Functional changes in the gut microbiome of Multiple Sclerosis patients come along with a striking Vancomycin-resistant gene profile
Background and Objectives: The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders, including Multiple Sclerosis (MS). However, due to the concept of most studies being single center based, include mostly patients under treatment and/or performing taxonomic evaluation based on 16S rDNA sequencing only, findings on the overall role microbial dysbiosis could play in the etiology of MS are inconsistent.   Methods: In our study, fecal samples of 61 treatment-naïve MS patients from two geographically distinct German regions were subjected to metagenomic sequencing and compared to samples from age- and gender-matched controls. In addition, fecal samples from 65 MS patients treated with Ocrelizumab from the same geographic regions were included in a subsequent metagenomic analysis.   Results: Bioinformatic analysis of metagenomic sequencing data confirmed earlier described decrease in microbial diversity (?-diversity) and significant changes in overall microbial taxonomy (?-diversity) within the fecal microbiome of treatment-naïve MS patients. Meta-analysis of differently abundant microbial species highlighted a consistent increase of Alistipes finegoldii and Bacteroides vulgatus and a decrease of several strains belonging to the Actinomycetota. Further functional profiling of fecal metagenomes revealed a significant decrease of microbial functions including Carbohydrate Biosynthesis and Degradation pathways. Interestingly however, higher biosynthesis of the non-essential amino acid L-citrulline and of the urea cycle pathway driven by Alistipes finegoldii were found in the gut microbiome of MS patients, which might replace arginine and thus leading to conformational changes of proteins. Noteworthy, a highly significant enrichment of numerous Vancomycin-resistant genes mainly driven by Bacteroides and Streptococcus was found, strongly indicating increased antibiotic target alterations of cell wall glycopeptides in MS patients. We finally included 65 MS patients treated with Ocrelizumab from the same geographic regions, which showed significant changes in the microbial functions though taxonomic differences were weak.   Discussion: The herein presented results of a fecal metagenome meta-analysis originating from treatment-naïve MS patients reveal evidence for dysbiotic changes probably caused by a specific antibiotic resistance pattern. The resulting functional changes, particularly in the synthesis of amino acids could be causal for autoimmune processes in MS and thus warrant further studies.