Table 1.

Bacterial genera significantly altered in MS

Genera	Abundance MS: controls	Reference(s) in which difference identified	Reference(s) in which opposite difference identified	Mechanistic understanding
Acidaminococcus	increased	[217]	[187]
Acinetobacter	increased	[187]		A. calcoaceticus reduced CD25+ FoxP3+ Tregs in human PBMCs [187] A. calcoaceticus increased differentiation of human peripheral blood CD4+ T cells to IFNγ-producing Th1 cells [187] Antibody cross-reactivity between Acinetobacter and myelin peptides [218]
Actinomyces	increased	[187]
Adlercreutzia	decreased	[185]
Akkermansia	increased	[217] [186] [187] [188]		A. muciniphila increased differentiation of human peripheral blood CD4+ T cells to IFNγ-producing Th1 cells [187]
Anaerococcus	increased	[187]
Anaerostipes	increased	[217]	[184]
Aquamonas	decreased	[187]
Atopobium	increased	[217]
Bacillus	decreased	[187]
Bacteroides	decreased	[217] [184] [187]	[217]	Decreased EAE severity via B. fragilis polysaccharide A-mediated induction of regulatory dendritic cells and Tregs and suppression of Th17s [177,219] B. fragilis expands of regulatory CD39+CD4+ T cells [220]
Barnesiella	decreased	[186]
Bifidobacterium	increased	[217] [187]	[187]	Supplementation of Bifidobacterium ameliorates EAE in Lewis rats [221] Supplementation of Bifidobacterium ameliorates EAE in C57BL/6 mice [182]
Bilophila	increased	[217]	[187]
Blautia	increased	[217] [185] [187]	[217] [187]
Bulleidia	increased	[187]
Buttiauxella	decreased	[186]
Butyricimonas	decreased	[217] [186] [187]
Catenibacterium	increased	[217]	[217]
Citrobacter	increased	[217] [187]		C. rodentium induces inflammatory Th17 cells [222]
Cloacibacillus	increased	[186]
Clostridium	decreased	[184] [187]	[187]	C. butyricum suppresses EAE associated with decreased Th17 and increased Treg [223] Clostridia consortia induces colonic Treg [224]
Collinsella	decreased	[185] [186] [187]
Coprobacillus	decreased	[185] [187]
Coprococcus	decreased	[217] [184] [187]	[217] [187]
Corynebacterium	increased	[187]
Dehalobacterium	increased	[217]
Desulfotomaculum	decreased	[184]
Desulfovibrio	increased	[217] [184] [186] [187]	[187]
Dialister	increased	[217] [187]	[217]
Dorea	decreased	[217] [187]	[185]
Eggerthella	increased	[184]
Enterobacter	increased	[187]		E. lenta does not affect human PBMC differentiation towards Th1 or Treg [187]
Eubacterium	increased	[217] [187]	[184] [187]
Faecalibacterium	decreased	[217] [187]	[187]	F. prausnitzii decreases Th17 differentiation and increases Treg differentiation in mouse CD4 + T cells va production of butyrate [225]
Flavobacterium	increased	[185]
Fusobacterium	decreased	[187]
Guggenheimella	decreased	[186]
Haemophilus	decreased	[185] [186]	[186]
Klebsiella	increased	[187]		Intratracheal infection with K. pneumoniae induces Th17 cells [226]
Lachnospira	decreased	[217] [184] [187]
Lactobacillus	decreased	[217] [185] [187]	[217]	L. reuteri ameliorates EAE with reduced Th1 and Th17 cells [178] L. paracasei DSM 13434, L. plantarum DSM 15312, and L. plantarum DSM 15313 ameliorate EAE via IL-10 producing Tregs and suppression of IFNy and IL-17 production [179] L. helviticus SBT2171 attenuates EAE by reducing IL-6 production, T cell infiltration into the spinal cord, and Th17 proportions [227] L. murinis ameliorates EAE by reducing Th17 cells through indole metabolites [117] L. paracasei ATCC27092 ameliorates EAE [181] L. plantarum A7 ameliorates EAE via induction of Tregs [182]
Megamonas	increased	[217] [186] [187]	[184]
Megasphaera	increased	[217] [186] [187]
Methanobrevibacter	increased	[217] [186]
Mitsuokella	decreased	[217]
Mogibacterium	increased	[187]
Mycoplana	increased	[185]
Odoribacter	increased	[187]	[187]
Oscillospira	decreased	[217] [187]	[217]
Oxalobacter	decreased	[187]
Parabacteroides	decreased	[185] [187]	[217]	P. distasonis increased differentiation of human peripheral blood CD4+ T cells to CD25+ IL-10+ T cells [187]
Paraprevotella	decreased	[217] [186] [187]	[217]
Pedobacter	increased	[185]
Peptostreptococcus	decreased	[217]
ph2	increased	[187]
Phascolarctobacterium	increased	[217]	[187]
Porphyromonas	increased	[217] [187]		Subcutaneous application of P. gingivalis A7436 five days after EAE induction exacerbates disease associated with increased nitric oxide and prostaglandin E2 production from glial cells [228]
Prevotella	decreased	[217] [184] [186] [187]	[217] [187]	Human gut-derived P. histolitica induced tolerogenic dendritic cells and Tregs and suppressed Th1 and Th1 7 response [183,229]
Providencia	increased	[217]
Pseudomonas	increased	[185] [187]	[187]
rc4–4	increased	[217] [187]
Ruminococcus	increased	[217] [187]	[217] [187]	R. gnavus produces a polysaccharide that induces TNFα production [230]
Sarcina	decreased	[186]
Serratia	decreased	[187]
Slackia	decreased	[186]
SMB53	increased	[187]
Sporanaerobacter	decreased	[186]
Streptococcus	increased	[217] [184]	[187]	S. pneumoniae infection seven days after EAE induction increases severity of EAE via a Toll-like receptor 2-dependent mechanism with increased serum TNFα and IL-6 and increased expression of MHC-II, CD80, and CD86 in splenic dendritic cells [231]
Succiniclastum	increased	[217]
Sutterella	decreased	[217] [184] [186] [187]	[217]
Trabulsiella	decreased	[217]
Varibaculum	increased	[187]
Veillonela	increased	[187]
WAL_855D	increased	[217] [187]