The faecal bacteriome in patients with irritable bowel syndrome

Faecal material for metagenomic seqeuncing was obtained from a double-blind, randomised, cross-over, placebo-controlled trial using two pairs of gut microbiota transplants in patients with diarrhoeal or mixed type of IBS (the MISCEAT study, ClinicalTrials ID NCT04899869). All study interventions were performed using the same faecal mixture - a large bulk of faeces from multiple donors was mixed under a nitrogen atmosphere and aliquoted into appropriately sized aliquots and deep-frozen in identical flasks labelled with non-revealing codes. Placebo aliquots were inactivated by autoclaving prior to freezing.Here we deposit the data of shotgun metagenomic sequencing of faecal samples collected at four time points (one week before and one month after each of the two FMT interventions).Data were analysed for taxonomic composition (MetaPhlAn), functional capacity (HUMAnN) and carriage of antibiotic resistance genes. Mixed effects log linear models were used to investigate the effect of the interventions on microbiome characteristics.Administration of live FMT was strongly associated with a subsequent increase in the alpha diversity of the faecal microbiome. The Sorensen and Bray-Curtis distance metrics indicated that after live microbiota FMT, the patients' faecal microbiota became more similar to the transplanted mixture, while administration of autoclaved placebo or the period between the two interventions were accompanied by apparently random, shorter trajectories within the multidimensional taxonomic space.