Worldwide T1D incidence has been steadily increasing annually over the past 30 years. The etiology of T1D is multifactorial, consisting of genetic susceptibility and environmental factors, including gut microbiota alterations. The comprehensive profiling of functional and metabolic dysbiosis of gut microbiota in T1D is lacking. To decipher the T1D-associated functional features of gut dysbiosis, we performed integrative metagenomic and metabolomic analyses in pediatric patients with new-onset T1D.