The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

• Published in: Cell host & microbe Vol. 17; no. 2; pp. 260 - 273
• Main Authors: Kostic, Aleksandar D., Gevers, Dirk, Siljander, Heli, Vatanen, Tommi, Hyötyläinen, Tuulia, Hämäläinen, Anu-Maaria, Peet, Aleksandr, Tillmann, Vallo, Pöhö, Päivi, Mattila, Ismo, Lähdesmäki, Harri, Franzosa, Eric A., Vaarala, Outi, de Goffau, Marcus, Harmsen, Hermie, Ilonen, Jorma, Virtanen, Suvi M., Clish, Clary B., Orešič, Matej, Huttenhower, Curtis, Knip, Mikael, Xavier, Ramnik J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 11.02.2015
• Subjects: Cohort Studies; Diabetes Mellitus, Type 1 - microbiology; Gastrointestinal Microbiome; Gastrointestinal Tract - microbiology; Humans; Infant
• ISSN: 1931-3128; 1934-6069; 1934-6069
• DOI: 10.1016/j.chom.2015.01.001

Colonization of the fetal and infant gut microbiome results in dynamic changes in diversity, which can impact disease susceptibility. To examine the relationship between human gut microbiome dynamics throughout infancy and type 1 diabetes (T1D), we examined a cohort of 33 infants genetically predisposed to T1D. Modeling trajectories of microbial abundances through infancy revealed a subset of microbial relationships shared across most subjects. Although strain composition of a given species was highly variable between individuals, it was stable within individuals throughout infancy. Metabolic composition and metabolic pathway abundance remained constant across time. A marked drop in alpha-diversity was observed in T1D progressors in the time window between seroconversion and T1D diagnosis, accompanied by spikes in inflammation-favoring organisms, gene functions, and serum and stool metabolites. This work identifies trends in the development of the human infant gut microbiome along with specific alterations that precede T1D onset and distinguish T1D progressors from nonprogressors. [Display omitted] •Gut microbial metabolic pathways but not taxonomies are stable throughout infancy•Strain composition of high-abundance species remains constant throughout infancy•Decreased community diversity occurs after seroconversion but before onset of T1D•T1D onset is preceded by increased inflammation-associated organisms and pathways Kostic et al. perform a microbiome analysis of type 1 diabetes (T1D), examining the infant gut microbiome as T1D develops. Microbial metabolic pathways remain remarkably stable throughout infancy. T1D onset is preceded by a drop in community diversity and a spike in inflammation-associated species and metabolic pathways.