Healthy infants harbor intestinal bacteria that protect against food allergy/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-30
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Mus musculus
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- milk allergic reaction milk allergic reaction,milk allergy,Milk Hypersensitivity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cows milk allergy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cows milk allergy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- 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).
- relative abundances
- 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
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex, Matched on: "mode of birth (human fecal transplant donors)" 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.mode of birth (human fecal transplant donors)
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-30
Source: Figure 2e
Description: LEfSe analysis of genera that are significantly enriched in healthy-colonized mice or cow milk allergy-colonized mice
Abundance in Group 1: increased abundance in cows milk allergy
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-30
Source: Figure 2e
Description: LEfSe analysis of genera that are significantly enriched in healthy-colonized mice or cow milk allergy-colonized mice
Abundance in Group 1: decreased abundance in cows milk allergy
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Streptococcus | ||
| Salmonella | ||
| unclassified Lachnospiraceae | ||
| unclassified Enterobacteriaceae |
