IRCI Article ID: IRCI-AR-0000000942

Early life inter-kingdom interactions shape the immunological environment of the airways

Journal: Microbiome

Publication: 2022-12-01 · Vol. 10 No. 1

DOI: 10.1186/s40168-021-01201-y

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Abstract

AbstractBackgroundThere is increasing evidence that the airway microbiome plays a key role in the establishment of respiratory health by interacting with the developing immune system early in life. While it has become clear that bacteria are involved in this process, there is a knowledge gap concerning the role of fungi. Moreover, the inter-kingdom interactions that influence immune development remain unknown. In this prospective exploratory human study, we aimed to determine early post-natal microbial and immunological features of the upper airways in 121 healthy newborns.ResultsWe found that the oropharynx and nasal cavity represent distinct ecological niches for bacteria and fungi. Breastfeeding correlated with changes in microbiota composition of oropharyngeal samples with the greatest impact upon the relative abundance ofStreptococcusspecies andCandida. Host transcriptome profiling revealed that genes with the highest expression variation were immunological in nature. Multi-omics factor analysis of host and microbial data revealed unique co-variation patterns.ConclusionThese data provide evidence of a diverse multi-kingdom microbiota linked with local immunological characteristics in the first week of life that could represent distinct trajectories for future respiratory health.Trial registrationNHS Health Research Authority, IRAS ID 199053. Registered 5 Oct 2016.https://www.hra.nhs.uk/planning-and-improving-research/application-summaries/research-summaries/breathing-together/

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Authors

Céline Pattaroni

Affiliation: Monash University

ORCID: 0000-0002-9920-1181

Matthew Macowan

Affiliation: Monash University

ORCID: 0000-0001-7721-1349

Roxanne Chatzis

Affiliation: Monash University

Carmel Daunt

Affiliation: Monash University

Adnan Custovic

Affiliation: Imperial College London; Royal College of Paediatrics and Child Health

ORCID: 0000-0001-5218-7071

Michael D. Shields

Affiliation: Queen's University Belfast

ORCID: 0000-0002-3793-3571

Ultan F. Power

Affiliation: Queen's University Belfast

Jonathan Grigg

Affiliation: Queen Mary University of London

Graham Roberts

Affiliation: University Hospital Southampton NHS Foundation Trust; NIHR Southampton Biomedical Research Centre; St Mary's Hospital; David Hide Asthma and Allergy Research Centre; St. Mary's Hospital; University of Southampton

ORCID: 0000-0003-2252-1248

Peter Ghazal

Affiliation: Cardiff University

ORCID: 0000-0003-0035-2228

Jürgen Schwarze

Affiliation: Centre for Inflammation Research; University of Edinburgh

ORCID: 0000-0002-6899-748X

Mindy Gore

Affiliation: Imperial College London; Royal College of Paediatrics and Child Health

ORCID: 0000-0002-1458-1438

Steve Turner

Affiliation: University of Aberdeen; NHS Grampian

Andrew Bush

Affiliation: Royal Brompton Hospital; Imperial College London; Royal College of Paediatrics and Child Health

ORCID: 0000-0001-6756-9822

Sejal Saglani

Affiliation: Royal Brompton Hospital; Imperial College London; Royal College of Paediatrics and Child Health

Clare M. Lloyd

Affiliation: Imperial College London

ORCID: 0000-0001-8977-6726

Benjamin J. Marsland

Affiliation: Monash University

ORCID: 0000-0003-1457-3160

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