed significant differences in composition by delivery mode at 10-days postpartum; however, this effect could not be explained by maternal vaginal microbiome composition and was vastly reduced by 3 months. Vaginal microbiome clusters were distributed across infant stool clusters in proportion to their frequency in the overall maternal population, indicating independence of the two communities. Intrapartum antibiotic administration was identified as a confounder of infant stool microbiome differences and was associated with lower abundances of Escherichia coli, Bacteroides vulgatus, Bifidobacterium longum and Parabacteroides distasonis. Our findings demonstrate that maternal vaginal microbiome composition at delivery does not affect infant stool microbiome composition and development, suggesting that practices to amend infant stool microbiome composition focus factors other than maternal vaginal microbes.

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Section: Resultsmentioning

confidence: 99%

Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life

Santos

Pakzad

Albert

et al. 2023

Front. Cell. Infect. Microbiol.

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“…Indeed, Enterobacter and Escherichia, commonly identified contaminants in laboratory and extraction kit reagents [65,66] have been reported as the most abundant genera detected in amniotic fluid [67,68] . Similarly, controlled studies have reported that the microbial content of meconium does not differ from negative controls [69,70] . A recent study claimed to have detected bacterial DNA and viable bacteria in the fetal intestine using 16S rRNA gene sequencing, qPCR, electron microscopy, and bacterial culture of Micrococcus luteus-related bacteria, which appeared to show adaptations to the fetal environment, re-igniting the controversy surrounding the existence of in utero microbiomes [71,72] .…”

Section: In Utero Microbiome Transfermentioning

confidence: 88%

First encounters of the microbial kind: perinatal factors direct infant gut microbiome establishment

Dempsey¹,

Ryan²,

Ross³

et al. 2022

MRR

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The human gut microbiome harbors a diverse range of microbes that play a fundamental role in the health and well-being of their host. The early-life microbiome has a major influence on human development and long-term health. Perinatal factors such as maternal nutrition, antibiotic use, gestational age and mode of delivery influence the initial colonization, development, and function of the neonatal gut microbiome. The perturbed early-life gut microbiome predisposes infants to diseases in early and later life. Understanding how perinatal factors guide and shape the composition of the early-life microbiome is essential to improving infant health. The following review provides a synopsis of perinatal factors with the most decisive influences on initial microbial colonization of the infant gut.

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“… 91 – 93 This “ in utero colonization theory” leaves open the possibility of a maternal–fetal efflux of commensal bacteria, 87 providing another framework of how prenatal air pollution exposure could more directly influence an infant’s intestinal microbiome. However, the presence of bacteria in meconium samples is also debated, because studies 94 , 95 reported that the bacteria found in the majority of the “dogma-challenging” studies originated from contamination from lab reagents and the environment. During childhood, black carbon particles may also be transported into the gut after mucociliary clearance of particles from the airways or systemic uptake after inhalation.…”

Section: Discussionmentioning

confidence: 99%

Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIR ON AGE Birth Cohort

Pee

Hogervorst

Dockx

et al. 2023

Environ Health Perspect

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Background: The gut microbiome plays an essential role in human health. Despite the link between air pollution exposure and various diseases, its association with the gut microbiome during susceptible life periods remains scarce. Objectives: In this study, we examined the association between black carbon particles quantified in prenatal and postnatal biological matrices and bacterial richness and diversity measures, and bacterial families. Methods: A total of 85 stool samples were collected from 4- to 6-y-old children enrolled in the ENVIRonmental influence ON early AGEing birth cohort. We performed 16S rRNA gene sequencing to calculate bacterial richness and diversity indices (Chao1 richness, Shannon diversity, and Simpson diversity) and the relative abundance of bacterial families. Black carbon particles were quantified via white light generation under femtosecond pulsed laser illumination in placental tissue and cord blood, employed as prenatal exposure biomarkers, and in urine, used as a post-natal exposure biomarker. We used robust multivariable-adjusted linear models to examine the associations between quantified black carbon loads and measures of richness (Chao1 index) and diversity (Shannon and Simpson indices), adjusting for parity, season of delivery, sequencing batch, age, sex, weight and height of the child, and maternal education. Additionally, we performed a differential relative abundance analysis of bacterial families with a correction for sampling fraction bias. Results are expressed as percentage difference for a doubling in black carbon loads with 95% confidence interval (CI). Results: Two diversity indices were negatively associated with placental black carbon [Shannon: (95% CI: , ); Simpson: (95% CI: , )], cord blood black carbon [Shannon: (95% CI: , ); Simpson: (95% CI: , )], and urinary black carbon [Shannon: (95% CI: , ); Simpson: (95% CI: , )]. The explained variance of black carbon on the above indices varied from 6.1% to 16.6%. No statistically significant associations were found between black carbon load and the Chao1 richness index. After multiple testing correction, placental black carbon was negatively associated with relative abundance of the bacterial families Defluviitaleaceae and Marinifilaceae , and urinary black carbon with Christensenellaceae and Coriobacteriaceae ; associations with cord blood black carbon were not statistically significant after correction. Conclusion: Black carbon particles quantified in prenatal and postnatal biological matrices were as...

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Early Neonatal Meconium Does Not Have a Demonstrable Microbiota Determined through Use of Robust Negative Controls with cpn 60-Based Microbiome Profiling

Cited by 15 publications

References 55 publications

Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life

Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life

First encounters of the microbial kind: perinatal factors direct infant gut microbiome establishment

Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIR ON AGE Birth Cohort

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