Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

Study information

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-6

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

28112736

DOI Digital object identifier for electronic documents.

10.1038/nm.4272

URI

https://www.nature.com/articles/nm.4272

Authors

Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM

Journal

Nature medicine

Year

2017

Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early third trimester (n = 81) were prospectively enrolled for longitudinal sampling through 6 weeks after delivery, and a second matched cross-sectional cohort (n = 81) was additionally recruited for sampling once at the time of delivery. Samples across multiple body sites, including stool, oral gingiva, nares, skin and vagina were collected for each maternal-infant dyad. Whole-genome shotgun sequencing and sequencing analysis of the gene encoding the 16S rRNA were performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R2 = 0.038), this was not true for neonatal stool (meconium; Mann-Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode. For infants at 6 weeks of age, the microbiota structure and function had expanded and diversified with demonstrable body site specificity (P < 0.001, R2 = 0.189) but without discernable differences in community structure or function between infants delivered vaginally or by cesarean surgery (P = 0.057, R2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes substantial reorganization, which is primarily driven by body site and not by mode of delivery.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-6

Curated date: 2022/03/02

Curator: Shaimaa

Revision editor(s): WikiWorks, Lwaldron, Shaimaa, Peace Sandy, Davvve

Subjects

Location of subjects

United States of America

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

Feces , Saliva , Anterior naris , Posterior fornix of vagina , Epithelium of elbow Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva,Anterior nostril,Anterior naris,anterior naris,Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina,Cubital region epithelial tissue,Cubital region epithelium,Elbow epithelial tissue,Elbow epithelium,Epithelial tissue of cubital region,Epithelial tissue of elbow,Epithelium of cubital region,Epithelium of elbow,epithelium of elbow

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Microbiome Microbiome,microbiome

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

Maternal samples taken at delivery.

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

Neonatal samples taken at delivery

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

Neonatal samples taken at delivery

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

82

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

82

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V3-V5

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)?

No

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

4

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-6

Curated date: 2024/02/06

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Fig. S3.

Description: Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (A) Maternal samples taken at delivery. (B) Neonatal samples taken at delivery.

Abundance in Group 1: increased abundance in Neonatal samples taken at delivery

NCBI	Quality Control	Links
Corynebacterium
Propionibacterium
Sphingomonas
Gardnerella
Prevotella
Lactobacillus
Enterobacteriaceae

Revision editor(s): Peace Sandy

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-6

Curated date: 2024/02/06

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Fig. S3

Description: Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (A) Maternal samples taken at delivery. (B) Neonatal samples taken at delivery.

Abundance in Group 1: decreased abundance in Neonatal samples taken at delivery

NCBI	Quality Control	Links
Corynebacterium
Actinomyces
Porphyromonas
Alloprevotella
Neisseria
Haemophilus
Veillonella
Streptococcus
Anaerococcus
Staphylococcus
Propionibacterium
Ruminococcus
Oscillospira
Parabacteroides
Faecalibacterium
Prevotella
Bacteroides
Gardnerella
Lactobacillus

Revision editor(s): Peace Sandy

Experiment 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-6

Curated date: 2024/02/06

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

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

Maternal samples taken at 6 weeks postpartum

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

Infant samples taken at 6 weeks postpartum

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

Infant samples taken at 6 weeks postpartum

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

60

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

60

Lab analysis

Statistical Analysis

Signature 1

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Curated date: 2024/02/06

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Fig. S3

Description: Fig. S3. Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (C) Maternal samples taken at 6 weeks postpartum (D) Infant samples taken at 6 weeks postpartum

Abundance in Group 1: increased abundance in Infant samples taken at 6 weeks postpartum

NCBI	Quality Control	Links
Corynebacterium
Veillonella
Streptococcus
Peptoniphilus
Finegoldia
Propionibacterium
Anaerococcus
Staphylococcus
Bifidobacterium
Clostridium
Klebsiella
Escherichia
Bacteroides

Revision editor(s): Peace Sandy

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-6

Curated date: 2024/02/06

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Fig. S3

Description: Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. . (C) Maternal samples taken at 6 weeks postpartum (D) Infant samples taken at 6 weeks postpartum.

Abundance in Group 1: decreased abundance in Infant samples taken at 6 weeks postpartum

NCBI	Quality Control	Links
Corynebacterium
Capnocytophaga
Actinomyces
Fusobacterium
Alloprevotella
Porphyromonas
Neisseria
Haemophilus
Veillonella
Streptococcus
Staphylococcus
Propionibacterium
Ruminococcus
Oscillospira
Parabacteroides
Roseburia
Faecalibacterium
Bacteroides
Megasphaera
Gardnerella
Atopobium
Lactobacillus

Revision editor(s): Peace Sandy