Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 11 November 2022
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Martin R, Makino H, Cetinyurek Yavuz A, Ben-Amor K, Roelofs M, Ishikawa E, Kubota H, Swinkels S, Sakai T, Oishi K, Kushiro A, Knol J
PloS one
Colonization of the infant gut is believed to be critically important for a healthy growth as it influences gut maturation, metabolic, immune and brain development in early life. Understanding factors that influence this process is important, since an altered colonization has been associated with a higher risk of diseases later in life. Fecal samples were collected from 108 healthy neonates in the first half year of life. The composition and functionality of the microbiota was characterized by measuring 33 different bacterial taxa by qPCR/RT qPCR, and 8 bacterial metabolites. Information regarding gender, place and mode of birth, presence of siblings or pets; feeding pattern and antibiotic use was collected by using questionnaires. Regression analysis techniques were used to study associations between microbiota parameters and confounding factors over time. Bacterial DNA was detected in most meconium samples, suggesting bacterial exposure occurs in utero. After birth, colonization by species of Bifidobacterium, Lactobacillus and Bacteroides was influenced by mode of delivery, type of feeding and presence of siblings, with differences found at species level and over time. Interestingly, infant-type bifidobacterial species such as B. breve or B. longum subsp infantis were confirmed as early colonizers apparently independent of the factors studied here, while B. animalis subsp. lactis presence was found to be dependent solely on the type of feeding, indicating that it might not be a common infant gut inhabitant. One interesting and rather unexpected confounding factor was gender. This study contributes to our understanding of the composition of the microbiota in early life and the succession process and the evolution of the microbial community as a function of time and events occurring during the first 6 months of life. Our results provide new insights that could be taken into consideration when selecting nutritional supplementation strategies to support the developing infant gut microbiome.

Experiment 1

Reviewed Marked as Reviewed by Claregrieve1 on 11 November 2022

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1


Location of subjects
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Meconium Meconium
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
cesarean section caesarean 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
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
babies that were delivered by c-section
Group 0 sample size Number of subjects in the control (unexposed) group
Group 1 sample size Number of subjects in the case (exposed) group
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
use of antibiotics between 2 weeks prior to delivery and 2 weeks after delivery, for any reason except for prophylactic use (e.g. cesarean section).

Lab analysis

Sequencing type
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Statistical Analysis

Statistical test
Mixed-Effects Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 11 November 2022

Curated date: 2020-02-23

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks743, Claregrieve1

Source: Figure 1

Description: Differential microbial abundance between infants born by vaginal delivery or C-section.

Abundance in Group 1: decreased abundance in C-section

NCBI Links
Bacteroides caccae
Bacteroides fragilis
Bacteroides ovatus
Bifidobacterium catenulatum
Bifidobacterium longum subsp. longum
Clostridium perfringens
Phocaeicola vulgatus
Bifidobacterium bifidum
Lactobacillus gasseri
Limosilactobacillus reuteri

Revision editor(s): WikiWorks743, Claregrieve1