Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA, Nagler CR
Journal
The ISME journal
Year
2016
Dietary intervention with extensively hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG (EHCF+LGG) accelerates tolerance acquisition in infants with cow's milk allergy (CMA). We examined whether this effect is attributable, at least in part, to an influence on the gut microbiota. Fecal samples from healthy controls (n=20) and from CMA infants (n=19) before and after treatment with EHCF with (n=12) and without (n=7) supplementation with LGG were compared by 16S rRNA-based operational taxonomic unit clustering and oligotyping. Differential feature selection and generalized linear model fitting revealed that the CMA infants have a diverse gut microbial community structure dominated by Lachnospiraceae (20.5±9.7%) and Ruminococcaceae (16.2±9.1%). Blautia, Roseburia and Coprococcus were significantly enriched following treatment with EHCF and LGG, but only one genus, Oscillospira, was significantly different between infants that became tolerant and those that remained allergic. However, most tolerant infants showed a significant increase in fecal butyrate levels, and those taxa that were significantly enriched in these samples, Blautia and Roseburia, exhibited specific strain-level demarcations between tolerant and allergic infants. Our data suggest that EHCF+LGG promotes tolerance in infants with CMA, in part, by influencing the strain-level bacterial community structure of the infant gut.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
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)
- 1 month
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
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 |
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
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 |
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