DOI: 10.7272/q6rx997g
title: Gut Microbiota from Multiple Sclerosis patients triggers spontaneous autoimmune encephalomyelitis in mice --16S data--

description: The commensal microbiota has emerged as a key factor influencing human
 health and has been associated with several diseases, including those of
 the central nervous system (CNS). To investigate the role of the
 microbiome in multiple sclerosis (MS), a complex autoimmune disorder
 shaped by a multitude of genetic and environmental factors, we recruited a
 cohort of 34 monozygotic twin pairs discordant for MS, and compared their
 gut microbial composition by 16S ribosomal RNA sequencing of stool
 samples. While no major differences in the microbial profiles between
 MS-affected twins and their healthy co-twins were detected, a significant
 increase in some taxa (including Akkermansia) was seen in affected
 untreated subjects. To search for possible functional differences, we used
 a transgenic mouse model, in which spontaneous anti-CNS autoimmunity is
 dependent on the commensal gut flora. Germ-free mice colonized with
 microbiota from MS-affected twins, developed the MS-like disease with a
 significantly higher incidence than mice colonized with healthy
 twin-derived microbiota. Although alpha diversity was reduced compared to
 human donors, the microbial profiles of the colonized mice showed high
 intraindividual, remarkable temporal stability and a high transfer rate,.
 Analysis of the transplanted mouse microbiome at the level of individual
 taxa revealed several differences, including a significantly reduced
 abundance of the potentially autoimmune-protective genus Sutterella in
 mice colonized with MS-twin-derived microbiota. These findings provide
 first evidence that MS-derived microbiota contain factors that precipitate
 an MS-like autoimmune disease in a transgenic mouse model. This model
 lends itself to identify protective and pathogenic microbial component in
 human MS.
description: Study design. MZ twins were recruited by
 launching a national televised appeal as well as internet notification in
 Germany with support from the German Multiple Sclerosis Society (DMSG).
 Inclusion criteria for study participation were met for MZ twins with an
 MS diagnosis according to the revised McDonald criteria or clinically
 isolated syndrome (CIS) in one twin only. Exclusion criteria were
 antibiotic, glucocorticosteroidal or immunosuppressive treatment,
 gastrointestinal infection or diet irregularities in the 3 months prior to
 study entry. In total, 34 pairs (see Table 1) visited the outpatient
 department at the Institute of Clinical Neuroimmunology in Munich for a
 detailed interview on past and present medical, family and social history,
 a neurological examination as well as a nutrition questionnaire. To
 confirm the MS diagnosis, medical records including MRI scans were
 obtained and reviewed. Fecal samples were either directly collected in
 hospital or taken at home, stored at -20°C and transferred to the hospital
 in cooling bags. Finally, all samples were stored at -80°C. Of all
 participants buccal swabs for zygosity testing were taken. The study was
 approved by the local Ethics Committee of the Ludwig-Maximilians
 University Munich and all participants gave written informed consent.
 16S rRNA Sequencing and Analysis.The
 V3-V5 region of bacterial 16S rRNA gene was amplified using the universal
 forward (5’-CCGTCAATTCMTTTGAGTTT-3’) and reverse primer (5’-ACTCCTA
 CGGGAGGCAGCAG-3’) incorporating the FLX Titanium adapters and a unique
 barcode sequence. PCR products were sequenced on a 454 GS FLX titanium
 pyrosequencer (454 Life Sciences, Branford, CT, USA) at BGI-Shenzhen.
 Analysis was performed using QIIME v1.9 as described (1). Essentially,
 amplicon sequences were quality-filtered and grouped to operational
 taxonomic units (OTUs) using SortMeRNA method (2) using GreenGenes version
 13.8 97% dataset for closed reference. Sequences that did not match
 reference sequences in the GreenGenes database were dropped from the
 analysis. Taxonomy was assigned to the retained OTUs based on the
 GreenGenes reference sequence and the GreenGenes tree was used for all
 downstream phylogenetic community comparisons. Samples were filtered to at
 least 10000 sequences per sample and OTUs were filtered to retain only
 OTUs present in at least 5% of samples, covering at least 0.01% of total
 reads. After filtering, human samples were rarefied to 10975 sequences,
 while mouse samples were rarefied to 8137 sequences per sample, which were
 the lowest number of sequences per sample, respectively. For comparison
 between human and mouse samples, the human and mouse datasets were
 combined before OTU filtering and rarefaction. The resulting OTUs were
 filtered as described above and samples were rarefied to 6200 sequences
 per sample. Alpha diversity was calculated using phylogenetic diversity
 index method (3). For analysis of beta diversity, pairwise distance
 matrices were generated by phylogenetic metric of weighted UniFrac (4) and
 used for PCoA. For comparison of individual taxa, samples were not
 rarefied. Instead, OTU abundances were normalized using
 variance-stabilizing transformation and taxa distributions were compared
 using the Wald negative binomial test from the R software package DESeq2
 (as described in (4, 5) with Benjamini-Hochberg correction for multiple
 comparisons. All statistical analyses of differences between individual
 bacterial species were performed using QIIME v.1.9 or R (packages DESeq2
 and phyloseq).
description: Two files are uploaded. The dataset contains both human and mice
 samples. Max_Planck_Twin_metadata.txt: Contains the
 sample metadataMax_Planck_Twin_OTU_table.txt: contains
 the normalized OTU abundances for each individualOTU
 abundances were normalized using variance-stabilizing transformation and
 taxa distributions were compared using the Wald negative binomial test
 from the R software package DESeq2 (as described in (4, 5) with
 Benjamini-Hochberg correction for multiple comparisons.