No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls

Abstract

Several studies have indicated that colonic microbiota may exhibit important differences between patients with irritable bowel syndrome (IBS) and healthy controls. Less is known about the microbiota of the small bowel. We used massive parallel sequencing to explore the composition of small bowel mucosa-associated microbiota in patients with IBS and healthy controls. We analysed capsule biopsies from the jejunum of 35 patients (26 females) with IBS aged 18-(36)-57 years and 16 healthy volunteers (11 females) aged 20-(32)-48 years. Sequences were analysed based on taxonomic classification. The phyla with the highest total abundance across all samples were: Firmicutes (43%), Proteobacteria (23%), Bacteroidetes (15%), Actinobacteria (9.3%) and Fusobacteria (7.0%). The most abundant genera were: Streptococcus (19%), Veillonella (13%), Prevotella (12%), Rothia (6.4%), Haemophilus (5.7%), Actinobacillus (5.5%), Escherichia (4.6%) and Fusobacterium (4.3%). We found no difference among major phyla or genera between patients with IBS and controls. We identified a cluster of samples in the small bowel microbiota dominated by Prevotella, which may represent a common enterotype of the upper small intestine. The remaining samples formed a gradient, dominated by Streptococcus at one end and Escherichia at the other.

Figure 1. Relative abundance of the five most common phyla among IBS patients and controls.

Figure 2. Relative abundance of the eight most common genera among IBS patients and controls.

Figure 3. Correlation between the relative abundance of Prevotella and Veillonella (Spearman rho = 0.55 ρ ≈ 0.55, p ≈ 4 × 10⁻⁵).

Figure 4. The relative abundance of Escherichia and Rothia exhibit a mutually exclusive relationship.

Figure 5. The relative abundance of Prevotella and Streptococcus exhibit an inverse relationship in samples with high total abundance of these two genera.

Figure 6. The distribution of Prevotella abundance is bimodal, indicating that samples may be naturally subdivided into two distinct subgroups according to whether they have low or high Prevotella abundance.

Figure 7. A principal component analysis of all samples.

The first two principal components were roughly organized along three directions determined by enrichment for Prevotella, Streptococcus or Escherichia.