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

Show simple item record Vatanen, Tommi en Plichta, Damian R en Somani, Juhi en Münch, Philipp C en Arthur, Timothy D en Hall, Andrew Brantley en Rudolf, Sabine en Oakeley, Edward J en Ke, Xiaobo en Young, Rachel A en Haiser, Henry J en Kolde, Raivo en Yassour, Moran en Luopajärvi, Kristiina en Siljander, Heli en Virtanen, Suvi M en Ilonen, Jorma en Uibo, Raivo en Tillmann, Vallo en Mokurov, Sergei en Dorshakova, Natalya en Porter, Jeffrey A en McHardy, Alice C en Lähdesmäki, Harri en Vlamakis, Hera en Huttenhower, Curtis en Knip, Mikael en Xavier, Ramnik J en 2019-03-20T04:15:33Z en 2019-03 en
dc.identifier.issn 2058-5276 en
dc.identifier.uri en
dc.description.abstract 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. en
dc.format.medium Print-Electronic en
dc.language eng en
dc.relation.ispartofseries Nature microbiology en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. en
dc.rights.uri en
dc.subject Feces en
dc.subject Humans en
dc.subject Bacteroides en
dc.subject Bacteriophages en
dc.subject Longitudinal Studies en
dc.subject Child Development en
dc.subject Age Factors en
dc.subject Adaptation, Physiological en
dc.subject Polymorphism, Single Nucleotide en
dc.subject Genome, Bacterial en
dc.subject Probiotics en
dc.subject Child, Preschool en
dc.subject Infant en
dc.subject Estonia en
dc.subject Russia en
dc.subject Finland en
dc.subject Female en
dc.subject Male en
dc.subject Metabolic Networks and Pathways en
dc.subject Genetic Variation en
dc.subject Metagenomics en
dc.subject Gastrointestinal Microbiome en
dc.subject Bifidobacterium bifidum en
dc.subject Bifidobacterium longum en
dc.title Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. en
dc.type Journal Article en
dc.identifier.doi 10.1038/s41564-018-0321-5 en
pubs.issue 3 en
pubs.begin-page 470 en
pubs.volume 4 en
dc.rights.holder Copyright: The author en
pubs.end-page 479 en
pubs.publication-status Published en
dc.rights.accessrights en
pubs.subtype Research Support, Non-U.S. Gov't en
pubs.subtype research-article en
pubs.subtype Journal Article en
pubs.subtype Research Support, N.I.H., Extramural en
pubs.elements-id 759198 en Liggins Institute en
dc.identifier.eissn 2058-5276 en
pubs.record-created-at-source-date 2018-12-19 en
pubs.dimensions-id 30559407 en

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