From the AGA Journals

Usefulness of IBD biomarker may vary based on microbiome

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Looking beyond endoscopic evaluation

The search continues for reliable, noninvasive methods for monitoring disease activity in inflammatory bowel disease (IBD). Noninvasive disease activity measures improve quality of care by facilitating more frequent assessment of therapeutic efficacy, which for IBD otherwise depends on periodic endoscopic evaluation and biopsy. Available tools such as fecal calprotectin are valuable and widely used but are imperfect.

Dr. Deborah C. Rubin, the William B. Kountz Professor of Medicine and professor of developmental biology in the division of gastroenterology at Washington University, St. Louis

Dr. Deborah C. Rubin

In this report by Kamp et al., the authors provide a potential explanation for variation in fecal calprotectin levels. They make the novel observation that calprotectin can be metabolized by components of the patient’s fecal microbiome. The authors generated an ex-vivo functional assay in which they anaerobically cultured fecal samples with or without calprotectin, and showed that Subdoligranulum species (Subdoligranulum variabile) when cultured in low–amino acid media, degraded calprotectin, yet another microbiome component, Akkermansia muciniphilia, did not. Subdoligranulum species were isolated from 17 of 22 patient microbiomes.

Of note, a patient with endoscopically active colitis and a relatively low fecal calprotectin level harbored Subdoligranulum species, which – when isolated and assayed ex vivo – degraded calprotectin. These studies suggest that individualized, patient microbiome–based calibration assays might help improve the sensitivity and specificity of fecal calprotectin levels for monitoring disease activity. As the authors note, more patients need to be studied, especially focusing on those with active disease and paradoxically low calprotectin levels.

Deborah C. Rubin, MD, AGAF, is the William B. Kountz Professor of Medicine and professor of developmental biology in the division of gastroenterology at Washington University, St. Louis. She had no conflicts of interest to disclose.



Levels of calprotectin, a biomarker used to detect intestinal inflammation, may vary in fecal samples based on an individual’s microbiome composition, according to researchers. The results, if confirmed, might help refine its use in monitoring inflammatory bowel disease (IBD).

Researchers used a new ex vivo functional assay to identify specific bacteria that degrade calprotectin and may play a role in variations found in vivo. “Microbiome-based calibration could improve sensitivity and specificity of fecal calprotectin readouts, thereby facilitating more reliable real-time monitoring and ultimately enabling more timely interventions,” the authors wrote in their research letter, which was published in Gastro Hep Advances.

The standard for diagnosing ulcerative colitis (UC) and Crohn’s disease (CD) is endoscopy and biopsy because it allows both visual and histological examination of the severity and extent of intestinal inflammation, but this cannot be used to monitor patients on an ongoing basis.

Calprotectin is a promising biomarker for intestinal inflammation, but a meta-analysis found that it has a pooled sensitivity of 85% and a pooled specificity of 75% for the diagnosis of endoscopically active inflammatory bowel disease.

The researchers investigated whether an individual’s microbiome can metabolize calprotectin, which would complicate measurement of fecal calprotectin. They recruited 22 individuals with IBD (64% female, 73% with colonic disease), who provided stool samples. They completed a symptom questionnaire in advance of a colonoscopy. Overall, 64% had endoscopically inactive disease, and 82% had clinically inactive disease.

At a cutoff of 50 mcg/g, 9 patients had normal fecal calprotectin levels, and 13 had elevated levels. Those with clinically or endoscopically active disease had higher levels of fecal calprotectin (P < .0001).

There was a significant but poor correlation between disease activity measures and fecal calprotectin levels in CD (r = 0.62; P = .008), but there was no statistically significant association for UC (r = –0.29; P = .6). Endoscopic disease activity was also significantly correlated with fecal calprotectin in CD (r = 0.83; P < .001), but not UC (r = 0.50; P = .4).

The researchers created an ex vivo functional assay to measure calprotectin metabolism by the microbiome. They anaerobically cultured fecal samples in the presence of calprotectin and measured levels of calprotectin after 24 hours. Control samples were grown without microbes, without calprotectin, or lacking both. The researchers tested samples in both standard media and in media with low levels of amino acids, reasoning that the latter condition might encourage catabolism of calprotectin. The cultures with low amino acid content had lower calprotectin levels than those with normal amino acid content (P < .0007).

The researchers found greater calprotectin degradation in the low amino acid media, and the difference was more pronounced among samples taken from individuals with UC than CD (P < .02).

They used metagenomic sequencing data from fecal samples to identify bacterial species associated with calprotectin metabolism. Similarly to previous reports, the researchers found that Firmicutes was dominant, while Subdoligranulum correlated with calprotectin degradation in low amino acid media (P = .04).

For 5 days, they cultured Subdoligranulum variabile in low amino acid media that also contained calprotectin. Calprotectin levels were lower than a control sample with cultured Akkermansia muciniphila, which was previously shown to not be associated with calprotectin degradation in low amino acid media (P = .03). Because Subdoligranulum species were not detectable in 5 of 22 fecal samples, the authors say they are unlikely to be the only species capable of metabolizing calprotectin.

Among IBD patients, only one had both endoscopically active colitis and a low fecal calprotectin level. The patient’s micobiome had Subdoligranulum present, and their fecal sample was able to metabolize calprotectin in the functional assay.

The study was limited by its small sample size, which prevented development of a calibration model for fecal calprotectin, and the researchers called for additional studies among individuals with active colitis.

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