Longitudinal Follow-Up of Gut and Salivary Microbiota in Children With Food Protein-Induced Enterocolitis Syndrome.

Abstract

Gut microbiota and their metabolites play a key role in digestive dysimmunity and tolerance breakdown, leading to pathologies such as food protein-induced enterocolitis syndrome (FPIES). This study aimed to compare both the gut and salivary microbiota over time between the allergic and tolerant patients and the matched controls. Faecal and salivary samples were collected longitudinally from FPIES allergic patients on an elimination diet, and after their natural tolerance acquisition, and from matched controls (1:1 ratio). 16S rRNA gene sequencing and biostatistical analyses (ALDEx2, ANCOM-BC, DESeq2, LEfSe, and MaAsLIN2) were used to compare microbiota composition between groups. The measurement of faecal short-chain fatty acids (SCFAs) using gas chromatography evaluated the gut microbiota functions. Thirty-eight allergic patients were included (median age: 1.3 years), and 22 became tolerant over time. Allergic patients exhibited lower gut and salivary alpha-diversities, and several different genera (12 in stools, including less Ruminococcus, and 2 in saliva), and higher relative abundance of acetate than the controls. With tolerance acquisition, faecal alpha-diversities partially increased, whereas SCFAs normalised. Ultimately, there were more differences in faecal and salivary microbiota in allergic patients versus after tolerance acquisition (i.e., more Blautia, Ruminococcus, Faecalibacterium, Prevotella-9, and less Escherichia-Shigella in tolerant patients) than between the controls over time. The faecal and salivary dysbiosis observed in allergic patients with FPIES partially resolved after tolerance acquisition. Understanding the underlying mechanisms of dysbiosis is crucial to prevent and help manage FPIES. A prolonged follow-up could determine whether dysbiosis resolution may be complete, and whether this early infancy dysbiosis has long-term consequences on health.