Individuality and convergence of the infant gut microbiota during the first year of life

Nat Commun. 2018 Jun 8;9(1):2233. doi: 10.1038/s41467-018-04641-7.


The human gut microbiota plays a vital role in health and disease, and microbial colonization is a key process in infant development. Here, we analyze 2684 fecal specimens from 12 infants during their first year of life, providing detailed insights into the human gut colonization process. Maturation of the gut microbial community shows strong temporal structure and specific developmental stages. At 2-4 months of age, there is a period of accelerated convergence concurrent with a bloom of Bifidobacterium, a genus associated with metabolism of oligosaccharides found in breast milk. The end of this period coincides with the introduction of solid food, a reduction in the relative abundance of Bifidobacterium, and an increase in several groups of Firmicutes. Our findings highlight the dynamic nature and individuality of the gut colonization process, and the need for high-frequency sampling over an extended period when designing and interpreting infant microbiome studies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / growth & development*
  • Bifidobacterium / growth & development
  • Feces / microbiology*
  • Female
  • Firmicutes / growth & development
  • Gastrointestinal Microbiome*
  • Gastrointestinal Tract / microbiology*
  • Humans
  • Individuality
  • Infant
  • Male
  • Milk, Human / chemistry
  • Oligosaccharides / metabolism
  • Population Dynamics
  • RNA, Ribosomal, 16S / genetics


  • Oligosaccharides
  • RNA, Ribosomal, 16S