Upper Airways Microbiota in Antibiotic-Naïve Wheezing and Healthy Infants from the Tropics of Rural Ecuador

Background Observations that the airway microbiome is disturbed in asthma may be confounded by the widespread use of antibiotics and inhaled steroids. We have therefore examined the oropharyngeal microbiome in early onset wheezing infants from a rural area of tropical Ecuador where antibiotic usage is minimal and glucocorticoid usage is absent. Materials and Methods We performed pyrosequencing of amplicons of the polymorphic bacterial 16S rRNA gene from oropharyngeal samples from 24 infants with non-infectious early onset wheezing and 24 healthy controls (average age 10.2 months). We analyzed microbial community structure and differences between cases and controls by QIIME software. Results We obtained 76,627 high quality sequences classified into 182 operational taxonomic units (OTUs). Firmicutes was the most common and diverse phylum (71.22% of sequences) with Streptococcus being the most common genus (49.72%). Known pathogens were found significantly more often in cases of infantile wheeze compared to controls, exemplified by Haemophilus spp. (OR = 2.12, 95% Confidence Interval (CI) 1.82–2.47; P = 5.46×10−23) and Staphylococcus spp. (OR = 124.1, 95%CI 59.0–261.2; P = 1.87×10−241). Other OTUs were less common in cases than controls, notably Veillonella spp. (OR = 0.59, 95%CI = 0.56–0.62; P = 8.06×10−86). Discussion The airway microbiota appeared to contain many more Streptococci than found in Western Europe and the USA. Comparisons between healthy and wheezing infants revealed a significant difference in several bacterial phylotypes that were not confounded by antibiotics or use of inhaled steroids. The increased prevalence of pathogens such as Haemophilus and Staphylococcus spp. in cases may contribute to wheezing illnesses in this age group.

[1]  Elmar Pruesse,et al.  SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes , 2012, Bioinform..

[2]  Kyle Bittinger,et al.  Topographical continuity of bacterial populations in the healthy human respiratory tract. , 2011, American journal of respiratory and critical care medicine.

[3]  K. McCoy,et al.  Dysregulation of allergic airway inflammation in the absence of microbial colonization. , 2011, American journal of respiratory and critical care medicine.

[4]  Harald Meier,et al.  46. ARB: A Software Environment for Sequence Data , 2011 .

[5]  Peer Bork,et al.  Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..

[6]  M. Kurrer,et al.  Bacterial-induced protection against allergic inflammation through a multicomponent immunoregulatory mechanism , 2011, Thorax.

[7]  B. Haas,et al.  Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. , 2011, Genome research.

[8]  Tanja Woyke,et al.  Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. , 2011, The Journal of allergy and clinical immunology.

[9]  D. Solé,et al.  International prevalence of recurrent wheezing during the first year of life: variability, treatment patterns and use of health resources , 2010, Thorax.

[10]  R. Knight,et al.  Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution , 2010, Nature Methods.

[11]  J. Just,et al.  Impact of Innate and Environmental Factors on Wheezing Persistence During Childhood , 2010, The Journal of asthma : official journal of the Association for the Care of Asthma.

[12]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[13]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[14]  Lior Pachter,et al.  Disordered Microbial Communities in Asthmatic Airways , 2010, PloS one.

[15]  Rob Knight,et al.  PyNAST: a flexible tool for aligning sequences to a template alignment , 2009, Bioinform..

[16]  R. Xavier,et al.  Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43 , 2009, Nature.

[17]  G. Huffnagle,et al.  Control of mucosal polymicrobial populations by innate immunity , 2009, Cellular microbiology.

[18]  M. Wechsler Managing asthma in primary care: putting new guideline recommendations into context. , 2009, Mayo Clinic proceedings.

[19]  Mihai Pop,et al.  Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples , 2009, PLoS Comput. Biol..

[20]  Gregory E. Jordan,et al.  Assigning strains to bacterial species via the internet , 2009, BMC Biology.

[21]  P J Cooper,et al.  Asthma in Latin America: a public heath challenge and research opportunity , 2009, Allergy.

[22]  James R. Cole,et al.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..

[23]  D. Artis Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut , 2008, Nature Reviews Immunology.

[24]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[25]  Hans Bisgaard,et al.  Childhood asthma after bacterial colonization of the airway in neonates. , 2007, The New England journal of medicine.

[26]  G. Macfarlane,et al.  Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples , 2007, Applied and Environmental Microbiology.

[27]  G. Weinmayr,et al.  Atopic sensitization and the international variation of asthma symptom prevalence in children. , 2007, American Journal of Respiratory and Critical Care Medicine.

[28]  Rob Knight,et al.  UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context , 2006, BMC Bioinformatics.

[29]  Dawn Field,et al.  Open software for biologists: from famine to feast , 2006, Nature Biotechnology.

[30]  G. Huffnagle,et al.  The ‘microflora hypothesis’ of allergic diseases , 2005, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[31]  T. Popović,et al.  High Level of Sequence Diversity in the 16S rRNA Genes of Haemophilus influenzae Isolates Is Useful for Molecular Subtyping , 2005, Journal of Clinical Microbiology.

[32]  Thomas Ludwig,et al.  RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees , 2005, Bioinform..

[33]  W. Cookson The immunogenetics of asthma and eczema: a new focus on the epithelium , 2004, Nature Reviews Immunology.

[34]  G. Huffnagle,et al.  Does the microbiota regulate immune responses outside the gut? , 2004, Trends in microbiology.

[35]  A. Macpherson,et al.  Interactions between commensal intestinal bacteria and the immune system , 2004, Nature Reviews Immunology.

[36]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[37]  S. Hellström,et al.  Is hydrogen peroxide responsible for the inhibitory activity of alpha-haemolytic streptococci sampled from the nasopharynx? , 2003, Acta oto-laryngologica.

[38]  M. Kraft,et al.  The role of bacterial infections in asthma. , 2000, Clinics in chest medicine.

[39]  C. Crowe,et al.  Bacterial interference. II. Role of the normal throat flora in prevention of colonization by group A Streptococcus. , 1973, The Journal of infectious diseases.

[40]  J. Stockman Exposure to Environmental Microorganisms and Childhood Asthma , 2012 .

[41]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[42]  Kenneth Jost Asthma Epidemic , 1999 .

[43]  A. Magurran Ecological Diversity and Its Measurement , 1988, Springer Netherlands.

[44]  J. T. Staley,et al.  Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. , 1985, Annual review of microbiology.

[45]  A. Chao Nonparametric estimation of the number of classes in a population , 1984 .

[46]  D. Savage Microbial ecology of the gastrointestinal tract. , 1977, Annual review of microbiology.