Methodological challenges in neonatal microbiome research

ABSTRACT

Following microbial colonization at birth, the gut microbiome plays a vital role in the healthy development of human neonates and impacts both health and disease in later life. Understanding the development of the neonatal gut microbiome and how it interacts with the neonatal host are therefore important areas of study. However, research within this field must address a range of specific challenges that impact the design and implementation of research methods. If not considered ahead of time, these challenges have the potential to introduce biases into studies, negatively affecting the relevance, reproducibility, and impact of any findings. This review outlines the nature of these challenges and points to current and future solutions, as outlined in the literature, to assist researchers in the early stages of study design.

KEYWORDS:

• Neonatal gut microbiome;
• neonatal health;
• gut microbiota composition;
• gut microbiome development;
• microbiome analytical methods;
• neonatal models;
• intestinal organoids;
• host microbiome interactions;
• study design

Disclosure statement

CJS declares performing consultancy for Astarte Medical and receiving lecture honoraria from Danone Early Life Nutrition and Nestle Nutrition Institute. He also supervises a BBSRC collaborative training partnership PhD student for which Nestlé are involved (no salary or other personal payment is provided by Nestlé). He has no share options or other conflicts. JAC reports no conflict of interest.

Additional information

Funding

This work was supported by the Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant Number 221745/Z/20/Z), a Newcastle University Academic career Track (NUAcT) Fellowship, and the 2021 Lister Institute Prize Fellow Award.