Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, Folakunmi

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

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Folakunmi

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 ControlLinks
Faecalibacterium
Lachnospiraceae
Oscillospiraceae
Ruminococcus

Revision editor(s): WikiWorks, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Folakunmi

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 ControlLinks
Bifidobacteriaceae
Bifidobacterium
Enterobacteriaceae
Enterococcaceae
Escherichia
Streptococcaceae

Revision editor(s): WikiWorks, Folakunmi

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2024/01/24

Curator: Folakunmi

Revision editor(s): Folakunmi

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

Curated date: 2024/01/24

Curator: Folakunmi

Revision editor(s): Folakunmi

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 ControlLinks
Blautia
Roseburia
Coprococcus

Revision editor(s): Folakunmi

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2024/01/24

Curator: Folakunmi

Revision editor(s): Folakunmi

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

Curated date: 2024/01/24

Curator: Folakunmi

Revision editor(s): Folakunmi

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 ControlLinks
Roseburia
Anaerofustis

Revision editor(s): Folakunmi