Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Italy
- 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
- 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 controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IgE mediated cow's milk allergy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- diagnosis of IgE mediated cow's milk allergy based on clinical history and level of IgE serum-specific anti-cow's milk proteins
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- Welch's T-Test
- 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
- age, body weight, sex
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 1d, Text ("The gut microbiota of cow's milk allergic infants exhibits significantly increased diversity and altered composition"), Supplemental Table 2
Description: Differentially abundant taxa between healthy and cow's milk allergy pre-treatment groups
Abundance in Group 1: increased abundance in IgE mediated cow's milk allergy
NCBI | Quality Control | Links |
---|---|---|
Faecalibacterium | ||
Lachnospiraceae | ||
Oscillospiraceae | ||
Ruminococcus |
Signature 2
Source: Figure 1d, Text("The gut microbiota of cow's milk allergic infants exhibits significantly increased diversity and altered composition"), Supplemental Table 2
Description: Differentially abundant taxa between healthy and cow's milk allergy pre-treatment groups
Abundance in Group 1: decreased abundance in IgE mediated cow's milk allergy
NCBI | Quality Control | Links |
---|---|---|
Bifidobacteriaceae | ||
Bifidobacterium | ||
Enterobacteriaceae | ||
Enterococcaceae | ||
Escherichia | ||
Streptococcaceae |
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre EHCF with LGG
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post EHCF with LGG
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cow milk allergic infants post treatment with EHCF with LGG
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: text ("Treatment with LGG-supplemented EHCF increases the relative abundance of butyrate-producing bacteria and fecal butyrate levels"), Supplemental Table 2
Description: Differentially abundant taxa between pre EHCF with LGG and post EHCF with LGG groups
Abundance in Group 1: increased abundance in post EHCF with LGG
NCBI | Quality Control | Links |
---|---|---|
Blautia | ||
Roseburia | ||
Coprococcus |
Revision editor(s): Folakunmi
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lactobacillus rhamnosus GG Lactobacillus rhamnosus ATCC 53103,Lactobacillus rhamnosus str. GG,Lactobacillus rhamnosus strain GG,Lactobacillus rhamnosus GG,lactobacillus rhamnosus GG
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Post EHCF treatment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post EHCF with LGG
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Within text result ("Treatment with LGG-supplemented EHCF increases the relative abundance of butyrate-producing bacteria and fecal butyrate levels", lines 10-12), supplemental table 2
Description: Differentially abundant taxa between Post EHCF and Post EHCF with LGG groups
Abundance in Group 1: increased abundance in Post EHCF with LGG
NCBI | Quality Control | Links |
---|---|---|
Roseburia | ||
Anaerofustis |
Revision editor(s): Folakunmi