Gut microbiome composition is associated with long-term disability worsening in multiple sclerosis

ABSTRACT

Predicting the long-term outcome of multiple sclerosis (MS) remains an important challenge to this day. As the gut microbiota is emerging as a potential player in MS, we investigated in this study whether gut microbial composition at baseline is related to long-term disability worsening in a longitudinal cohort of 111 MS patients. Fecal samples and extensive host metadata were collected at baseline and 3 months post-baseline, with additional repeated neurological measurements performed over (median) 4.4 y. Worsening (with EDSS-Plus) occurred in 39/95 patients (outcome undetermined for 16 individuals). The inflammation-associated, dysbiotic Bacteroides 2 enterotype (Bact2) was detected at baseline in 43.6% of worsened patients, while only 16.1% of non-worsened patients harbored Bact2. This association was independent of identified confounders, and Bact2 was more strongly associated with EDSS-Plus than neurofilament light chain (NfL) plasma levels. Furthermore, using fecal sampling performed 3 months post-baseline, we observed Bact2 to be relatively stable, suggesting its potential use as a prognostic biomarker in MS clinical practice.

KEYWORDS:

• multiple sclerosis
• gut microbiome
• Bacteroides 2
• neurofilament light chain
• EDSS-Plus
• long-term disability worsening

Acknowledgments

We thank all study participants for their valuable contribution. We sincerely appreciate all who provided logistic support for sample collection (nurses and health practitioners in the National MS Center as well as Annick Van Merhaegen-Wieleman and Tatjana Reynders in University Hospital Brussels). We are grateful for the support of Chloë Verspecht, Duyen Nguyen, Leen Rymenans, Lindsey De Commer and other members of the Raes Lab for assistance in laboratory work and logistics or participation in helpful discussions. We thank Kristin Verbeke for facilitating measurements of moisture content in fecal samples.

Disclosure statement

JR, LD, MD, JDK, GF, SVS are inventors on the patent EP2018/084920: A new inflammation associated, low cell count enterotype issued to VIB VZW, Katholieke Universiteit Leuven, KU Leuven and Vrije Universiteit Brussel. JR is inventor on patent EP14184535.4 - 12/09/2014: Biological sampling and storage container, International patent application on 14/09/2015: PCT/EP2015/070977 issued to VIB VZW, Vrije Universiteit Brussel and LRD.

Inclusion and ethics

Study procedures were compliant with all relevant ethical regulations, aligning with the Declaration of Helsinki and Belgian privacy laws. Study procedures were approved by the medical ethics committee of the UZB (approval number B.U.N. 143201317985) and of the NMSC. Informed consent was obtained from all participants. The study protocol was registered at https://ClinicalTrials.gov under trial identifier NCT04929145.

Availability of data and materials

Raw 16S rRNA amplicon sequencing and selected host metadata will be available immediately following publication at the European Nucleotide Archive (ENA) via https://www.ebi.ac.uk/ena/browser/home under accession number PRJEB45550. Other individual de-identified participant data underlying the results reported in this article (text, tables, figures and appendix) will be shared upon reasonable request. Researchers who provide a methodologically sound proposal can request the data by contacting the corresponding authors.

Code availability

An open-source R script for obtaining QMP matrices is available on https://raeslab.org/software/QMP and the Github repository (https://github.com/raeslab/QMP).

Authors’ contributions

Laboratory experiments, flow cytometry analysis, preprocessing of raw sequencing data and statistical analyses were carried out by LD with guidance from GF and SVS. Cleaning of metadata was done by LD and AP. Clinical assessment of participants during study visits was performed by MD, AP and AVR. Patient data from in-between study visits was collected and quality checked by AP. Evaluation of sustained worsening for each patient was performed by AP. Sampling of cohorts was carried out by AVR. The study was designed by MD and JR, with help of JDK and GN. The manuscript was drafted by LD, AP, JR and MD, with critical revision by GF, SVS, JDK, GN. All authors approved the final version for publication.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2180316

Additional information

Funding

This work was co-funded by the Vlaams instituut Biotechnologie; the Rega Institute for Medical Research, KU Leuven, and an FWO research grant (G038318N) awarded to MD and JR; Research Foundation Flanders.