Dataset supporting the article 'Fermentation of human milk oligosaccharides using faecal microbiota from healthy and Irritable Bowel Syndrome donors using in vitro batch cultures'

This dataset presents the statistical analysis results from a study exploring the effects of different human milk oligosaccharides (HMOs), solely and in combination, on the gut microbiome and short-chain fatty acid (SCFA) production using 280ml anaerobic in vitro batch culture fermenters. 7 IBS and 3 healthy volunteers were included and samples from each fermentation were taken at timepoints 0, 4, 8, 24 and 48 hours. The aim was to assess prebiotic effects of HMOs in faecal samples from Irritable Bowel Syndrome (IBS) and healthy controls, and to determine a best-performing HMO in IBS. Fluorescence in situ hybridisation coupled with flow cytometry was utilised to study the microbiota at 0 and 24 hours. SCFA production was assessed by gas chromatography at 0, 8, 24 and 48 hours. The data outputs were kept separately for both laboratory techniques. Baseline microbial profiles were analysed to determine whether there were significant differences between healthy and IBS volunteers and whether there was an IBS signature. IBS donors had different starting microbial profiles compared to healthy controls, and lower levels of SCFA. In response to HMOs, there was a shift in both the healthy and IBS faecal microbiomes. In IBS donors, Bifidobacterium, Faecalibacterium and total bacterial numbers significantly increased post-HMO intervention. There was a shift in both the healthy and IBS faecal microbiomes and an increase in SCFA production at 24 hours.