Biesbroek G, Tsivtsivadze E, Sanders EAM, Montijn R, Veenhoven RH, Keijser BJF, et al. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Am J Respir Crit Care Med. 2014;190:1283–92 [cited 2020 Nov 25]. Available from: http://www.atsjournals.org/doi/full/10.1164/rccm.201407-1240OC.
Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17:704–15.
Article
CAS
Google Scholar
Bosch AATM, Levin E, van Houten MA, Hasrat R, Kalkman G, Biesbroek G, et al. Development of upper respiratory tract microbiota in infancy is affected by mode of delivery. EBioMedicine. 2016;9:336–45 [cited 2021 Jan 29]. Available from: http://www.sciencedirect.com/science/article/pii/S2352396416302250.
Article
Google Scholar
Bosch AATM, de Steenhuijsen Piters WAA, van Houten MA, Chu MLJN, Biesbroek G, Kool J, et al. Maturation of the infant respiratory microbiota, environmental drivers, and health consequences. A prospective cohort study. Am J Respir Crit Care Med. 2017;196:1582–90.
Article
Google Scholar
Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med. 2017;23:314–26 Nature Publishing Group. [cited 2020 Dec 15]. Available from: http://www.nature.com/articles/nm.4272.
Pattaroni C, Watzenboeck ML, Schneidegger S, Kieser S, Wong NC, Bernasconi E, et al. Early-life formation of the microbial and immunological environment of the human airways. Cell Host Microbe. 2018;24:857–865.e4.
Article
CAS
Google Scholar
Teo SM, Tang HHF, Mok D, Judd LM, Watts SC, Pham K, et al. Airway microbiota dynamics uncover a critical window for interplay of pathogenic bacteria and allergy in childhood respiratory disease. Cell Host Microbe. 2018;24:341–352.e5.
Article
CAS
Google Scholar
de Steenhuijsen Piters WAA, Binkowska J, Bogaert D. Early life microbiota and respiratory tract infections. Cell Host Microbe. 2020;28:223–32.
Article
Google Scholar
Ta LDH, Yap GC, Tay CJX, Lim ASM, Huang C-H, Chu CW, et al. Establishment of the nasal microbiota in the first 18 months of life: correlation with early-onset rhinitis and wheezing. J Allergy Clin Immunol. 2018;142:86–95.
Article
Google Scholar
Thorsen J, Rasmussen MA, Waage J, Mortensen M, Brejnrod A, Bønnelykke K, et al. Infant airway microbiota and topical immune perturbations in the origins of childhood asthma. Nat Commun. 2019;10:5001 Nature Publishing Group. [cited 2021 Jan 28]. Available from: http://www.nature.com/articles/s41467-019-12989-7.
Mansbach JM, Luna PN, Shaw CA, Hasegawa K, Petrosino JF, Piedra PA, et al. Increased Moraxella and Streptococcus species abundance after severe bronchiolitis is associated with recurrent wheezing. J Allergy Clin Immunol. 2020;145:518–527.e8 [cited 2021 Jan 28]. Available from: http://www.sciencedirect.com/science/article/pii/S0091674919315167.
Article
CAS
Google Scholar
Gollwitzer ES, Saglani S, Trompette A, Yadava K, Sherburn R, McCoy KD, et al. Lung microbiota promotes tolerance to allergens in neonates via PD-L1. Nat Med. 2014;20:642–7.
Article
CAS
Google Scholar
Olszak T, An D, Zeissig S, Vera MP, Richter J, Franke A, et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012;336:489–93 American Association for the Advancement of Science. [cited 2020 Nov 27]. Available from: http://www.science.sciencemag.org/content/336/6080/489.
Russell SL, Gold MJ, Hartmann M, Willing BP, Thorson L, Wlodarska M, et al. Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep. 2012;13:440–7 John Wiley & Sons, Ltd. [cited 2020 Nov 27]. Available from: http://www.embopress.org/doi/full/10.1038/embor.2012.32.
Man WH, Clerc M, de Steenhuijsen Piters WAA, van Houten MA, Chu MLJN, Kool J, et al. Loss of microbial topography between oral and nasopharyngeal microbiota and development of respiratory infections early in life. Am J Respir Crit Care Med. 2019;200:760–70.
Article
CAS
Google Scholar
Turner S, Custovic A, Ghazal P, Grigg J, Gore M, Henderson J, et al. Pulmonary epithelial barrier and immunological functions at birth and in early life - key determinants of the development of asthma? A description of the protocol for the Breathing Together study. Wellcome Open Res. 2018;3:60.
Article
Google Scholar
Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6:226.
Article
Google Scholar
Marsh RL, Kaestli M, Chang AB, Binks MJ, Pope CE, Hoffman LR, et al. The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. Microbiome. 2016;4:37 [cited 2020 Nov 11]. Available from: https://doi.org/10.1186/s40168-016-0182-1.
Article
CAS
Google Scholar
Bassis CM, Erb-Downward JR, Dickson RP, Freeman CM, Schmidt TM, Young VB, et al. Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals. mBio [Internet]. American Society for Microbiology; 2015 [cited 2020 Nov 11];6. Available from: http://www.mbio.asm.org/content/6/2/e00037-15.
Barberán A, Dunn RR, Reich BJ, Pacifici K, Laber EB, Menninger HL, et al. The ecology of microscopic life in household dust. Proc Biol Sci. 2015;282:20151139. Available from: https://doi.org/10.1098/rspb.2015.1139.
Rocchi S, Valot B, Reboux G, Millon L. DNA metabarcoding to assess indoor fungal communities: electrostatic dust collectors and Illumina sequencing. J Microbiol Methods. 2017;139:107–12.
Article
CAS
Google Scholar
Adams RI, Bhangar S, Pasut W, Arens EA, Taylor JW, Lindow SE, et al. Chamber bioaerosol study: outdoor air and human occupants as sources of indoor airborne microbes. PloS One. 2015;10:e0128022.
Article
Google Scholar
Yan D, Zhang T, Su J, Zhao L-L, Wang H, Fang X-M, et al. Diversity and composition of airborne fungal community associated with particulate matters in Beijing during haze and non-haze days. Front Microbiol. 2016;7:487.
PubMed
PubMed Central
Google Scholar
Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11:e1004226.
Tipton L, Müller C, Kurtz ZD, Huang L, Kleerup E, Morris A, et al. Fungi stabilize connectivity in the lung and skin microbial ecosystems. Microbiome. 2018;6:12. Available from: https://doi.org/10.1186/s40168-017-0393-0.
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci [Internet]. National Academy of Sciences; 2010 [cited 2020 Nov 25];107:11971–5. Available from: http://www.pnas.org/content/107/26/11971.
Argelaguet. Multi-Omics Factor Analysis—a framework for unsupervised integration of multi-omics data sets. Mol Syst Biol [Internet]. John Wiley & Sons, Ltd; 2018 [cited 2021 Sep 22];14:e8124. Available from: http://www.embopress.org/doi/full/10.15252/msb.20178124.
Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC, et al. MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data. Genome Biol. 2020;21:111 [cited 2021 Sep 22]. Available from: https://doi.org/10.1186/s13059-020-02015-1.
Article
Google Scholar
Halayko AJ, Ghavami S. S100A8/A9: a mediator of severe asthma pathogenesis and morbidity?This article is one of a selection of papers published in a special issue celebrating the 125th anniversary of the Faculty of Medicine at the University of Manitoba. Can J Physiol Pharmacol. 2009;87:743–55 NRC Research Press. [cited 2021 Sep 22]. Available from: http://www.cdnsciencepub.com/doi/abs/10.1139/y09-054.
Park J-S, Lee T-H, Shin H-R, Song HJ, Kim J-D, Park C-S. Relationship of S100A9 (S100 Calcium binding Protein A9) with neutophilic inflammation in murine asthma model. J Allergy Clin Immunol. 2015;135:AB243 Elsevier. [cited 2021 Sep 22]. Available from: http://www.jacionline.org/article/S0091-6749(14)03510-6/fulltext#relatedArticles.
Quoc QL, Choi Y, Thi Bich TC, Yang E-M, Shin YS, Park H-S. S100A9 in adult asthmatic patients: a biomarker for neutrophilic asthma. Exp Mol Med. 2021;53:1170–9 [cited 2021 Sep 22]. Available from: http://www.nature.com/articles/s12276-021-00652-5.
Gould HJ, Sutton BJ. IgE in allergy and asthma today. Nat Rev Immunol. 2008;8:205–17 [cited 2021 Sep 29]. Available from: http://www.nature.com/articles/nri2273.
van Tilburg BE, Pettersen VK, Gutierrez MW, Laforest-Lapointe I, Jendzjowsky NG, Cavin J-B, et al. Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Nat Commun. 2020;11:2577 Nature Publishing Group. [cited 2020 Dec 4]. Available from: http://www.nature.com/articles/s41467-020-16431-1.
Budden KF, Shukla SD, Rehman SF, Bowerman KL, Keely S, Hugenholtz P, et al. Functional effects of the microbiota in chronic respiratory disease. Lancet Respir Med. 2019;7:907–20 [cited 2021 May 27]. Available from: http://www.linkinghub.elsevier.com/retrieve/pii/S2213260018305101.
van Tilburg BE, Gutierrez MW, Arrieta M-C. The fungal microbiome and asthma. Front Cell Infect Microbiol. 2020;10 Frontiers. [cited 2020 Dec 4]. Available from: http://www.frontiersin.org/articles/10.3389/fcimb.2020.583418/full.
Cui L, Lucht L, Tipton L, Rogers MB, Fitch A, Kessinger C, et al. Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease. Am J Respir Crit Care Med. 2015;191:932–42.
Article
Google Scholar
Mac Aogáin M, Chandrasekaran R, Lim AYH, Low TB, Tan GL, Hassan T, et al. Immunological corollary of the pulmonary mycobiome in bronchiectasis: the CAMEB study. Eur Respir J. 2018;52:1800766.
Article
Google Scholar
Huang C, Yu Y, Du W, Liu Y, Dai R, Tang W, et al. Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma. Clin Transl Allergy. 2020;10:42 [cited 2021 Sep 29]. Available from: https://doi.org/10.1186/s13601-020-00345-8.
Article
CAS
Google Scholar
Vandenborght L-E, Enaud R, Urien C, Coron N, Girodet P-O, Ferreira S, et al. Type 2-high asthma is associated with a specific indoor mycobiome and microbiome. J Allergy Clin Immunol. 2021;147:1296–1305.e6.
Article
CAS
Google Scholar
Tiew PY, Dicker AJ, Keir HR, Poh ME, Pang SL, Mac Aogáin M, et al. A high-risk airway mycobiome is associated with frequent exacerbation and mortality in COPD. Eur Respir J. 2021;57:2002050.
Article
CAS
Google Scholar
Deo PN, Deshmukh R. Oral microbiome: unveiling the fundamentals. J Oral Maxillofac Pathol. 2019;23:122–8 [cited 2020 Dec 4]. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503789/.
Gonia S, Tuepker M, Heisel T, Autran C, Bode L, Gale CA. Human milk oligosaccharides inhibit Candida albicans invasion of human premature intestinal epithelial cells. J Nutr. 2015;145:1992–8 Oxford Academic. [cited 2020 Dec 4]. Available from: http://www.academic.oup.com/jn/article/145/9/1992/4585751.
Bisgaard H, Hermansen MN, Buchvald F, Loland L, Halkjaer LB, Bønnelykke K, et al. Childhood Asthma after Bacterial Colonization of the Airway in Neonates. N Engl J Med [Internet]. Massachusetts Medical Society; 2007 [cited 2021 Sep 29];357:1487–95. Available from: https://doi.org/10.1056/NEJMoa052632.
Edwards MR, Strong K, Cameron A, Walton RP, Jackson DJ, Johnston SL. Viral infections in allergy and immunology: How allergic inflammation influences viral infections and illness. J Allergy Clin Immunol [Internet]. 2017 [cited 2021 Sep 29];140:909–20. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173222/.
Rapin A, Pattaroni C, Marsland BJ, Harris NL. Microbiota analysis using an Illumina MiSeq platform to sequence 16S rRNA genes. Curr Protoc Mouse Biol. 2017;7:100–29.
Article
CAS
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Article
Google Scholar
Eren AM, Vineis JH, Morrison HG, Sogin ML. A filtering method to generate high quality short reads using illumina paired-end technology. PloS One. 2013;8:e66643.
Article
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal [Internet]. 2011 [cited 2020 Nov 5];17:10–2. Available from: http://www.journal.embnet.org/index.php/embnetjournal/article/view/200.
Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses. F1000Research [Internet]. 2016 [cited 2020 Nov 6];5:1492. Available from: http://www.f1000research.com/articles/5-1492/v2.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS One. 2013;8:e61217.
Article
Google Scholar
Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10:1200–2.
Article
CAS
Google Scholar
Tian L, Su S, Dong X, Amann-Zalcenstein D, Biben C, Seidi A, et al. scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data. PLoS Comput Biol. 2018;14:e1006361.
Article
Google Scholar
Liao Y, Smyth GK, Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res. 2019;47:e47.
54. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinforma Oxf Engl. 2010;26:139–40.
Article
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinforma Oxf Engl. 2010;26:139–40.
Article
CAS
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol [Internet]. 2014 [cited 2021 Sep 30];15:550. Available from: https://doi.org/10.1186/s13059-014-0550-8.
Mallick H, Rahnavard A, McIver L. Maaslin2: Maaslin2 [Internet]. Bioconductor version: Release (3.12); 2020 [cited 2020 Nov 5]. Available from: http://www.bioconductor.org/packages/Maaslin2/.