Temporal development of the gut microbiome in early childhood from the TEDDY study

• DOI: 10.1038/s41586-018-0617-x
• Publication Date: 2018-10-18T16:45:03Z
• Authors: Christopher J. St...; Nadim J. Ajami; Jacqueline L. O’B...; Diane S. Hutchinson; Daniel P. Smith; Matthew C. Wong; Matthew C. Ross; Richard E. Lloyd; HarshaVardhan Dod...; Ginger A. Metcalf; Donna Muzny; Richard A. Gibbs; Tommi Vatanen; Curtis Huttenhower; Ramnik J. Xavier; Marian Rewers; William Hagopian; Jorma Toppari; Anette-G. Ziegler; Jin-Xiong She; Beena Akolkar; Ake Lernmark; Heikki Hyoty; Kendra Vehik; Jeffrey P. Krischer; Joseph F. Petrosino
• Keywords: Bacteroides fragilis; Bifidobacterium bifidum

The development of the microbiome from infancy to childhood is dependent on a range factors, with microbial–immune crosstalk during this time thought be involved in pathobiology later life diseases1–9 such as persistent islet autoimmunity and type 1 diabetes10–12. However, our knowledge, no studies have performed extensive characterization early large, multi-centre population. Here we analyse longitudinal stool samples 903 children between 3 46 months age by 16S rRNA gene sequencing (n = 12,005) metagenomic 10,867), part Environmental Determinants Diabetes Young (TEDDY) study. We show that developing gut undergoes three distinct phases progression: developmental phase (months 3–14), transitional 15–30), stable 31–46). Receipt breast milk, either exclusive or partial, was most significant factor associated structure. Breastfeeding higher levels Bifidobacterium species (B. breve B. bifidum), cessation milk resulted faster maturation microbiome, marked phylum Firmicutes. Birth mode also significantly phase, driven Bacteroides (particularly fragilis) infants delivered vaginally. increased diversity maturation, regardless birth mode. factors including geographical location household exposures (such siblings furry pets) represented important covariates. A nested case–control analysis revealed subtle associations microbial taxonomy diabetes. These data determine structural functional assembly provide foundation for targeted mechanistic investigation into consequences long-term health. Metagenomic TEDDY study shows breastfeeding structure, microbiome.