Metagenomic data (ECOBABe trial)

The ECOBABe Trial was a single-blinded randomised placebo-controlled pilot trial that assessed whether oral administration of maternal vaginal microbes could restore gut microbiome development in infants born by caesarean section (CS).

The trial recruited 25 women having an elective CS and randomised their neonates 1:1 to receive a 3 ml solution of maternal vaginal microbes (CS-seeded, n=12) or sterile water (CS-placebo, n=13). A group of vaginally born infants served as a reference control (VB, n=22).

Shotgun metagenomics was performed on a total of 116 samples. This included 45 infant stool samples collected at 1 month of age, 46 infant stool samples collected at 3 months of age, and 25 maternal vaginal samples (from CS mothers).

This dataset contains:

1. Sample metadata

2. KneadData read count table

3. MetaPhlAn2 relative abundance taxonomy table

4. HUMAnN2 gene families table (normalised to CPM)

5. HUMAnN2 pathways abundance table (normalised to CPM)

6. StrainPhlAn FASTA files (SNP haplotypes)