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Background  As little is known of association(s) between gut microbiota profiles and host immunological markers, we explored these in children with and without multiple sclerosis (MS).    Methods  Children ≤18 years provided stool and blood. MS cases were within 2-years of onset. Fecal 16S rRNA gene profiles were generated on an Illumina Miseq platform. Peripheral blood mononuclear cells were isolated, and Treg (CD4 + CD25 hi CD127 low FoxP3 + ) frequency and CD4 +  T-cell intracellular cytokine production evaluated by flow cytometry. Associations between microbiota diversity, phylum-level abundances and immune markers were explored using Pearson’s correlation and adjusted linear regression.    Results  Twenty-four children (15 relapsing-remitting, nine controls), averaging 12.6 years were included. Seven were on a disease-modifying drug (DMD) at sample collection. Although immune markers (e.g. Th2, Th17, Tregs) did not differ between cases and controls ( p  > 0.05), divergent gut microbiota associations occurred; richness correlated positively with Th17 for cases ( r  = +0.665,  p  = 0.018), not controls ( r  = −0.644,  p  = 0.061).  Bacteroidetes  inversely associated with Th17 for cases ( r  = −0.719,  p  = 0.008), not controls ( r  = +0.320,  p  = 0.401).  Fusobacteria  correlated with Tregs for controls ( r  = +0.829,  p  = 0.006), not cases ( r  = −0.069,  p  = 0.808).    Conclusions  Our observations motivate further exploration to understand disruption of the microbiota-immune balance so early in the MS course.    Electronic supplementary material  The online version of this article (doi:10.1186/s12883-016-0703-3) contains supplementary material, which is available to authorized users.

Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls