Fecal microbiome and metabolome differ in healthy and food-allergic twins
Riyue Bao, … , Kari C. Nadeau, Cathryn R. Nagler
Riyue Bao, … , Kari C. Nadeau, Cathryn R. Nagler
Published January 19, 2021
Citation Information: J Clin Invest. 2021;131(2):e141935. https://doi.org/10.1172/JCI141935.
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Clinical Research and Public Health Immunology

Fecal microbiome and metabolome differ in healthy and food-allergic twins

Abstract

BACKGROUND There has been a striking generational increase in the prevalence of food allergies. We have proposed that this increase can be explained, in part, by alterations in the commensal microbiome.METHODS To identify bacterial signatures and metabolic pathways that may influence the expression of this disease, we collected fecal samples from a unique, well-controlled cohort of twins concordant or discordant for food allergy. Samples were analyzed by integrating 16S rRNA gene amplicon sequencing and liquid chromatography–tandem mass spectrometry metabolite profiling.RESULTS A bacterial signature of 64 operational taxonomic units (OTUs) distinguished healthy from allergic twins; the OTUs enriched in the healthy twins were largely taxa from the Clostridia class. We detected significant enrichment in distinct metabolite pathways in each group. The enrichment of diacylglycerol in healthy twins is of particular interest for its potential as a readily measurable fecal biomarker of health. In addition, an integrated microbial-metabolomic analysis identified a significant association between healthy twins and Phascolarctobacterium faecium and Ruminococcus bromii, suggesting new possibilities for the development of live microbiome-modulating biotherapeutics.CONCLUSION Twin pairs exhibited significant differences in their fecal microbiomes and metabolomes through adulthood, suggesting that the gut microbiota may play a protective role in patients with food allergies beyond the infant stage.TRIAL REGISTRATION Participants in this study were recruited as part of an observational study (ClinicalTrials.gov NCT01613885) at multiple sites from 2014 to 2018.FUNDING This work was supported by the Sunshine Charitable Foundation; the Moss Family Foundation; the National Institute of Allergy and Infectious Diseases (NIAID) (R56AI134923 and R01AI 140134); the Sean N. Parker Center for Allergy and Asthma Research; the National Heart, Lung, and Blood Institute (R01 HL 118612); the Orsak family; the Kepner family; and the Stanford Institute for Immunity, Transplant and Infection.

Authors

Riyue Bao, Lauren A. Hesser, Ziyuan He, Xiaoying Zhou, Kari C. Nadeau, Cathryn R. Nagler

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Figure 2

Relative abundance of microbial composition of healthy and allergic twins does not differ at the family level.

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Relative abundance of microbial composition of healthy and allergic twin...
(A) Relative abundance of taxonomy at the family level. Sample IDs are shown on the x axis (n = 34). Discordant twins (12 pairs, n = 24), for which one member was healthy and the other member was allergic; concordant twins (5 pairs, n = 10), for which both members were allergic. Of 36 total samples in the twin cohort, 1 sample (S5077) failed sequencing and yielded 0 reads, hence the corresponding twin pair (no. 13) was excluded from 16S analysis. (B and C) Correlation of OTU abundance between members from each twin pair, with the comparison between concordant and discordant twin pairs shown in B and the comparison between dizygotic and monozygotic twins shown in C. Each dot denotes 1 twin pair (17 pairs shown). (D and E) Shannon α diversity index between healthy and allergic groups, with all samples are shown in D (n = 34) and only discordant twins shown in E (n = 24). Each dot denotes 1 sample. In B–E, the bounds of the boxes represent the 25th and 75th percentiles, the horizontal centers line indicate the medians, and the whiskers extend to data points within a maximum of 1.5 times the IQR. Two-tailed Wilcoxon’s rank-sum test was used in B–D, and two-tailed Wilcoxon’s signed-rank test was used in E.