title: The developing hypopharyngeal microbiota in early life.
abstract: The airways of healthy humans harbor a distinct microbial community. Perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a healthy airway microbiota in early life. Our goal was to understand the establishment of the airway microbiota within the first 3 months of life. We investigated the hypopharyngeal microbiota in the unselected COPSAC2010cohort of 700 infants, using 16S rRNA gene sequencing of hypopharyngeal aspirates from 1 week, 1 month, and 3 months of age.
  
  
  
  Our analysis shows that majority of the hypopharyngeal microbiota of healthy infants belong to each individual's core microbiota and we demonstrate five distinct community pneumotypes. Four of these pneumotypes are dominated by the genera Staphylococcus, Streptococcus, Moraxella, and Corynebacterium, respectively. Furthermore, we show temporal pneumotype changes suggesting a rapid development towards maturation of the hypopharyngeal microbiota and a significant effect from older siblings. Despite an overall common trajectory towards maturation, individual infants' microbiota are more similar to their own, than to others, over time.
  
  
  
  Our findings demonstrate a consolidation of the population of indigenous bacteria in healthy airways and indicate distinct trajectories in the early development of the hypopharyngeal microbiota.
authors.affiliation: Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark.
authors.forename: Martin Steen
authors.initials: MS
authors.lastname: Mortensen
authors.affiliation: Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark.
authors.forename: Asker Daniel
authors.initials: AD
authors.lastname: Brejnrod
authors.affiliation: Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark.
authors.forename: Michael
authors.initials: M
authors.lastname: Roggenbuck
authors.affiliation: Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark.
authors.forename: Waleed
authors.initials: W
authors.lastname: Abu Al-Soud
authors.affiliation: Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark.
authors.forename: Christina
authors.initials: C
authors.lastname: Balle
authors.affiliation: Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark.
authors.forename: Karen Angeliki
authors.initials: KA
authors.lastname: Krogfelt
authors.affiliation: Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark.
authors.forename: Jakob
authors.initials: J
authors.lastname: Stokholm
authors.affiliation: Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Thorsen
authors.affiliation: Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark.
authors.forename: Johannes
authors.initials: J
authors.lastname: Waage
authors.affiliation: Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark.|Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg C, Denmark.
authors.forename: Morten Arendt
authors.initials: MA
authors.lastname: Rasmussen
authors.affiliation: Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark.
authors.forename: Hans
authors.initials: H
authors.lastname: Bisgaard
authors.affiliation: Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark. sjs@bio.ku.dk.
authors.forename: Søren Johannes
authors.initials: SJ
authors.lastname: Sørensen
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D005260:Female; D006801:Humans; D007013:Hypopharynx / Q000382:microbiology*; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D064307:Microbiota / Q000235:genetics*; D011446:Prospective Studies; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Airway microbiome; Infant microbiome; Microbiome development