Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery/Experiment 2

From BugSigDB


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

Curated date: 2024/02/06

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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 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

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

Needs review

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 ControlLinks
Corynebacterium
Veillonella
Streptococcus
Peptoniphilus
Finegoldia
Propionibacterium
Anaerococcus
Staphylococcus
Bifidobacterium
Clostridium
Klebsiella
Escherichia
Bacteroides

Revision editor(s): Peace Sandy

Signature 2

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 ControlLinks
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