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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12-17

AUTHORS

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 Mokurov, Natalya Dorshakova, Jeffrey A. Porter, Alice C. McHardy, Harri Lähdesmäki, Hera Vlamakis, Curtis Huttenhower, Mikael Knip, Ramnik J. Xavier

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. More... »

PAGES

470-479

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  • Journal

    TITLE

    Nature Microbiology

    ISSUE

    3

    VOLUME

    4

    Author Affiliations

  • Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Department of Computer Science, Aalto University, Espoo, Finland
  • Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, Munich, Germany
  • Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
  • Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
  • Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
  • Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
  • Department of Pediatrics, Tampere University Hospital, Tampere, Finland
  • Science Centre, Pirkanmaa Hospital District and Research Center for Child Health, University Hospital, Tampere, Finland
  • Clinical Microbiology, Turku University Hospital, Turku, Finland
  • Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
  • Department of Pediatrics, University of Tartu and Tartu University Hospital, Tartu, Estonia
  • Ministry of Health and Social Development, Karelian Republic of the Russian Federation, Petrozavodsk, Russia
  • Petrozavodsk State University, Department of Family Medicine, Petrozavodsk, Russia
  • Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Brunswick, Germany
  • Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
  • Folkhälsan Research Center, Helsinki, Finland
  • Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41564-018-0321-5

    DOI

    http://dx.doi.org/10.1038/s41564-018-0321-5

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1110423599

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30559407


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