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 Uniform resource identifier for web resources.

Authors

Feehley T., Plunkett C.H., Bao R., Choi Hong S.M., Culleen E., Belda-Ferre P., Campbell E., Aitoro R., Nocerino R., Paparo L., Andrade J., Antonopoulos D.A., Berni Canani R., Nagler C.R.

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

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees, Chikamso, Joan Chuks

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: 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,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 Infants-colonised mice

Group 1 name Corresponds to the case (exposed) group for case-control studies: cow’s milk allergic (CMA) infants-colonized mice

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Germ-free mice colonised with human feces from cow’s milk allergic (CMA) infant donors

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, mode of birth, sex

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

Edit History Delete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Atrayees, Joan Chuks

Source: Figure 2e

Description: LEfSe analysis of genera that are differentially abundant in cow milk allergy-colonized mice compared to healthy infant-colonized mice

Abundance in Group 1: increased abundance in cow’s milk allergic (CMA) infants-colonized mice

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

Revision editor(s): WikiWorks, Atrayees, Joan Chuks

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Atrayees, Joan Chuks

Source: Figure 2e

Description: LEfSe analysis of genera that are differentially abundant in cow milk allergy-colonized mice compared to healthy infant-colonized mice

Abundance in Group 1: decreased abundance in cow’s milk allergic (CMA) infants-colonized mice

NCBI	Quality Control	Links
Enterobacteriaceae
Salmonella
Streptococcus
unclassified Enterobacteriaceae
unclassified Lachnospiraceae

Revision editor(s): WikiWorks, Atrayees, Joan Chuks