Bifidobacteria support optimal infant vaccine responses/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by KateRasheed on 2025-7-8

Curated date: 2025/04/07

Curator: ShadeAkinremi

Revision editor(s): Chloe, Victoria, KateRasheed, ShadeAkinremi

Subjects

Location of subjects
Australia
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 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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Response to antibiotic Response to antibiotic,response to antibiotic
Group 0 name Corresponds to the control (unexposed) group for case-control studies
No Antibiotic (No-ABX) group [Week-1]
Group 1 name Corresponds to the case (exposed) group for case-control studies
Intrapartum Antibiotic (IP-ABX) group [Week-1]
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants whose mothers received intrapartum antibiotics (within 28 days before or during delivery) and had no direct infant antibiotic exposure up to 6 weeks of age.
Group 0 sample size Number of subjects in the control (unexposed) group
80
Group 1 sample size Number of subjects in the case (exposed) group
49

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).
centered log-ratio
Statistical test
Linear Regression
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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
formula feeding, sex, Confounders controlled for: "collection day" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.collection day

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-7-8

Curated date: 2025/04/10

Curator: ShadeAkinremi

Revision editor(s): ShadeAkinremi, Victoria, KateRasheed

Source: Extented figure 6(g, h, i) And Supplementary Table 11a&b

Description: Differentially abundant microbial species in stool samples collected from IP-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.

Abundance in Group 1: increased abundance in Intrapartum Antibiotic (IP-ABX) group [Week-1]

NCBI Quality ControlLinks
Atlantibacter hermannii
Citrobacter amalonaticus
Citrobacter freundii
Citrobacter koseri
Citrobacter youngae
Enterobacter
Enterobacter chengduensis
Enterobacter cloacae
Enterobacter hormaechei
Enterobacter ludwigii
Enterococcus raffinosus
Haemophilus
Haemophilus parainfluenzae
Klebsiella aerogenes
Klebsiella pneumoniae
Neisseria subflava
Pantoea septica
Schaalia odontolytica
Streptococcus infantis
Streptococcus peroris
Veillonella sp900550175Veillonella sp900550175
Haemophilus sp900756875Haemophilus sp900756875
Haemophilus sp900755445Haemophilus sp900755445
Lancefieldella sp000564995Lancefieldella sp000564995
Haemophilus sp. CCUG 60358
Haemophilus sp. HMSC068C11
Neisseria mucosa C102
Veillonella sp. T11011-6

Revision editor(s): ShadeAkinremi, Victoria, KateRasheed

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-7-8

Curated date: 2025/04/10

Curator: ShadeAkinremi

Revision editor(s): ShadeAkinremi, Victoria, KateRasheed

Source: Extented figure 6(g, h, i) And Supplementary Table 11a&b

Description: Differentially abundant microbial species in stool samples collected from IP-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.

Abundance in Group 1: decreased abundance in Intrapartum Antibiotic (IP-ABX) group [Week-1]

NCBI Quality ControlLinks
Bacteroides
Bifidobacterium
Bifidobacterium breve
Bifidobacterium catenulatum
Bifidobacterium longum subsp. infantis
Bifidobacterium pseudocatenulatum
Parabacteroides
Phocaeicola
Bifidobacterium sp. N4G05

Revision editor(s): ShadeAkinremi, Victoria, KateRasheed