1. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life
- Author
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Sabine Rudolf, Natalya Dorshakova, Edward J. Oakeley, Andrew Brantley Hall, Raivo Uibo, Juhi Somani, Timothy D. Arthur, Henry J. Haiser, Raivo Kolde, Vallo Tillmann, Moran Yassour, Jorma Ilonen, Damian R. Plichta, Suvi M. Virtanen, Ramnik J. Xavier, Heli Siljander, Hera Vlamakis, Mikael Knip, Alice C. McHardy, Harri Lähdesmäki, Xiaobo Ke, Curtis Huttenhower, Jeffrey A. Porter, Rachel A. Young, Kristiina Luopajärvi, Philipp C. Münch, Sergei Mokurov, Tommi Vatanen, Broad Institute, Centre of Excellence in Molecular Systems Immunology and Physiology Research Group, SyMMys, Helmholtz Centre for Infection Research, Novartis, Novartis USA, University of Helsinki, National Institute for Health and Welfare, University of Turku, University of Tartu, Russian Ministry of Health, Petrozavodsk State University, Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto-yliopisto, Aalto University, BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany., HUS Children and Adolescents, Diabetes and Obesity Research Program, Children's Hospital, Research Programs Unit, Lastentautien yksikkö, Clinicum, and Mikael Knip / Principal Investigator
- Subjects
DYNAMICS ,Male ,Bifidobacterium longum ,AUTOIMMUNITY ,ved/biology.organism_classification_rank.species ,BIFIDOBACTERIA ,Applied Microbiology and Biotechnology ,Russia ,law.invention ,Feces ,Probiotic ,Child Development ,3123 Gynaecology and paediatrics ,law ,Bacteroides ,Bacteriophages ,Longitudinal Studies ,1183 Plant biology, microbiology, virology ,Finland ,2. Zero hunger ,Genetics ,0303 health sciences ,Strain (biology) ,Age Factors ,food and beverages ,ASSOCIATION ,Adaptation, Physiological ,READ ALIGNMENT ,INSIGHTS ,BACTERIAL TRANSMISSION ,Child, Preschool ,Female ,ACCURATE ,Metabolic Networks and Pathways ,Estonia ,Microbiology (medical) ,BODY SITES ,Immunology ,Single-nucleotide polymorphism ,Biology ,Polymorphism, Single Nucleotide ,Microbiology ,Article ,03 medical and health sciences ,REVEALS ,Humans ,Microbiome ,030304 developmental biology ,Bifidobacterium bifidum ,030306 microbiology ,ved/biology ,Probiotics ,Genetic Variation ,Infant ,Cell Biology ,biology.organism_classification ,Gastrointestinal Microbiome ,Metagenomics ,3111 Biomedicine ,Adaptation ,human activities ,Genome, Bacterial - 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. Integration of longitudinal gut metagenomic datasets from children in Finland, Estonia and Russian Karelia reveals high strain-level diversity, which consequently impacts the functional capabilities of the early life microbiome.
- Published
- 2018
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