SGD_gutmicro_2026

Data and code for the paper: "Gut Microbiota in Preterm infants with different weight gain outcomes"

Procedure

You must run the R markdowns (Scripts/Rmds) in the following order so that the appropriate RData files are generated:

1. Shotgun_preamble.Rmd
2. Shotgun_taxonomic_growth_analysis.Rmd
3. Download the KEGG data files from Zenodo and place in Data/
4. Shotgun_gene_abundance_analysis.Rmd
5. Shotgun_metabolomic_analysis.Rmd
6. Shotgun_random_forest_analysis.Rmd
7. FIGURESANDTABLES.Rmd
8. The Rmds in sensitivity/

Source data

Decontaminated Fastq's are available from the following BioProjects:

• https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1301887
• https://www.ncbi.nlm.nih.gov/bioproject/PRJNA872399

Metabolomic data is under Data/

Manuscript

[TBD]