Food Science and Technology Department


Department of Food Science and Technology: Faculty Publications

Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study

Thomas Auchtung, University of Nebraska - Lincoln
Christopher J. Stewart, Baylor College of Medicine, Houston, TX
Daniel P. Smith, Baylor College of Medicine, Houston, TX
Eric W. Triplett, University of Florida
Daniel Agardh, Skåne University Hospital, Malmö, Sweden
William A. Hagopian, Pacific Northwest Research Institute, Seattle, WA
Anette G. Ziegler, Technische Universität München
Marian J. Rewers, University of Colorado, Aurora
Jin-Xiong She, Medical College of Georgia, Augusta University
Jorma Toppari, University of Turku
Åke Lemmark, Lund University/CRC, Skane University Hospital, Malmö, Sweden
Beena Akolkar, National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD
Jeffrey P. Krischer, Morsani College of Medicine, University of South Florida
Kendra Vehik, Morsani College of Medicine, University of South Florida
Jennifer Auchtung, University of Nebraska - Lincoln
Nadfim J. Ajami, Baylor College of Medicine, Houston, TX
Joseph F. Petrosino, Baylor College of Medicine, Houston

Document Type Article

U.S. government work

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,


Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over time, in contrast with the increase in bacterial diversity. Fungal profiles had high temporal variation, but there was less variation from month-to-month in an individual than among different children of the same age. Fungal composition varied with geography, diet, and the use of probiotics. Multiple Candida spp. were at higher relative abundance in children than adults, while Malassezia and certain food-associated fungi were lower in children. There were only subtle fungal differences associated with the subset of children that developed islet autoimmunity or type 1 diabetes. Having proper fungal exposures may be crucial for children to establish appropriate responses to fungi and limit the risk of infection: the data here suggests those gastrointestinal exposures are limited and variable.