NEW YORK (GenomeWeb) – A team from the Netherlands and the US has profiled gut microbial features in individuals with inflammatory bowel disease (IBD) or irritable bowel syndrome (IBS), including gut microbes that differ between the two common gut conditions.
"By combining species-level profiles and strain-level profiles with bacterial growth rates, metabolic functions, antibiotic resistance, and virulence factor analyses, we identified key bacterial species that may be involved in two common gastrointestinal diseases," corresponding author Rinse Weersma, a gastroenterology and hepatology researcher at the University of Groningen, and his co-authors wrote.
As they reported online today in Science Translational Medicine, the researchers performed metagenomic sequencing on stool samples from 355 individuals with IBD (Crohn's disease or ulcerative colitis), 412 individuals with IBS, and 1,025 unaffected, healthy controls, searching for microbial species and strains associated with one or both inflammatory gut conditions.
Together with association analyses and bacterial data ranging from growth rates and metabolism to virulence and drug response profiles, the team's results revealed gut microbial species and strains that overlap and differ between IBD and IBS, including candidates for distinguishing between the two conditions.
"Our results suggest that in the future, the use of probes directed at key bacterial species could complement fecal [inflammation biomarker] calprotectin measurements in distinguishing the diagnosis of IBS and IBD," the authors wrote.
Along with microbial features meant to inform IBD or IBS diagnoses, the team explained, the current study included a search for microbe-based treatment targets, based on additional microbial pathway, drug resistance, and virulence clues.
Using Illumina instruments, the researchers performed shotgun metagenomic sequencing on microbial DNA in home-collected stool samples from 1,792 well-phenotyped cases and controls from three cohorts from the Netherlands.
The team's sequence data led to 219 Crohn's disease-related taxa, 102 taxa associated with ulcerative colitis, and 66 taxa with apparent ties to IBS. There was some overlap between conditions: Within IBD, for example, at least 87 of the microbes implicated in ulcerative colitis also turned up in individuals with Crohn's disease.
On the strain side, meanwhile, the researchers noted that the diversity of strains within beneficial bacterial species, such as Faecalibacterium prausnitzii, tended to wane in the guts of individuals with IBD or IBS relative to the unaffected controls. They also saw shifts in strain diversity for 21 bacterial species in individuals with Crohn's disease, compared to strain diversity changes in 15 species in those with ulcerative colitis and one species in the IBS group.
The team also estimated growth rates for a subset of the gut microbial species, identifying small sets of species that seemed to have altered abundance in each of the conditions. In addition, they dug deeper into differences in bacterial composition, gene content, and gene functions in the IBD and IBS cases.
"The changes we identified in gut microbiota composition and functional potential in patients with IBD and IBS could lead to new tools that assist diagnosis in clinical practice," the authors wrote. Still, they cautioned that "more additional evidence is required" and said that the "relevance of the microbial pathways described in this study needs to be supported by metatranscriptomics and metabolomics data, as well as functional experiments."