Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis/Experiment 1
Curated date: 2023/10/09
Curator: Tolulopeo
Revision editor(s): LGeistlinger, Peace Sandy, Tolulopeo, Fiddyhamma
Subjects
- Location of subjects
- United States of America
- 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
- Ulcerative proctosigmoiditis chronic ulcerative rectosigmoiditis (disorder),Proctocolitis,proctosigmoiditis,Proctosigmoiditis (disorder),ulcerative (chronic) proctosigmoiditis,ulcerative proctosigmoiditis,Ulcerative proctosigmoiditis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants diagnosed without food protein-induced allergic proctocolitis (FPIAP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP) who had a minimum of 4 longitudinal stool samples in the first year. FPIAP was diagnosed by the treating physician and confirmed by comprehensive study staff chart review.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 81
- Group 1 sample size Number of subjects in the case (exposed) group
- 79
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NIL
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).
- arcsine square-root
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.20
- 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
- age, Matched on: "disease status" 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.disease status
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- diet, Confounders controlled for: "symptoms" 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.symptoms, Confounders controlled for: "Probiotics use in the first year of life" 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.Probiotics use in the first year of life, age, mode of birth
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Fig 3 (A) and 3 (B)
Description: Summary of key differential taxa between infants with FPIAP and healthy controls. A Significantly different taxa comparing infants with FPIAP to healthy controls (q < 0.20; absolute coefficient > = 0.05) when looking at sample subsets: 0–2 months, last pre-symptomatic, first symptomatic, and first resolved. Bars to the right are enriched in infants with FPIAP, while bars to the left are enriched in the controls. Number of samples in each group is shown under the name of the subset analyzed in that model (FPIAP, control). B Significantly different taxa (q < 0.20) when comparing infants with FPIAP to matched controls before their symptom onset (top section) and then during the symptomatic period (lower section) over the first 2 months of age. Association directionality and numbers are as in (A).
Abundance in Group 1: increased abundance in Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| unclassified Eubacteriales |
Revision editor(s): Tolulopeo, Peace Sandy
Signature 2
Source: Figure 3 (A) and (B)
Description: Summary of key differential taxa between infants with FPIAP and healthy controls. A Significantly different taxa comparing infants with FPIAP to healthy controls (q < 0.20; absolute coefficient > = 0.05) when looking at sample subsets: 0–2 months, last pre-symptomatic, first symptomatic, and first resolved. Bars to the right are enriched in infants with FPIAP, while bars to the left are enriched in the controls. Number of samples in each group is shown under the name of the subset analyzed in that model (FPIAP, control). B Significantly different taxa (q < 0.20) when comparing infants with FPIAP to matched controls before their symptom onset (top section) and then during the symptomatic period (lower section) over the first 2 months of age. Association directionality and numbers are as in (A).
Abundance in Group 1: decreased abundance in Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Lactobacillus |
Revision editor(s): Peace Sandy
