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The individual-specific and diverse nature of the preterm infant microbiota
  1. Eoin Barrett1,2,
  2. Colm Kerr3,
  3. Kiera Murphy1,4,
  4. Orla O'Sullivan1,2,
  5. C Anthony Ryan3,
  6. Eugene M Dempsey3,
  7. Brendan P Murphy3,
  8. Paul W O'Toole2,4,
  9. Paul D Cotter1,2,
  10. Gerald F Fitzgerald2,4,
  11. R Paul Ross1,2,
  12. Catherine Stanton1,2
  1. 1Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
  2. 2Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, National University of Ireland, Cork, Ireland
  3. 3Department of Neonatology, Cork University Maternity Hospital and Department of Paediatrics and Child Health, University College Cork, National University of Ireland, Cork, Ireland
  4. 4Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
  1. Correspondence to Professor Catherine Stanton, Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; catherine.stanton{at}teagasc.ie

Abstract

Objective To examine the composition of the evolving microbiota of preterm infants at weeks 2 and 4 of life.

Settings The paediatric intensive care unit of the Cork University Maternity Hospital.

Methods The microbial diversity of faecal samples from 10 preterm infants was determined using 16S rRNA amplicon pyrosequencing technology.

Results In total, 452 863 sequences were obtained from 20 faecal samples collected from 10 preterm infants, allowing a level of analysis not previously reported. The preterm infant microbiota samples were dominated by Proteobacteria (46%), followed by Firmicutes (45%), while the phyla Actinobacteria (2%) and Bacteroidetes (7%) were detected at much lower levels at week 2 of life. This colonisation pattern was similar at week 4 of life. At the family level, Enterobacteriaceae were detected at 50% and 58% at weeks 2 and 4, respectively. The preterm infants were characterised by a lack of detectable Bifidobacterium and Lactobacillus genera commonly associated with the infant gut. In addition to the dominance of the Proteobacteria, a high level of interindividual variation was observed, indeed the relative proportions of different phyla, families and genera in different infants ranged from <1% to >90%.

Conclusions The results indicate that in addition to an uncharacteristic microbiota relative to that reported for healthy term infants, there was a large interindividual variation in the faecal microbiota diversity of preterm infants suggesting that the preterm microbiota is individual-specific and does not display a uniformity among infants.

  • Molecular Biology
  • Microbiology

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