Initial meconium microbiome in Chinese neonates delivered naturally or by cesarean section

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

29459704

DOI Digital object identifier for electronic documents.

10.1038/s41598-018-21657-7

URI

Authors

Shi YC, Guo H, Chen J, Sun G, Ren RR, Guo MZ, Peng LH, Yang YS

Journal

Scientific reports

Year

2018

Previous studies have revealed significant differences in microbiome compositions between infants delivered via cesarean section (C-section) and natural vaginal birth. However, the importance of the delivery mode in the first days of life remains unclear. Importantly, this stage is minimally affected by infant feeding. Here, we used a metagenomic sequencing technique to characterize the meconium microbiome from the feces of a Chinese cohort of vaginally and C-section-delivered infants, including in vitro fertilization (IVF) newborns, during the first 24 h after birth. Meconium microbiome diversity was higher in vaginally delivered infants than that in C-section-delivered infants. Propionibacterium species were most abundant in the vaginally delivered infants, whereas the C-section group had high levels of Bacillus licheniformis. The two IVF newborns delivered by C-section harbored microbial communities similar to the vaginal microbiome in terms of taxonomic composition. Metabolic functions of the C-section group suffered more from the influence of the dominant group (B. licheniformis), whereas the vaginal group was more homogeneous, with a metabolism dominated by multi-microbes. Moreover, different modes of delivery affected the antibiotic resistance gene (ARG) prevalence. These findings provide novel information for the development of strategies to guide a healthy mode of delivery and promote the formation of healthy microbiota.

Experiment 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Shaimaa, WikiWorks, Victoria

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Meconium Meconium,meconium

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Cesarean section caesarean section,Cesarean section,cesarean section

Group 0 name Corresponds to the control (unexposed) group for case-control studies: vaginal delivery

Group 1 name Corresponds to the case (exposed) group for case-control studies: C-section

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: the first-pass meconium stools from within 24 h of delivery

Group 0 sample size Number of subjects in the control (unexposed) group: 8

Group 1 sample size Number of subjects in the case (exposed) group: 10

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None of VD mothers received antibiotics during delivery. CSD mothers recieved prophylactic antibiotics after delivery.

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3.5

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2021/08/7

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Fatima, WikiWorks

Source: Figure 1

Description: Comparison of the microbiome of vaginally delivered and C-section-delivered newborns

Abundance in Group 1: increased abundance in C-section

NCBI	Quality Control	Links
Aeromonas veronii
Alphaproteobacteria
Bacillaceae
Bacillales
Bacilli
Bacillus
Bacillus amyloliquefaciens
Bacillus licheniformis
Deinococcaceae
Deinococcales
Deinococci
Deinococcus
Deinococcota
Eubacteriaceae
Eubacterium
Faecalibacterium
Faecalibacterium prausnitzii
Bacillota
Phocaeicola vulgatus
Stenotrophomonas
Lysobacteraceae
Lysobacterales
Agathobacter rectalis

Revision editor(s): Fatima, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure 1

Description: ComparisonofthemicrobiomesofvaginallydeliveredandC-section-deliverednewborns

Abundance in Group 1: decreased abundance in C-section

NCBI	Quality Control	Links
Actinomycetes
Actinomycetota
Actinomycetales
Propionibacteriaceae
Gammaproteobacteria
Cutibacterium acnes
Propionibacterium
Pseudomonadales
Pseudonocardiaceae
Burkholderiales
Betaproteobacteria
Comamonas
Comamonadaceae
Comamonas testosteroni
Pseudomonas

Revision editor(s): WikiWorks