Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children

From BugSigDB
Needs review
study design
case-control
Citation
PMID
URI
Authors
Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S, Davis CM
Journal
Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology
Year
2018
BACKGROUND: Intestinal microbes have been shown to influence predisposition to atopic disease, including food allergy. The intestinal microbiome of food-allergic children may differ in significant ways from genetically similar non-allergic children and age-matched controls. The aim was to characterize fecal microbiomes to identify taxa that may influence the expression of food allergy. METHODS: Stool samples were collected from children with IgE-mediated food allergies, siblings without food allergy, and non-allergic controls. Stool microbiome characterization was performed via next-generation sequencing (Illumina) of the V1V3 and V4 variable regions of the 16S rRNA gene. Bacterial diversity, evenness, richness, and relative abundance of the operational taxonomic units (OTUs) were evaluated using QIIME. ANOVA and Welch's t test were utilized to compare groups. RESULTS: Sixty-eight children were included: food-allergic (n = 22), non-food-allergic siblings (n = 25), and controls (n = 21). When comparing fecal microbial communities across groups, differences were noted in Rikenellaceae (P = .035), Actinomycetaceae (P = .043), and Pasteurellaceae (P = .018), and nine other distinct OTUs. Food-allergic subjects had enrichment for specific microbes within the Clostridia class and Firmicutes phylum (Oscillobacter valericigenes, Lachnoclostridium bolteae, Faecalibacterium sp.) compared to siblings and controls. Identification of Clostridium sp. OTUs revealed differences in specific Clostridia drive the separation of the allergic from the siblings and controls. Alistipes sp. were enriched in non-allergic siblings. CONCLUSIONS: Comparisons in the fecal microbiome of food-allergic children, siblings, and healthy children point to key differences in microbiome signatures, suggesting the role of both genetic and environmental contributors in the manifestation of food-allergic disease.

Experiment 1


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)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
food allergy Food Hypersensitivity,Food intolerance,food allergy
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
child with food allergy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
child with food allergy
Group 0 sample size Number of subjects in the control (unexposed) group
21
Group 1 sample size Number of subjects in the case (exposed) group
22

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
Mann-Whitney (Wilcoxon)
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
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2020-03-20

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

Source: Figure 3, Figure 4, Figure 5

Description: Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls

Abundance in Group 1: increased abundance in child with food allergy

NCBI Links
Oscillibacter valericigenes
Faecalibacterium sp.
s__Lachnoclostridium_bolteaes__Lachnoclostridium_bolteae

Revision editor(s): WikiWorks743

Signature 2

Needs review

Curated date: 2020-03-20

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

Source: Figure 3, Figure 4, Figure 5

Description: Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls

Abundance in Group 1: decreased abundance in child with food allergy

NCBI Links
Blautia sp.

Revision editor(s): WikiWorks743

Experiment 2


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)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
food allergy Food Hypersensitivity,Food intolerance,food allergy
Group 0 name Corresponds to the control (unexposed) group for case-control studies
healthy sibling
Group 1 name Corresponds to the case (exposed) group for case-control studies
child with food allergy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
child with food allergy
Group 0 sample size Number of subjects in the control (unexposed) group
25
Group 1 sample size Number of subjects in the case (exposed) group
22

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
16S
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
Mann-Whitney (Wilcoxon)
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


Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2020-03-20

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

Source: Figure 3, Figure 5

Description: Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings

Abundance in Group 1: increased abundance in child with food allergy

NCBI Links
s__Lachnoclostridium_bolteaes__Lachnoclostridium_bolteae

Revision editor(s): WikiWorks743

Signature 2

Needs review

Curated date: 2020-03-20

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

Source: Figure 3, Figure 5

Description: Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings

Abundance in Group 1: decreased abundance in child with food allergy

NCBI Links
Alistipes putredinis
Alistipes sp.

Revision editor(s): WikiWorks743

Experiment 3


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)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
food allergy Food Hypersensitivity,Food intolerance,food allergy
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
healthy sibling
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
sibling with no food allergy
Group 0 sample size Number of subjects in the control (unexposed) group
21
Group 1 sample size Number of subjects in the case (exposed) group
25

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
16S
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
Mann-Whitney (Wilcoxon)
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


Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2020-03-20

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

Source: Figure 3, Figure 4, Figure 5

Description: Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls

Abundance in Group 1: increased abundance in healthy sibling

NCBI Links
Oscillibacter valericigenes
Faecalibacterium sp.
Alistipes putredinis
Alistipes sp.

Revision editor(s): WikiWorks743

Signature 2

Needs review

Curated date: 2020-03-20

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

Source: Figure 3, Figure 4, Figure 5

Description: Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls

Abundance in Group 1: decreased abundance in healthy sibling

NCBI Links
Blautia sp.

Revision editor(s): WikiWorks743

Experiment 4


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)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
age age
Group 0 name Corresponds to the control (unexposed) group for case-control studies
<7 years
Group 1 name Corresponds to the case (exposed) group for case-control studies
7-18 years
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
child age 7-18
Group 0 sample size Number of subjects in the control (unexposed) group
26
Group 1 sample size Number of subjects in the case (exposed) group
42

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
16S
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
Mann-Whitney (Wilcoxon)
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



Signature 1

Needs review

Curated date: 2020-03-20

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

Source: Text

Description: Differentially abundant taxons in children <7 years compared to children 7-18 years

Abundance in Group 1: increased abundance in 7-18 years

NCBI Links
Bacteroidetes

Revision editor(s): WikiWorks743

Signature 2

Needs review

Curated date: 2020-03-20

Curator: Lucy Mellor

Revision editor(s): WikiWorks743

Source: Text

Description: Differentially abundant taxons in children <7 years compared to children 7-18 years

Abundance in Group 1: decreased abundance in 7-18 years

NCBI Links
Firmicutes
Proteobacteria
Erysipelotrichaceae
Lachnospiraceae
Peptostreptococcaceae

Revision editor(s): WikiWorks743