The Relevance of the Bacterial Microbiome, Archaeome and Mycobiome in Pediatric Asthma and Respiratory Disorders

Bacteria, as well as eukaryotes, principally fungi, of the upper respiratory tract play key roles in the etiopathogenesis of respiratory diseases, whereas the potential role of archaea remains poorly understood. In this review, we discuss the contribution of all three domains of cellular life to human naso- and oropharyngeal microbiomes, i.e., bacterial microbiota, eukaryotes (mostly fungi), as well as the archaeome and their relation to respiratory and atopic disorders in infancy and adolescence. With this review, we aim to summarize state-of-the-art contributions to the field published in the last decade. In particular, we intend to build bridges between basic and clinical science.

• Publication year

  2022

• Venue

  Cells

• Publication date

  2022-04-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.3390/cells11081287PMID 35455967PMCID 9024940
• 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.

• Going Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease

  2021cited by this paper
• Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19

  2021cited by this paper
• Low-Abundant Microorganisms: The Human Microbiome’s Dark Matter, a Scoping Review

  2021cited by this paper
• Vast (but avoidable) underestimation of global biodiversity

  2021cited by this paper
• Diversity, ecology and evolution of Archaea

  2020cited by this paper
• Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk

  2020cited by this paper
• Managing adult asthma: The 2019 GINA guidelines.

  2020influential reference
• A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis

  2020influential reference
• Anatomy, Head and Neck, Nasopharynx

  2020cited by this paper
• Nasopharyngeal Microbiota Profiles in Rural Venezuelan Children Are Associated With Respiratory and Gastrointestinal Infections

  2020influential reference
• The Oral Archaeome: A Scoping Review

  2020cited by this paper
• Subgingival fungi, Archaea, and viruses under the omics loupe.

  2020cited by this paper
• Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease

  2020cited by this paper
• Lophomonas blattarum: A new flagellate causing respiratory tract infections

  2020cited by this paper
• Viral respiratory infections and the oropharyngeal bacterial microbiota in acutely wheezing children

  2019cited by this paper
• Severe bronchiolitis profiles and risk of recurrent wheeze by age 3 years

  2019influential reference
• Environment and Host-Genetic Determinants in Early Development of Allergic Asthma: Contribution of Fungi

  2019cited by this paper
• Lung Microbiota Contribute to Pulmonary Inflammation and Disease Progression in Pulmonary Fibrosis

  2019cited by this paper
• Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body

  2019cited by this paper
• Pathogenic Fungal Infection in the Lung

  2019cited by this paper
• Impaired Tumor‐Necrosis‐Factor‐&agr;‐driven Dendritic Cell Activation Limits Lipopolysaccharide‐Induced Protection from Allergic Inflammation in Infants

  2019cited by this paper
• Temporal association of the development of oropharyngeal microbiota with early life wheeze in a population-based birth cohort

  2019cited by this paper
• The sinonasal mycobiota in chronic rhinosinusitis and control patients.

  2019cited by this paper
• Loss of Microbial Topography between Oral and Nasopharyngeal Microbiota and Development of Respiratory Infections Early in Life.

  2019cited by this paper
• A census-based estimate of Earth's bacterial and archaeal diversity

  2019cited by this paper
• Distinct Nasopharyngeal and Oropharyngeal Microbiota of Children with Influenza A Virus Compared with Healthy Children

  2018cited by this paper
• The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis

  2018influential reference
• Development of the Human Mycobiome over the First Month of Life and across Body Sites

  2018influential reference
• Nasopharyngeal Lactobacillus is associated with a reduced risk of childhood wheezing illnesses following acute respiratory syncytial virus infection in infancy

  2018cited by this paper
• Allergic fungal rhinosinusitis.

  2018cited by this paper
• The nasal microbiome mirrors and potentially shapes olfactory function

  2018cited by this paper
• Archaea Are Interactive Components of Complex Microbiomes.

  2018cited by this paper
• The Microbiome – The Unscheduled Parameter for Future Therapies

  2018cited by this paper
• Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease

  2018influential reference
• Diversity and Niche of Archaea in Bioremediation

  2018cited by this paper
• Allergy in severe asthma

  2017cited by this paper
• Etiology and clinical features of viral bronchiolitis in infancy

  2017cited by this paper
• Corticosteroid treatment is associated with increased filamentous fungal burden in allergic fungal disease

  2017influential reference
• The lung mycobiome in the next-generation sequencing era

  2017cited by this paper
• The significance of Candida in the human respiratory tract: our evolving understanding

  2017cited by this paper
• Dynamic oropharyngeal and faecal microbiota during treatment in infants hospitalized for bronchiolitis compared with age-matched healthy subjects

  2017cited by this paper
• A genome Tree of Life for the Fungi kingdom

  2017cited by this paper
• The role of the microbiome in human health and disease: an introduction for clinicians

  2017cited by this paper
• Characterization of the oropharynx: anatomy, histology, immunology, squamous cell carcinoma and surgical resection

  2017influential reference
• Archaea: Essential inhabitants of the human digestive microbiota

  2017cited by this paper
• Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

  2017cited by this paper
• Fungi that Infect Humans

  2017influential reference
• First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

  2017cited by this paper
• Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis

  2017cited by this paper
• Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting

  2017cited by this paper
• Archaea and the origin of eukaryotes

  2017cited by this paper
• Fungal Microbiota in Chronic Airway Inflammatory Disease and Emerging Relationships with the Host Immune Response

  2017cited by this paper
• Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection

  2017influential reference
• Asgard archaea illuminate the origin of eukaryotic cellular complexity

  2017cited by this paper
• Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children

  2017cited by this paper
• The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana

  2017influential reference
• The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies

  2017cited by this paper
• Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis

  2016cited by this paper
• Neonatal gut microbiota associates with childhood multi–sensitized atopy and T–cell differentiation

  2016cited by this paper
• Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota

  2016cited by this paper
• Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children.

  2016cited by this paper
• Pediatric severe asthma with fungal sensitization is mediated by steroid-resistant IL-33

  2015cited by this paper
• The Repertoire of Archaea Cultivated from Severe Periodontitis

  2015cited by this paper
• Archaea associated with human surfaces: not to be underestimated.

  2015influential reference
• The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development

  2015influential reference
• Kopf, Hals und Neuroanatomie: LernAtlas Anatomie

  2015cited by this paper
• Airway surface mycosis in chronic TH2-associated airway disease.

  2014influential reference
• The Evolution of Respiratory Cryptosporidiosis: Evidence for Transmission by Inhalation

  2014cited by this paper
• The eukaryotic tree of life from a global phylogenomic perspective.

  2014influential reference
• Childhood asthma-predictive phenotype.

  2014cited by this paper
• Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal

  2014influential reference
• The fungal microbiome in chronic rhinosinusitis: richness, diversity, postoperative changes and patient outcomes

  2014influential reference
• Archaea on Human Skin

  2013cited by this paper
• The human mycobiome in health and disease

  2013cited by this paper
• Insights into the phylogeny and coding potential of microbial dark matter

  2013cited by this paper
• An archaeal origin of eukaryotes supports only two primary domains of life

  2013cited by this paper
• Lophomonas blattarum and bronchopulmonary disease.

  2013cited by this paper
• Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study

  2013influential reference
• Treatment options in severe fungal asthma and allergic bronchopulmonary aspergillosis

  2013cited by this paper
• Upper Airways Microbiota in Antibiotic-Naïve Wheezing and Healthy Infants from the Tropics of Rural Ecuador

  2012cited by this paper
• The domain Archaea in human mucosal surfaces.

  2012cited by this paper
• The Malassezia Genus in Skin and Systemic Diseases

  2012cited by this paper
• Archaea — timeline of the third domain

  2011influential reference
• The human metagenome: our other genome?

  2011cited by this paper
• How Many Species Are There on Earth and in the Ocean?

  2011cited by this paper
• Archaea as emerging organisms in complex human microbiomes.

  2011cited by this paper
• Methanogenic Archaea and oral infections — ways to unravel the black box

  2011influential reference
• Moving pictures of the human microbiome

  2011cited by this paper
• Emerging and established parasitic lung infestations.

  2010influential reference
• A human gut microbial gene catalogue established by metagenomic sequencing

  2010cited by this paper
• Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals

  2010influential reference
• Classification of Bacteria and Archaea: past, present and future.

  2009cited by this paper
• Prevalence and molecular diversity of Archaea in subgingival pockets of periodontitis patients.

  2009cited by this paper
• The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease

  2008cited by this paper
• Pathogenic and opportunistic free-living amoebae: Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri, and Sappinia diploidea.

  2007cited by this paper
• Methanogenic Archaea and human periodontal disease.

  2004cited by this paper
• Normal endoscopic anatomy of the pharynx and larynx.

  2003cited by this paper
• Pathogenic archaea: do they exist?

  2003cited by this paper
• Thoracic amebiasis.

  2002cited by this paper
• Georgis' Parasitology for Veterinarians

  1995cited by this paper

• First Report of the Pulmonary Parasite Lophomonas blattarum in Ahvaz Province, Khuzestan: Case Report and Literature Review

  2025cites this paper
• The Respiratory Tract Microbiome and Human Health

  2025cites this paper
• Cutting-edge research frontiers in oral cavity vaccines for respiratory diseases: a roadmap for scientific advancement

  2024cites this paper
• The Footprint of Microbiome in Pediatric Asthma—A Complex Puzzle for a Balanced Development

  2023cites this paper
• The respiratory microbiome in childhood asthma.

  2023cites this paper
• The Overlooked Microbiome—Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes

  2023cites this paper
• Metatranscriptome Analysis of Nasopharyngeal Swabs across the Varying Severity of COVID-19 Disease Demonstrated Unprecedented Species Diversity

  2023cites this paper
• A Commentary on the Potential Use of Oral Microbiome in Prediction, Diagnosis or Prognostics of a Distant Pathology

  2022cites this paper