Analyzing the intestinal microbiome in inflammatory bowel disease: From RNA to multiomics

Some of the species that were unique to ulcerative colitis were the complex sugar‐metabolizing bacteria Bacteoides uniformis 6and Bifidobacterium bifidum. 7 In contrast, patients with CD were found to have a decrease in bacteria such as Faecalibacterium prausnitzii, a butyrate‐producing bacteria with anti‐inflammatory properties, and Bifidobacterium longum, bacteria known to protect against infection by harmful bacteria. CD patients also had an increase in the Enterobacteriacea species, Escheria and Shigella, both known to cause damage to the gut epithelium. 5 In addition to examining the abundance of bacterial species in IBD, the authors went on to investigate how disease states impact strain level diversity, finding 21 species in CD and 15 species in UC that had alterations in their strain level diversity. 5 Of note was a decrease in the strain diversity of Faecalibacterium prausnitzii, which, as mentioned above, also had a decrease in abundance. The findings of dysregulation of short‐chain fatty acids and secondary bile acids are replicated in other studies. 10,11 The authors also identified previously undescribed metabolic changes such as enrichment of acylcarnitines, a class of compounds associated with energy metabolism, which have also been found to be pro‐inflammatory. Research on IBD still has some way to go, a situation it shares with many other chronic inflammatory disorders. 1 TableSummary of the findings of different methods of examining the IBD microbiome Method Principle Conclusions in IBD 16s RNA sequencing Sequences the 16s ribosomal RNA of bacteria, which permit identification and quantification of bacteria down to the genus level, depending on the sequence conservation in a given phylum. ↑ Firmicutes ↑ Actinobacteria ↓ Bacilli ↓ Bifidobacteriaceae ↕ Bacteroidete ↓ Microbiome diversity Metagenomics Using high‐throughput methods, all DNA in a sample is sequenced.