Healthy infants harbor intestinal bacteria that protect against food allergy/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-30
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Atrayees, Chikamso, Joan Chuks
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- 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,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Milk allergic reaction milk allergic reaction,milk allergy,Milk Hypersensitivity,Milk allergic reaction
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy Infants-colonised mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cow’s milk allergic (CMA) infants-colonized mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free mice colonised with human feces from cow’s milk allergic (CMA) infant donors
- 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
- 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
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, mode of birth, sex
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 differentially abundant in cow milk allergy-colonized mice compared to healthy infant-colonized mice
Abundance in Group 1: increased abundance in cow’s milk allergic (CMA) infants-colonized mice
Revision editor(s): WikiWorks, Atrayees, Joan Chuks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-30
Source: Figure 2e
Description: LEfSe analysis of genera that are differentially abundant in cow milk allergy-colonized mice compared to healthy infant-colonized mice
Abundance in Group 1: decreased abundance in cow’s milk allergic (CMA) infants-colonized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Salmonella | ||
| Streptococcus | ||
| unclassified Enterobacteriaceae | ||
| unclassified Lachnospiraceae |
Revision editor(s): WikiWorks, Atrayees, Joan Chuks
