20% of Healthy Adults Have Elevated Gut Inflammation Markers, and Their Microbiomes Look Different

One in five adults who feel perfectly healthy may carry elevated signs of intestinal inflammation, according to a new study published in iScience. Researchers from the Parma Microbiota Project measured fecal calprotectin and gut microbiome composition in 515 adults from northern Italy with no known intestinal disease, finding that elevated calprotectin tracks with a distinct microbial fingerprint, one dominated by opportunistic pathogens and depleted of bacteria that help keep the gut lining healthy.

Elevated Calprotectin in One-Fifth of Symptom-Free Adults

Fecal calprotectin is a protein released by neutrophils into the intestinal lumen when inflammation is active. It chelates divalent metals like calcium, iron, and zinc, limiting bacterial growth in the process, and resists digestion by proteases, making it stable enough to measure reliably in stool. In clinical settings, it is widely used to detect intestinal inflammation and to distinguish inflammatory bowel disease from functional disorders. The healthy reference range typically sits between 10 and 50 micrograms per gram of stool.

In this cohort, the median fecal calprotectin (FC) was 23.6 micrograms per gram, comfortably within that healthy range. But 20% of participants had readings above 50 micrograms per gram, suggesting possible subclinical intestinal alterations in a population that had no diagnosed gut disease. The researchers also noted that chronic use of proton pump inhibitors correlated with elevated FC, though PPI use did not appear to alter microbiome composition independently.

Butyrate Producers Drop as Calprotectin Climbs

The most striking microbial pattern was the inverse relationship between calprotectin and butyrate-producing bacteria. Species including Lachnospira, Hungatella, Clostridium, and Roseburia hominis were all more abundant in individuals whose FC sat within the normal range. Butyrate is the primary fuel for colonocytes, the cells lining the colon, and its production is closely linked to the integrity of the gut barrier. Fewer butyrate producers may mean a less well-nourished epithelium, which could in turn permit low-grade inflammation to take hold.

Flip the picture and you see the opposite pattern in the high-FC group. Opportunistic pathogens, including Haemophilus parainfluenzae, Klebsiella variicola, Escherichia albertii, Streptococcus salivarius, and Proteus mirabilis, were enriched in individuals with elevated calprotectin. Many of these belong to the Pseudomonadota phylum, organisms commonly associated with infection and inflammatory responses. Increased Klebsiella and Escherichia in particular may reflect gut dysbiosis, a shift in the microbial balance that makes the intestinal environment more hospitable to organisms that do not belong there in large numbers.

Despite these compositional differences, the team found no significant changes in total bacterial load, and alpha- and beta-diversity measures did not differ meaningfully between the normal and high FC groups. The story is not about how many microbes are present, but about which ones.

How 515 Healthy Participants Were Studied

The Parma Microbiota Project enrolled 515 adults from northern Italy with no known intestinal pathologies. Fecal samples were analyzed using shallow shotgun metagenomics, sequencing 100,000 reads per sample and classifying them against a curated genome database using METAnnotatorX2 software. Calprotectin was measured by ELISA assay. A subset of 40 samples also underwent bacterial cell density measurement by flow cytometry to verify that total bacterial abundance was not confounding the compositional findings.

Functional prediction drew on the Rhea database, covering 184 enzyme reactions relevant to human health, using samples with at least five million reads. The statistical approach combined relative abundance comparisons, Mann-Whitney U tests, PLS-DA, and Spearman correlations, and the team controlled for confounders including BMI, chronic disease, anxiety and depressive disorders, smoking, alcohol use, and dietary supplements.

Functional analysis added another layer to the picture. Elevated FC was associated with increased bacterial capacity to degrade polyamines, compounds like spermidine and spermine that are linked to epithelial damage and inflammatory responses. Normal FC, by contrast, was associated with enzymatic activities including inositol-polyphosphate 5-phosphatase and cysteine dioxygenase. Propionate production and cGMP degradation, both associated with gut homeostasis, were negatively correlated with FC. The team also observed a positive correlation between FC and bacterial magnesium transport, which they interpret as a possible microbial compensatory response to calprotectin's metal-chelating activity.

What This Study Cannot Yet Tell Us

The cross-sectional design is the central limitation here. Because all measurements were taken at a single point in time, it is impossible to determine whether the microbial differences cause elevated calprotectin, result from it, or simply coexist with it. The authors are explicit that their findings are hypothesis-generating, not causal.

Dietary habits were accounted for only partially, and diet is one of the most powerful drivers of microbiome composition. The shallow shotgun approach, while practical for a 515-person cohort, may miss low-abundance taxa that play important functional roles. And defining what a truly healthy microbiome looks like remains an open problem in the field; there is no universally accepted baseline against which to compare these findings. Single-center studies also carry inherent geographic and dietary homogeneity that limits how broadly the results can be applied.

What Comes Next for Microbiome-Based Calprotectin Research

Longitudinal follow-up is the obvious next step: tracking the same individuals over time would begin to untangle whether microbial shifts precede or follow changes in calprotectin. External validation in geographically diverse cohorts would help address the generalizability problem.

Longer term, the findings point toward a more nuanced use of fecal calprotectin as a clinical tool. Microbiome-based calibration of calprotectin readouts could, in principle, improve how reliably the test distinguishes true subclinical inflammation from inter-individual variation driven by microbiome composition. That kind of refinement would matter enormously in primary care, where calprotectin is increasingly used as a first-pass screen before more invasive investigations. Translating gut microbiome science into practical clinical tools requires exactly the kind of large, well-characterized healthy-cohort data that studies like this one are beginning to build.

The broader implication is that the microbiome may be doing something measurable even before overt disease appears. Subclinical inflammation detectable only through a biomarker, paired with a microbial signature that has shifted away from butyrate producers and toward opportunistic organisms, suggests a gut environment in transition. Whether that transition leads anywhere clinically meaningful is what the next round of research will need to answer.

Evidence rating

EMERGING — 80/100

Caveats:

• Cross-sectional design: the study shows associations, not causation — it cannot determine whether microbial shifts drive inflammation or result from it.
• Single-center Italian cohort only; findings require validation in diverse independent populations.
• Microbial functional profiles are computationally predicted from metagenomic reads, not measured directly as metabolic outputs.
• Shallow shotgun sequencing (100,000 reads/sample) may miss low-abundance taxa and underrepresent functional diversity.
• Funding source was not disclosed by the authors.

Cross-sectional observational study of 515 healthy adults using shallow shotgun metagenomics. Findings reflect associations between fecal calprotectin levels and microbial taxa and predicted enzymatic functions; causality cannot be established. Results have not yet been independently replicated and the authors note the need for longitudinal validation.

References

1. Giuseppe Taurino, Leonardo Mancabelli, Christian Milani, et al. (2026). Fecal calprotectin and gut microbiome in a cohort without intestinal pathologies from northern Italy. iScience. https://doi.org/10.1016/j.isci.2026.116578
2. Almina Jukic, Latifa Bakiri, Erwin F. Wagner, Herbert Tilg, Timon E. Adolph (2021). Calprotectin: from biomarker to biological function. Gut. https://doi.org/10.1136/gutjnl-2021-324855
3. Amir Mari (2019). Clinical utility of fecal calprotectin: potential applications beyond inflammatory bowel disease for the primary care physician. Annals of Gastroenterology. https://doi.org/10.20524/aog.2019.0394
4. Shuting Xia, Diya Jiang, Qianyi Zhou, et al. (2025). Unlocking the healthy human microbiome: Redefining core microbial signatures. Acta Pharmaceutica Sinica B. https://doi.org/10.1016/j.apsb.2025.01.001
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