Deconfounded, quantitative microbiome profiling identifies robust multiple sclerosis markers and clinical covariate associations

Pauwels, A; Devolder, L; Falony, G; D'haeseleer, M; Nagels, G; Van Remoortel, A; Derrien, M; D'hooghe, M; Raes, J

Journal article

Deconfounded, quantitative microbiome profiling identifies robust multiple sclerosis markers and clinical covariate associations

Abstract:: Despite a wealth of gut microbiota studies in multiple sclerosis (MS), consistent results are lacking. Here, we study confounder effects and use of quantitative microbiome profiling (QMP) in 228 MS patients (103 untreated) and 2860 population controls (Flemish Gut Flora Project (FGFP)). Total bacterial load was lower in relapsing remitting (RR)MS, while strong fecal moisture effects, indicative of longer transit times, in MS vs. FGFP, were driven by primary progressive (PP)MS. Applying cell count and moisture in deconfounded QMP, we identified 21 differentially abundant genera in MS, with a.o. Lachnobacterium, Blautia enriched, and Clostridium, Bacteroides depleted. Deconfounded QMP across 10 published studies (1065 patients, 874 controls) did not confirm commonly detected markers (Akkermansia, Roseburia), yet lowered Bacteroides, and higher Blautia and Methanobrevibacter emerged as robust MS biomarkers. Lowered butyrate producers (Butyricicoccus, Butyricimonas) merit further investigation. Enterotype stratification linked the low cell count Bacteroides 2 enterotype to low-efficacy DMTs, and the Prevotella enterotype to lower disease severity. Serum glial fibrillary acidic protein (GFAP), a disease progression biomarker, was identified as a covariate of gut microbial variation and inversely correlated with Faecalibacterium and Roseburia abundance in PPMS. Overall, our study provides robust disease markers and emphasizes the importance of QMP and confounder control.

Publication status:: Published

Peer review status:: Peer reviewed

Actions

Email

Email this record

Send the bibliographic details of this record to your email address.

Your Email
Please enter the email address that the record information will be sent to.

-
Your message (optional)
Please add any additional information to be included within the email.
Share
Cite

Cite this record

APA Style

Pauwels, A., Devolder, L., Falony, G., D'haeseleer, M., Nagels, G., Van Remoortel, A., Derrien, M., D'hooghe, M., & Raes, J. (2026). Deconfounded, quantitative microbiome profiling identifies robust multiple sclerosis markers and clinical covariate associations. Gut Microbes, 18(1), 2681876.

MLA Style

Pauwels, A, et al. “Deconfounded, Quantitative Microbiome Profiling Identifies Robust Multiple Sclerosis Markers and Clinical Covariate Associations.” Gut Microbes, vol. 18, no. 1, 2026, p. 2681876.

Chicago Style

Pauwels, A, L Devolder, G Falony, et al. 2026. “Deconfounded, Quantitative Microbiome Profiling Identifies Robust Multiple Sclerosis Markers and Clinical Covariate Associations.” Gut Microbes 18 (1): 2681876.
Print