Metagenomic data (Gut Bugs Trial)

The gut microbiome is a contributing factor in the development of metabolic disorders. The Gut Bugs Trial was conducted to assess the efficacy of using lean multi-donor fecal microbiota transplantation (FMT) to treat adolescents with obesity.

The Gut Bugs Trial recruited 87 adolescents with obesity and randomised them 1:1 to receive a single dose of either FMT or placebo capsules. FMT capsules contained concentrated fecal material derived from 4 sex-matched lean donors. Placebo capsules contained saline. Recipients were clinically assessed at baseline, and at 6-, 12-, and 26-weeks post-treatment. The primary objective was a change in BMI SDS at week 6. Secondary objectives included a variety of metabolic health parameters, body composition, and gut microbiome alterations.

Microbial DNA was extracted from stool samples collected from donors and recipients throughout the study. Shotgun metagenomic sequencing was performed on 381 samples using an Illumina platform (150bp paired end reads). Raw sequencing files were processed with bioBakery workflows using docker images available at http://huttenhower.sph.harvard.edu/biobakery_workflows. Quality control and pre-processing steps involved removal of adaptor sequences using Trim Galore! followed by removal of low-quality reads and human sequences with KneadData. Taxonomic profiling was performed using MetaPhlAn2; Strain profiling was performed using StrainPhlAn; and functional profiling was performed using HUMAnN2.

This dataset contains:

(i) Sample metadata

(ii) KneadData read count table

(iii) MetaPhlAn2 relative abundance table

(iv) MetaCyc pathways abundance table (HUMAnN2)

(v) SNP haplotype FASTA files (StrainPhlAn)