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

Céline Pattaroni, Matthew Macowan, Roxanne Chatzis, Carmel Daunt, Adnan Custovic, Michael D. Shields, Ultan F. Power, Jonathan Grigg, Graham Roberts, Peter Ghazal, Jürgen Schwarze, Mindy Gore, Steve Turner, Andrew Bush, Sejal Saglani, Clare M. Lloyd, Benjamin J. Marsland

Research output: Contribution to journalArticleResearchpeer-review

13 Citations (Scopus)


Background: There 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. Results: We 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 of Streptococcus species and Candida. 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. Conclusion: These 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 registration: NHS 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/ [MediaObject not available: see fulltext.]

Original languageEnglish
Article number34
Number of pages16
Issue number1
Publication statusPublished - Dec 2022

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