To Probiotic or not to probiotic: using metagenomics to compare the gut microbiome of infants who fulfill probiotic-treatment criteria with those who do not.

Microbiome analyses and supplementary data for the manuscript titled above.

Summary of study:

Preterm birth is associated with the development of acute and chronic disease, potentially, through the disruption of normal gut microbiome development. Probiotic treatment may correct for disrupted microbial imbalances and mitigate disease risk but is only targeted at the most premature of infants. This project used both 16S rRNA gene amplicon and shotgun metagenomic (shotgun performed by Microba) sequencing to compare the gut microbiome of infants who fulfil the criteria for probiotic-treatment and those who do not. We used several mixed effects models to account for variation imparted by known clinical co-variates of the infant gut microbiome. The aim of the study was to determine if late-preterm infants are at a disadvantage due to the current criteria for probiotic treatment.

Preterm infants were recruited in North Queensland, Australia, and stool samples collected just before the infants were discharged (~ 36 weeks gestation). Mixed effects modelling demonstrated that probiotic treatment had a significant effect on overall community composition (beta diversity), characterised by lower alpha diversity and differing abundances of several tax in those infants not treated. However, differing abundances of probiotic-taxa were not observed, suggesting transient colonisation. Late preterm-infants who go without probiotic-treatment may be missing out on stabilising-effects provided through increased alpha diversity, via the use of probiotic-treatment.

The manuscript is published here.