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Acquisition and Development of the Extremely Preterm Infant Microbiota Across Multiple Anatomical Sites

Young, Gregory R.*; van der Gast, Christopher J.; Smith, Darren L.*; Berrington, Janet E.; Embleton, Nicholas D.; Lanyon, Clare*

Journal of Pediatric Gastroenterology and Nutrition: November 9, 2019 - Volume Publish Ahead of Print - Issue - p
doi: 10.1097/MPG.0000000000002549
Original Article: Gastroenterology: PDF Only

Objectives: Microbial communities influencing health and disease are being increasingly studied in preterm neonates. However, there exists little data detailing longitudinal microbial acquisition, especially in the most extremely preterm (<26 weeks gestation). This study aims to characterise the development of the microbiota in this previously under-represented cohort.

Methods: Seven extremely preterm infant-mother dyads (mean gestation 23.6 weeks) were recruited from a single neonatal intensive care unit. Oral and endotracheal secretions, stool and breast milk (n = 157 total), were collected over the first 60 days of life. Targeted 16S rRNA gene sequencing identified bacterial communities present.

Results: Microbiota of all body sites were most similar immediately following birth and diverged longitudinally. Throughout the sampling period Escherichia, Enterococcus, Staphylococcus and an Enterobacteriaceae were dominant and well dispersed across all sites. Temporal divergence of the stool from other microbiota was driven by decreasing diversity and significantly greater proportional abundance of Bifidobacteriaceae compared to other sites.

Conclusions: Four taxa dominated all anatomical sampling sites. Rare taxa promoted dissimilarity. Cross- seeding between upstream communities and the stool was demonstrated, possibly relating to buccal colostrum / breast milk exposure and indwelling tubes. Given the importance of dysbiosis in health and disease of extremely preterm infants better understanding of microbial acquisition within this context may be of clinical benefit.

*Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.

Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom.

Newcastle Neonatal Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.

Address correspondence and reprint requests to Gregory R. Young, Northumbria University, Newcastle upon Tyne, Tyne & Wear United Kingdom (e-mail:

Received 21 June, 2019

Accepted 22 October, 2019

Supplemental digital content is available for this article. Direct URL citations appear in the printed text, and links to the digital files are provided in the HTML text of this article on the journal's Web site (

Conflicts of Interest and Source of Funding: This work was supported by Northumbria University [grant number 10031605/2 awarded to GY]. The authors declare that they have no competing interests.

Ethics approval and consent to participate: This study was carried out in accordance with the recommendations of “NRES Committee North East – Newcastle & North Tyneside 2” with written informed consent from all subjects. All subjects gave written informed consent in accordance with the Declaration of Helsinki. The protocol was approved by the “NRES Committee North East – Newcastle & North Tyneside 2.”

Availability of data & materials: The datasets generated and/or analysed during the current study are available in the EBI Metagenomic portal (MGnify) repository, [ht**tps://] under the study accession number PRJEB27807.

This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

© 2019 by European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology,