Early infancy dysbiosis in food protein-induced enterocolitis syndrome: A prospective cohort study

Allergy. 2023 Jun;78(6):1595-1604. doi: 10.1111/all.15644. Epub 2023 Jan 24.


Background: The microbiome associations of food protein-induced enterocolitis syndrome (FPIES) are understudied. We sought to prospectively define the clinical features of FPIES in a birth cohort, and investigate for the evidence of gut dysbiosis.

Methods: We identified children diagnosed with FPIES in the Gastrointestinal Microbiome and Allergic Proctocolitis Study, a healthy infant cohort. Children were assessed and stools were collected at each well child visit. The clinical features of the children with FPIES were summarized. Stool microbiome was analyzed using 16S rRNA sequencing comparing children with and without FPIES.

Results: Of the 874 children followed up for 3 years, 8 FPIES cases (4 male) were identified, yielding a cumulative incidence of 0.92%. The most common triggers were oat and rice (n = 3, each) followed by milk (n = 2). The children with FPIES were more likely to have family history of food allergy (50% vs. 15.9% among unaffected, p = .03). The average age of disease presentation was 6 months old. During the first 6 months of life, stool from children with FPIES contained significantly less Bifidobacterium adolescentis, but more pathobionts, including Bacteroides spp. (especially Bacteroides fragilis), Holdemania spp., Lachnobacterium spp., and Acinetobacter lwoffii. The short-chain fatty acid (SCFA)-producing Bifidobacterium shunt was expressed significantly less in the stool from FPIES children.

Conclusions: In this cohort, the cumulative incidence over the 3-year study period was 0.92%. During the first 6 months of life, children with FPIES had evidence of dysbiosis and SCFA production pathway was expressed less in their stool, which may play an important role in the pathogenesis of FPIES.

Keywords: FPIES; Stool microbiome; birth cohort study; food allergy; food protein-induced enterocolitis syndrome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Allergens
  • Child
  • Dietary Proteins / adverse effects
  • Dysbiosis
  • Enterocolitis* / diagnosis
  • Enterocolitis* / epidemiology
  • Enterocolitis* / etiology
  • Food Hypersensitivity* / diagnosis
  • Humans
  • Infant
  • Male
  • Prospective Studies
  • RNA, Ribosomal, 16S / genetics
  • Syndrome


  • RNA, Ribosomal, 16S
  • Dietary Proteins
  • Allergens