Experiment 1
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 vaccine Response to vaccine,response to vaccine
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infacts exposed to antibiotics
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infacts not exposed to antibiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These are infacts that were not exposed to antibiotics at peripartum period.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 111
- Group 1 sample size Number of subjects in the case (exposed) group
- 80
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
- metagenomeSeq
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- mode of birth
Signature 1
Source: Figure 4D
Description: Comparison of the centered log-ratio abundance of taxa in the faecal microbiota of Neo-ABX, IP-ABX and PN-ABX infants, relative to No-ABX infants in week 1.
Abundance in Group 1: increased abundance in Infacts not exposed to antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium breve | ||
| Bifidobacterium longum subsp. infantis | ||
| Bifidobacterium pseudocatenulatum | ||
| Collinsella aerofaciens |
Revision editor(s): ShadeAkinremi
Signature 2
Source: Figure 4D
Description: Comparison of the centered log-ratio abundance of taxa in the faecal microbiota of Neo-ABX, IP-ABX and PN-ABX infants, relative to No-ABX infants in week 1.
Abundance in Group 1: decreased abundance in Infacts not exposed to antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus sp. | ||
| Edwardsiella sp. (in: enterobacteria) | ||
| Streptococcus sp. |
Revision editor(s): ShadeAkinremi
Signature 3
Source: Figure 4E
Description: Comparison of the centered log-ratio abundance of taxa in the faecal microbiota of Neo-ABX, IP-ABX and PN-ABX infants, relative to No-ABX infants in week 2.
Abundance in Group 1: increased abundance in Infacts not exposed to antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium breve | ||
| Bifidobacterium bifidum | ||
| Bifidobacterium pseudocatenulatum | ||
| Collinsella aerofaciens |
Revision editor(s): ShadeAkinremi
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 sample size Number of subjects in the control (unexposed) group
- 124
- Group 1 sample size Number of subjects in the case (exposed) group
- 79
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6G, 6H, GI
Description: Extended analyses of the centered-log ratio (CLR) abundance of selected differentially abundant taxa in the faecal microbiota of Neo-ABX, IP-ABX and PN-ABX infants, relative to No-ABX infants in week 1.
Abundance in Group 1: increased abundance in Infacts not exposed to antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium breve | ||
| Bifidobacterium bifidum | ||
| Bifidobacterium longum | ||
| Bifidobacterium longum subsp. infantis |
Revision editor(s): ShadeAkinremi
Signature 2
Source: Figure 6G, 6H, GI
Description: Extended analyses of the centered-log ratio (CLR) abundance of selected differentially abundant taxa in the faecal microbiota of Neo-ABX, IP-ABX and PN-ABX infants, relative to No-ABX infants in week 1.
Abundance in Group 1: decreased abundance in Infacts not exposed to antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter cloacae |
Revision editor(s): ShadeAkinremi
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infacts exposed to antibiotics through their mothers during labor.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 55
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Source: Figure 6G, 6H
Description: Extended analyses of the centered-log ratio (CLR) abundance of selected differentially abundant taxa in the faecal microbiota of IP-ABX relative to No-ABX infants in week 1.
Abundance in Group 1: decreased abundance in Infacts not exposed to antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter | ||
| Klebsiella | ||
| Haemophilus | ||
| Citrobacter | ||
| Streptococcus |
Revision editor(s): ShadeAkinremi
