Exploring the microbiome of probiotic-treated preterm infants

This PhD project used metagenomics to explore the gut microbiome of preterm infants in North Queensland, Australia. It explored potential covariates and the effect of probiotic prophylaxis.The dataset consists of the microbiome analyses and associated data for 3 studies/manuscripts: 1. GitHub repository: https://github.com/JacobAFW/NICU_Microbiome_Study This repo contains supplementary data for the manuscript "The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge" This includes: The full workflow, from raw reads to analysis The metadata (deidentified) Summary of the metadata A summary of the methods is also included in the README. The raw sequence reads (Accession PRJNA687291) are available from the NCBI: https://www.ncbi.nlm.nih.gov/bioproject/687291 2. https://github.com/JacobAFW/SCN_vs_NICU_probiotic_study This repo is associated with the manuscript "To probiotic or pot to probiotic: A metagenomic comparison of the discharge gut microbiome of infants supplemented with probiotics in NICU and those who are not" The metagenome (Accession PRJNA751712) is available from the NCBI: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA751712 3. GitHub repository: https://github.com/JacobAFW/Long_term_effects_of_probiotics Microbiome analyses and supplementary data for a pilot study exploring if differences observed in probiotic-supplemented and non-supplemented infants at discharge persist beyond the first year of life. This work has been divided into two separate papers: A validation of at-home infant stool sample collection devices for determining the faecal microbiome (accepted for publication) Exploring the long-term colonisation and persistence of probiotic-prophylaxis species on the gut microbiome of preterm infants: a pilot study This study includes data from the sequence repositories referred to above (PRJNA687291 and PRJNA751712) as well PRJNA805057 available from the NCBI: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA805057