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)
