Microbiota modulates the differentiation T helper cells in the pathogenic conditions of autoimmune diseases. The critical interaction between gut microbiota and immune cells in autoimmune diseases. The outcome of gut microbiota-mediated inflammation by the different subsets of CD4+ cells in the specific tissue. In T1D, the augmented expression of bacteria from Akkermansia, Clostridiales, Lachnospiraceae, Prevotellaceae, and Rikenellaceae in the gut can promote the Th17 cell differentiation, whereas the decrease of Bifidobacterium, Escherichia, Lactobacillus, and Sutterella contribute to the downregulated expression of Treg cells. In MS, the enhanced expressions of L. reuteri, A. calcoaceticus, A. muciniphila, Streptococcus modulate the expansion of intestinal Th17 cells, whereas the upregulation of L. murinus, L. helveticus, P. histicola and Bifidobacteria is able to augment the expression of the anti-inflammatory cytokine IL-10 in Th cells. In RA, bacteria of Prevotella, Lautia, Clostridium XIVa, and Ruminococcus can promote the differentiation of Th17 or Tfh cells.