Healthy infants harbor intestinal bacteria that protect against food allergy

Study information

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

30643289

DOI Digital object identifier for electronic documents.

10.1038/s41591-018-0324-z

URI

Authors

Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R, Nagler CR

Journal

Nature medicine

Year

2019

There has been a striking generational increase in life-threatening food allergies in Westernized societies1,2. One hypothesis to explain this rising prevalence is that twenty-first century lifestyle practices, including misuse of antibiotics, dietary changes, and higher rates of Caesarean birth and formula feeding have altered intestinal bacterial communities; early-life alterations may be particularly detrimental3,4. To better understand how commensal bacteria regulate food allergy in humans, we colonized germ-free mice with feces from healthy or cow's milk allergic (CMA) infants5. We found that germ-free mice colonized with bacteria from healthy, but not CMA, infants were protected against anaphylactic responses to a cow's milk allergen. Differences in bacterial composition separated the healthy and CMA populations in both the human donors and the colonized mice. Healthy and CMA colonized mice also exhibited unique transcriptome signatures in the ileal epithelium. Correlation of ileal bacteria with genes upregulated in the ileum of healthy or CMA colonized mice identified a clostridial species, Anaerostipes caccae, that protected against an allergic response to food. Our findings demonstrate that intestinal bacteria are critical for regulating allergic responses to dietary antigens and suggest that interventions that modulate bacterial communities may be therapeutically relevant for food allergy.

Experiment 1

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Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): Mus musculus

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: milk allergic reaction milk allergic reaction,milk allergy,Milk Hypersensitivity

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: cows milk allergy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: cows milk allergy
Group 0 sample size Number of subjects in the control (unexposed) group: 8
Group 1 sample size Number of subjects in the case (exposed) group: 9

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

LEfSe

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
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2
Matched on Factors on which subjects have been matched on in a case-control study: age, sex, Matched on: "mode of birth (human fecal transplant donors)" 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.mode of birth (human fecal transplant donors)

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

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Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/01/10

Curator: Lucy Mellor

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Source: Figure 2e

Description: LEfSe analysis of genera that are significantly enriched in healthy-colonized mice or cow milk allergy-colonized mice

Abundance in Group 1: increased abundance in cows milk allergy

NCBI	Quality Control	Links
Enterococcus
Ruminococcus
Oscillospiraceae
Coprobacillus
Clostridiaceae
Eubacteriales
Blautia
Parabacteroides
unclassified Oscillospiraceae
unclassified Barnesiellaceae
unclassified Eubacteriales