Noninvasive Microbiome Test May Identify Crohn’s and UC

International researchers have uncovered potentially diagnostic gut microbiome signatures and metabolic pathways associated specifically with ulcerative colitis (UC) and Crohn’s disease (CD).

Targeted droplet digital polymerase chain reaction (ddPCR)‒based quantification of bacterial species led to convenient inflammatory bowel disease (IBD) diagnostic assays that “are sufficiently robust, sensitive and cost-effective for clinical application,” the investigators wrote in a recent study published in Nature Medicine.

“Although traditional modalities used for diagnosis of IBD, including colonoscopy and cross-sectional imaging, are well established, the inconvenience of bowel preparation and radiation represents relevant concerns,” senior author Siew C. Ng, MBBS, PhD, a professor in the Department of Medicine and Therapeutics at the Chinese University of Hong Kong, said in an interview. “Furthermore, existing serological and fecal markers indicate inflammation but lack specificity for IBD.”

Identifying reproducible bacterial biomarkers specific to CD and IBD should enable precise and personalized approaches to detection and management.

As a starting point, the researchers hypothesized that changes in the gut microbiome of IBD patients may reflect underlying functional associations, if not causes, of the disease, said Ng, who is also director of Hong Kong’s Microbiota I-Center (MagIC). “Unlike inflammation, which is a manifestation of the disease, the gut microbiome may serve as a more reliable biomarker less affected by the disease’s fluctuating cycle.”

The study findings showed that bacterial markers remain consistent even during the inactive disease phase. Additionally, the results are reproducible across different populations, suggesting that these markers are true indicators of IBD, she added. “With a better performance than the commonly used noninvasive test, fecal calprotectin, we believe the test will be a valuable addition to clinician’s toolbox and a strong option for first-line diagnostics.”

The Study

The group used metagenomic data from 5979 fecal samples from persons with and without IBD from different regions (including the United States) and of different ethnicities. Identifying several microbiota alterations in IBD, they selected bacterial species to construct diagnostic models for UC (n = 10) and CD (n = 9). Some species were deleted and some were enriched in IBD.

Metagenomic findings confirmed, for example, enrichments of Escherichia coli and Bacteroides fragilis in the guts of CD patients, with adherent invasive E coli present in more than half of these. This pathogen has been linked to mucosal dysbiosis and functional alteration, and has been associated with disease activity and endoscopic recurrence following surgery. B fragilis may induce intestinal inflammation through toxin production.

The researchers also identified a new oral bacterium, Actinomyces species oral taxon 181, which was significantly enriched in stool samples with both CD and UC.

The diagnostic models achieved areas under the curve of >.90 for distinguishing IBD patients from controls in the discovery cohort and maintained satisfactory performance in transethnic validation cohorts from eight populations.

Ng’s group further developed a multiplex droplet digital PCR test targeting selected IBD-associated bacterial species. Models based on this test showed numerically higher performance than fecal calprotectin in discriminating UC and CD samples from controls. These universally IBD-associated bacteria suggest the potential applicability of a biomarker panel for noninvasive diagnosis.

Commenting on the paper but not involved in it, Ashwin N. Ananthakrishnan, MBBS, MPH, director of the Crohn’s and Colitis Center at Massachusetts General Hospital in Boston and an associate professor of medicine at Harvard Medical School, called it “a very important study that highlights the potential role of a microbiome-based diagnostic for screening. It could have application in a wide variety of settings and is very promising.”

More work, however, is necessary to clarify such testing’s role. “The study’s validation in independent cohorts is an important strength, but the sizes of those cohorts are still quite small,” he said in an interview. “It’s important to understand its accuracy across a spectrum of IBD phenotypes and severity.”

Furthermore, endoscopic evaluation at diagnosis is important to establish severity and extent of disease. “It’s not clear this diagnostic biomarker can help supplant that role. But I see potential value to it for patients for whom we may not be considering endoscopy yet but who would like to risk-stratify.”

The Test’s Future

“We expect to see a real shift in clinical practice,” Ng said. “As a cost-effective test, it will help millions of people dealing with nonspecific gastrointestinal symptoms get the diagnoses they need.” Because the bacterial test can identify IBD at an inactive stage, it has the potential for early diagnosis. “This capability allows clinicians to initiate treatment sooner, helping to prevent progression from subclinical to clinical stages of the disease.”

The next research steps involve prospective studies with a larger and more diverse group of patients with various gastrointestinal symptoms. “This will enable a comprehensive evaluation of bacterial biomarkers in real-world populations,” she said. In vivo and in vitro experiments are expected to provide mechanistic insights into the causal role of these bacteria and metabolic dysregulations in the pathogenesis of IBD, as well as their future clinical utility in disease monitoring and predicting treatment response.

Her group plans to work with the biotech industry and regulatory agencies to transform these biomarkers into an approved test kit. “The rollout is likely to be gradual, but we’re optimistic that supportive international and national guidelines will be developed and will pave the way for widespread implementation.”

This study was supported by various academic, charitable, and governmental research-funding bodies, including the governments of Hong Kong and the People’s Republic of China. 

Dr Ng has served as an advisory board member or speaker for Pfizer, Ferring, Janssen, AbbVie, Tillotts, Menarini, and Takeda. She has received research grants through her institutions from Olympus, Ferring, and AbbVie and is a founding member and shareholder of GenieBiome Ltd. She receives patent royalties through her institutions, including MagIC, which holds patents on the therapeutic and diagnostic use of the microbiome in IBD. 

Several co-authors reported various relationships, including patent holding, with private-sector companies. 

Dr Ananthakrishnan had no relevant competing interests.