Fecal Microbiome and Metabolome Differ in Healthy and Food-Allergic Twins

Abstract

In this study, the authors characterize fecal microbiomes to identify bacterial taxa and their products that may influence the expression of food allergies in children and adults.Participants included a cohort of 18 twin pairs across a broad age range, 13 of which were discordant twin pairs (one sibling had a food allergy and the other was healthy) and 5 of which were concordant twin pairs (both siblings had a food allergy).First, fecal samples were collected from the twin pairs who lived in the same household, in which they equally avoided the foods to which the affected twin was found to be allergic. 16S ribosomal RNA gene amplicon sequencing was performed on the fecal samples from the 12 discordant twin pairs and 5 concordant twin pairs, and the microbial composition between the twin pairs was compared. For each twin pair, the authors compared the relative abundance of operational taxonomic units (OTUs) and then calculated an OTU correlation score. Next, liquid chromatography-tandem mass spectrometry was used to measure the abundance of metabolic compounds in the same set of fecal samples. Finally, the authors compared the microbial taxa and their metabolites and correlated the data sets to identify any bacterial species or metabolites that may be mechanistically related to health.The healthy and allergic twins exhibited distinct fecal microbial profiles. A bacterial signature of 64 OTUs distinguished healthy from allergic twins; the OTUs enriched in the healthy twins were largely taxa from the Clostridia class. Healthy and allergic twins also exhibit differential enrichment in fecal metabolic pathways, most notably with the enrichment of diacylglycerol in healthy twins. Next, there was a significant association between healthy twins and Phascolarctobacterium faecium and Ruminococcus bromii. These are species from a taxon not previously associated with protection against allergies.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.With this study, the authors are one of the first to offer unique insight into the fecal microbiome and metabolome in allergic and nonallergic patients. By identifying bacterial species and metabolites that may be mechanistically related to health, it may be possible in the future to integrate live microbiome-modulating biotherapies into the treatment of food allergies. Oral immunotherapy, which typically achieves only short-term desensitization and often is accompanied by gastrointestinal symptoms, can potentially be targeted with biotherapeutics to ultimately improve its efficacy and safety. Further investigation is warranted to determine if or how the identified metabolites contribute to protection against allergies.