The development of food allergy has been reported to be related with the changes in the gut microbiome, however the specific microbe associated with the pathogenesis of food allergy remains elusive. This study aimed to comprehensively characterize the gut microbiome and iden-tify individual or group gut microbes relating to food‐allergy using 16S rRNA gene sequencing with network analysis. Faecal samples were collected from children with IgE‐mediated food allergies (n = 33) and without food allergy (n = 27). Gut microbiome was profiled by 16S rRNA gene sequencing. OTUs obtained from 16S rRNA gene sequencing were then used to construct a co‐abundance network using Weighted Gene Co‐expression Network Analysis (WGCNA) and mapped onto Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We identified a co‐abundance network module to be positively correlated with IgE‐mediated food allergy and this module was characterized by a hub taxon, namely Ruminococcaceae UCG‐002 (phylum Firmicutes). Functional pathway analysis of all the gut microbiome showed enrichment of methane metabolism and glycerolipid metabolism in the gut microbiome of food‐allergic children and enrichment of ubiquinone and other terpenoid‐quinone biosynthesis in the gut microbiome of non‐food allergic children. We concluded that Ruminococcaceae UCG‐002 may play determinant roles in gut microbial community structure and function leading to the development of IgE‐mediated food allergy.