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Paediatrician’s perspective of infant gut microbiome research: current status and challenges
  1. Paul MacDaragh Ryan1,
  2. Catherine Stanton2,3,
  3. R Paul Ross3,
  4. Alan L Kelly4,
  5. Eugene Dempsey5,6,
  6. C Anthony Ryan5,6
  1. 1 School of Medicine, University College Cork, Cork, Ireland
  2. 2 Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
  3. 3 APC Microbiome Ireland, University College Cork, Cork, Ireland
  4. 4 School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
  5. 5 Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
  6. 6 Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
  1. Correspondence to Prof C Anthony Ryan, Paediatrics and Child Health, University College Cork National University of Ireland, Cork, Ireland; tony.ryan{at}


Due to its innately intriguing nature and recent genomic technological advances, gut microbiome research has been at the epicentre of medical research for over a decade now. Despite the degree of publicisation, a comprehensive understanding and, therefore, acceptance of the area as a whole may be somewhat lacking within the broader medical community. This paper summarises the main analytical techniques and tools currently applied to compositional microbiome research. In addition, we outline five major lessons learnt from a decade of infant microbiome research, along with the current research gaps. Finally, we aim to provide an introduction and general guidelines relating to infant gut microbiome research for the practising paediatrician.

  • microbiome
  • microbiota
  • infant

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  • Contributors CAR conceived the idea for the manuscript; PMR and CAR drafted the manuscript; and CS, RPR, ALK and ED contributed edits to the manuscript.

  • Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

  • Competing interests None declared.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Patient consent for publication Not required.