Review Article

The Gut Microbiome in Inflammatory Bowel Disease—Avenues for Microbial Management

J. McIlroy; G. Ianiro; I. Mukhopadhya; R. Hansen; G. L. Hold


Aliment Pharmacol Ther. 2018;47(1):26-42. 

In This Article

Mucosal vs Faecal Microbial Populations

When considering the issue of mucosal vs faecal populations, there is limited comparison of both sample types within the same patient cohort, highlighting a gap in our understanding. The current evidence would indicate that only limited differences exist between different mucosal sites, or between inflamed and uninflamed mucosa, but significant differences exist between mucosal and luminal microbial populations—even within healthy individuals.[34,38,39] Table 1 summarises publications which describe microbial composition between IBD (either CD or ulcerative colitis) and healthy controls, where next-generation sequencing was used as the principal analysis tool (Table 1). In CD, a systematic review, published in 2015, documented the microbial alterations seen in luminal (faecal) vs mucosal samples.[40] In total 73 studies were included with 6 or more CD patients compared to healthy controls. Post-operative CD was not included in the review. In both luminal and mucosal samples, a reduction in microbial richness was apparent and mainly attributed to reduction of diversity within the Firmicutes phylum. Increases in Bacteroidetes and Enterobacteriaceae (Proteobacteria phylum) were seen, with E. coli specifically noted to rise in both tissue and faecal samples, relative to healthy controls. Reductions in the Firmicutes member F. prausnitzii were also noted, particularly in ileal CD.[40]

Abnormalities in the intestinal microbiota have also been reported in ulcerative colitis, although to a lesser degree compared to CD. Less diverse microbiota profiles have been demonstrated in ulcerative colitis patient samples, and in particular, the finding of increased Clostridium perfringens in faeces suggests a role in disease exacerbation.[41] A decrease in Fusicatenibacter saccharivorans in patients with active ulcerative colitis has also been reported, in contrast to the increase observed in patients with quiescent disease.[42]