Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study

Maureen M. Leonard, Francesco Valitutti, Hiren Karathia, Meritxell Pujolassos, Victoria Kenyon, Brian Fanelli, Jacopo Troisi, Poorani Subramanian, Stephanie Camhi, Angelo Colucci, Gloria Serena, Salvatore Cucchiara, Chiara Maria Trovato, Basilio Malamisura, Ruggiero Francavilla, Luca Elli, Nur A. Hasan, Ali R. Zomorrodi, Rita Colwell, Alessio Fasano

Research output: Contribution to journalArticlepeer-review


Other than exposure to gluten and genetic compatibility, the gut microbiome has been suggested to be involved in celiac disease (CD) pathogenesis by mediating interactions between gluten/environmental factors and the host immune system. However, to establish disease progression markers, it is essential to assess alterations in the gut microbiota before disease onset. Here, a prospective metagenomic analysis of the gut microbiota of infants at risk of CD was done to track shifts in the microbiota before CD development. We performed cross-sectional and longitudinal analyses of gut microbiota, functional pathways, and metabolites, starting from 18 mo before CD onset, in 10 infants who developed CD and 10 matched nonaffected infants. Cross-sectional analysis at CD onset identified altered abundance of six microbial strains and several metabolites between cases and controls but no change in microbial species or pathway abundance. Conversely, results of longitudinal analysis revealed several microbial species/strains/pathways/metabolites occurring in increased abundance and detected before CD onset. These had previously been linked to autoimmune and inflammatory conditions (e.g., Dialister invisus, Parabacteroides sp., Lachnospiraceae, tryptophan metabolism, and metabolites serine and threonine). Others occurred in decreased abundance before CD onset and are known to have anti-inflammatory effects (e.g., Streptococcus thermophilus, Faecalibacterium prausnitzii, and Clostridium clostridioforme). Additionally, we uncovered previously unreported microbes/pathways/ metabolites (e.g., Porphyromonas sp., high mannose–type N-glycan biosynthesis, and serine) that point to CD-specific biomarkers. Our study establishes a road map for prospective longitudinal study designs to better understand the role of gut microbiota in disease pathogenesis and therapeutic targets to reestablish tolerance and/or prevent autoimmunity.

Original languageEnglish
Article numbere2020322118
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number29
Publication statusPublished - Jul 20 2021


  • Autoimmunity
  • Celiac disease
  • Gut microbiome
  • Multiomics analysis

ASJC Scopus subject areas

  • General


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