The developing hypopharyngeal microbiota in early life

BackgroundThe 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 COPSAC2010 cohort of 700 infants, using 16S rRNA gene sequencing of hypopharyngeal aspirates from 1 week, 1 month, and 3 months of age.ResultsOur 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.ConclusionsOur 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.

• Publication year

  2016

• Venue

  Microbiome

• Publication date

  2016-12-30

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1186/s40168-016-0215-9PMID 28038686PMCID 5203717
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• "Finding Groups in Data": Cluster Analysis Extended Rousseeuw etal.

  2015cited by this paper
• The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development

  2015influential reference
• Dynamics of the nasal microbiota in infancy: a prospective cohort study.

  2015cited by this paper
• Lung microbiota across age and disease stage in cystic fibrosis

  2015cited by this paper
• Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals

  2015cited by this paper
• Surface area of the digestive tract – revisited

  2014cited by this paper
• The impact of breastfeeding on nasopharyngeal microbial communities in infants.

  2014influential reference
• Lung microbiota promotes tolerance to allergens in neonates via PD-L1

  2014cited by this paper
• Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children.

  2014influential reference
• Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes

  2014cited by this paper
• 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters.

  2013cited by this paper
• phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

  2013cited by this paper
• UPARSE: highly accurate OTU sequences from microbial amplicon reads

  2013cited by this paper
• The airway microbiome and disease.

  2013cited by this paper
• Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

  2012cited by this paper
• Low diversity of the gut microbiota in infants with atopic eczema.

  2012cited by this paper
• Reciprocal interactions of the intestinal microbiota and immune system

  2012cited by this paper
• Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.

  2011cited by this paper
• Enterotypes of the human gut microbiome

  2011cited by this paper
• Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age.

  2011cited by this paper
• An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

  2011influential reference
• Toward defining the autoimmune microbiome for type 1 diabetes

  2011cited by this paper
• Topographical continuity of bacterial populations in the healthy human respiratory tract.

  2011cited by this paper
• Association of bacteria and viruses with wheezy episodes in young children: prospective birth cohort study

  2010cited by this paper
• Disordered Microbial Communities in Asthmatic Airways

  2010cited by this paper
• A Persistent and Diverse Airway Microbiota Present during Chronic Obstructive Pulmonary Disease Exacerbations

  2010cited by this paper
• R Development Core Team (2010): R: A language and environment for statistical computing

  2010cited by this paper
• QIIME allows analysis of high-throughput community sequencing data

  2010cited by this paper
• PyNAST: a flexible tool for aligning sequences to a template alignment

  2009cited by this paper
• FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

  2009cited by this paper
• The importance of the development of the intestinal microbiota in infancy

  2009cited by this paper
• Associations between species and groups of sites: indices and statistical inference.

  2009cited by this paper
• Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

  2009cited by this paper
• Early differences in fecal microbiota composition in children may predict overweight.

  2008cited by this paper
• Development of the Human Infant Intestinal Microbiota

  2007cited by this paper
• Childhood asthma after bacterial colonization of the airway in neonates.

  2007cited by this paper
• Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction.

  2005cited by this paper
• The Copenhagen Prospective Study on Asthma in Childhood (COPSAC): design, rationale, and baseline data from a longitudinal birth cohort study.

  2004cited by this paper
• A proposal for the secondary structure of a variable area of eukaryotic small ribosomal subunit RNA involving the existence of a pseudoknot.

  1990cited by this paper
• Silhouettes: a graphical aid to the interpretation and validation of cluster analysis

  1987cited by this paper
• The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life.

  1982cited by this paper
• The internal surface area of the adult human lung.

  1972cited by this paper
• Edinburgh Research Explorer Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery

  year unknowncited by this paper
• Original Article Epidemiology of Allergic Disease Deep Phenotyping of the Unselected Copsac 2010 Birth Cohort Study

  year unknowninfluential reference

• Metagenomic analysis of the nasopharyngeal microbiomes and resistomes in asthma, COVID-19 infected, and healthy individuals

  2026cites this paper
• Corynebacterium drakensteinense sp. nov., isolated from the nasopharynx of a healthy South African infant

  2026cites this paper
• Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing

  2025cites this paper
• Bacterial dynamics and biotic sources in the developing swimming crab embryos

  2024cites this paper
• Early Succession of Community Structures and Biotic Interactions of Gut Microbes in Eriocheir sinensis Megalopa after Desalination

  2024cites this paper
• Reassembly and biotic sources of carapace bacterial community of Portunus trituberculatus after host molting

  2024cites this paper
• Atopic diseases—Diagnostics, mechanisms, and exposures

  2024cites this paper
• Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau

  2023cites this paper
• Characterization of Lung and Oral Microbiomes in Lung Cancer Patients Using Culturomics and 16S rRNA Gene Sequencing

  2023cites this paper
• Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics

  2023cites this paper
• Oropharyngeal Microbiota Clusters in Children with Asthma/Wheeze Associate with Allergy, Blood Transcriptomic Immune Pathways and Exacerbations Risk.

  2023cites this paper
• The Role of the Microbiome in Asthma Inception and Phenotype

  2022cites this paper
• Asthma and Wheeze Severity and the Oropharyngeal Microbiota in Children and Adolescents.

  2022cites this paper
• The developing airway and gut microbiota in early life is influenced by age of older siblings

  2022influential citation
• Role of the Microbiota in Lung Cancer: Insights on Prevention and Treatment

  2022cites this paper
• Succession, sources, and assembly of bacterial community in the developing crab larval microbiome

  2022cites this paper
• Prophages in the infant gut are largely induced, and may be functionally relevant to their hosts

  2021cites this paper
• The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition.

  2021cites this paper
• Related Factors to Streptococcus pneumoniae Invasive Infection and Clinical Manifestations: The Potential Role of Nasopharyngeal Microbiome

  2021cites this paper
• Interactions of Bacteriophages and Bacteria at the Airway Mucosa: New Insights Into the Pathophysiology of Asthma

  2021cites this paper
• Modeling transfer of vaginal microbiota from mother to infant in early life

  2021cites this paper
• Exploring the nasopharyngeal microbiota composition in infants with whooping cough: A test-negative case-control study

  2021cites this paper
• Urbanized microbiota in infants, immune constitution and later risk of atopic diseases.

  2020cites this paper
• Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial

  2020cites this paper
• Stability of the vaginal microbiota during pregnancy and its importance for early infant colonization

  2020cites this paper
• Season of Birth Impacts the Neonatal Nasopharyngeal Microbiota

  2020cites this paper
• Ecological succession in the vaginal microbiota during pregnancy and birth

  2020cites this paper
• Early life bacterial airway colonization, local immune mediator response and risk of otitis media.

  2020cites this paper
• The microbiome of captive hamadryas baboons

  2020cites this paper
• Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age.

  2020cites this paper
• Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota

  2020cites this paper
• The infant pharyngeal microbiomes: origin, impact and manipulation

  2020cites this paper
• Delivery mode and gut microbial changes correlate with an increased risk of childhood asthma

  2020cites this paper
• Environmental shaping of the bacterial and fungal community in 1 infant bed dust and correlations with the airway microbiota 2

  2020cites this paper
• Infant airway microbiota and topical immune perturbations in the origins of childhood asthma

  2019cites this paper
• Bacterial community analysis for investigating bacterial transfer from tonsils to the pig carcass.

  2019cites this paper
• Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects

  2019cites this paper
• Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing

  2019cites this paper
• Special Considerations in Preschool Age

  2019cites this paper
• Bronchiolitis needs a revisit: Distinguishing between virus entities and their treatments

  2018cites this paper
• Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome

  2018cites this paper
• Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics

  2018cites this paper
• Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial

  2018cites this paper
• Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities

  2018cites this paper
• Microbiomes in Dishwashers: Analysis of the microbial diversity and putative opportunistic 1 pathogens in dishwasher biofilm communities

  2018cites this paper
• long-term impacts of azithromycin treatment on the gut microbiota in children

  2018cites this paper
• Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study

  2018influential citation
• Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial

  2018cites this paper
• Development of Microbiota in Infants and its Role in Maturation of Gut Mucosa and Immune System.

  2017cites this paper
• The role of respiratory tract infections and the microbiome in the development of asthma: A narrative review

  2017cites this paper