Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

Tommi Vatanen, Damian R. Plichta, Juhi Somani, Philipp C. Münch, Timothy D. Arthur, Andrew Brantley Hall, Sabine Rudolf, Edward J. Oakeley, Xiaobo Ke, Rachel A. Young, Henry J. Haiser, Raivo Kolde, Moran Yassour, Kristiina Luopajärvi, Heli Siljander, Suvi M. Virtanen, Jorma Ilonen, Raivo Uibo, Vallo Tillmann, Sergei MokurovNatalya Dorshakova, Jeffrey A. Porter, Alice C. McHardy, Harri Lähdesmäki, Hera Vlamakis, Curtis Huttenhower, Mikael Knip, Ramnik J. Xavier*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

138 Scopus citations


The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.

Original languageAmerican English
Pages (from-to)470-479
Number of pages10
JournalNature Microbiology
Issue number3
StatePublished - 1 Mar 2019
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2018, The Author(s), under exclusive licence to Springer Nature Limited.


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