Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid

Study information

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

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

27001291

DOI Digital object identifier for electronic documents.

10.1038/srep23129

URI

Authors

Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S

Journal

Scientific reports

Year

2016

Interaction with intestinal microbes in infancy has a profound impact on health and disease in later life through programming of immune and metabolic pathways. We collected maternal faeces, placenta, amniotic fluid, colostrum, meconium and infant faeces samples from 15 mother-infant pairs in an effort to rigorously investigate prenatal and neonatal microbial transfer and gut colonisation. To ensure sterile sampling, only deliveries at full term by elective caesarean section were studied. Microbiota composition and activity assessment by conventional bacterial culture, 16S rRNA gene pyrosequencing, quantitative PCR, and denaturing gradient gel electrophoresis revealed that the placenta and amniotic fluid harbour a distinct microbiota characterised by low richness, low diversity and the predominance of Proteobacteria. Shared features between the microbiota detected in the placenta and amniotic fluid and in infant meconium suggest microbial transfer at the foeto-maternal interface. At the age of 3-4 days, the infant gut microbiota composition begins to resemble that detected in colostrum. Based on these data, we propose that the stepwise microbial gut colonisation process may be initiated already prenatally by a distinct microbiota in the placenta and amniotic fluid. The link between the mother and the offspring is continued after birth by microbes present in breast milk.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Subjects

Location of subjects: Finland

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: placenta

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: meconium samples

Group 0 sample size Number of subjects in the control (unexposed) group: 15

Group 1 sample size Number of subjects in the case (exposed) group: 15

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): prior to or during c-section

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

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)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Richness Number of species: unchanged

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Figure 4B

Description: Differentially abundant bacteria in meconium sample compared to placenta sample from LEfSe analysis

Abundance in Group 1: increased abundance in meconium

NCBI	Quality Control	Links
Bacillaceae
Streptococcaceae

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Figure 4B

Description: Differentially abundant bacteria in meconium sample compared to placenta sample from LEfSe analysis

Abundance in Group 1: decreased abundance in meconium

NCBI	Quality Control	Links
Enterobacteriaceae

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: maternal colostrum samples