Healthy infants harbor intestinal bacteria that protect against food allergy/Experiment 1

From BugSigDB


Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects Country from which study subjects were recruited
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 Experimental technique used for quantifying microbial abundance
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

Statistical test Statistical test or computational tool used for differential abundance testing
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, sex, "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 for the "Matched on" property.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

Needs review

Curated date: 2020-04-16

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

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

NCBI Links
Enterococcus
Barnesiellaceae
Ruminococcus
Oscillospiraceae
Coprobacillus
Clostridiaceae
Eubacteriales
Blautia
Parabacteroides

Revision editor(s): WikiWorks743

Signature 2

Needs review

Curated date: 2020-04-16

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

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 Links
Lachnospiraceae
Erysipelotrichaceae
Enterobacteriaceae
Streptococcus
Salmonella

Revision editor(s): WikiWorks743